references to publications of - university of south carolinapeople.math.sc.edu/laszlo/cita.pdf ·...

119
References to publications of L. A. Sz´ ekely November 24, 2010 1./ L. A. Sz´ ekely, Remarks on the chromatic number of geometric graphs, in: Graphs and Other Topics (ed. M. Fiedler), Teubner- Texte zur Mathematik, Band 59, Leipzig, l983, 312–315. References 1. Fernando Mario de Oliveira Filho, New Bounds for Geometric Packing and Coloring via Harmonic Analysis and Optimization, Ph.D. Thesis, Centrum Wiskunde & Informatica in Amsterdam, 2009. 2. FERNANDO MARIO DE OLIVEIRA FILHO AND FRANK VAL- LENTIN, A QUANTITATIVE VERSION OF STEINHAUS THEO- REM FOR COMPACT, CONNECTED, RANK-ONE SYMMETRIC SPACES, arXiv:1005.0471v1 [math.CO] 4 May 2010 3. Hart, Derrick, Explorations of geometric combinatorics in vector spaces over finite fields, Ph.D., UNIVERSITY OF MISSOURI - COLUMBIA, 2008, 70 pages 4. Hart D, Iosevich A, Ubiquity of simplices in subsets of vector spaces over finite fields, ANALYSIS MATHEMATICA Volume: 34 Issue: 1 Pages: 29-38 Published: JAN 2008 5. M. S. Payne, D. Coulson, A dense distance 1 excluding set in R 3 , Austr. Math. Soc. Gaz. 34 (2) (2007), 97–102. 6. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry, 2005, 499 pages. 7. P. Erd˝ os, Some combinatorial, geometric, and set theoretic problems in measure theory, in: Measure Theory, Oberwolfach, 1983, eds. D. olzow, D. Maharam-Stone, Springer Lecture Notes in Mathematics Vol. 1089, Springer-Verlag, 1984, 321–327. 8. K. J. Falconer, The realization of small distances in plane sets of pos- itive measure, Bull. London Math. Soc. 18(1986), 471–474. 9. K. J. Falconer, J. M. Marstrand, Plane sets of positive density at infin- ity contain all large distances, Bull. London Math. Soc. 18(1986), 475–477. 1

Upload: others

Post on 01-Jun-2020

1 views

Category:

Documents


0 download

TRANSCRIPT

Page 1: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References to publications of

L. A. Szekely

November 24, 2010

1./ L. A. Szekely, Remarks on the chromatic number of geometricgraphs, in: Graphs and Other Topics (ed. M. Fiedler), Teubner-Texte zur Mathematik, Band 59, Leipzig, l983, 312–315.

References

1. Fernando Mario de Oliveira Filho, New Bounds for Geometric Packingand Coloring via Harmonic Analysis and Optimization, Ph.D. Thesis,Centrum Wiskunde & Informatica in Amsterdam, 2009.

2. FERNANDO MARIO DE OLIVEIRA FILHO AND FRANK VAL-LENTIN, A QUANTITATIVE VERSION OF STEINHAUS THEO-REM FOR COMPACT, CONNECTED, RANK-ONE SYMMETRICSPACES, arXiv:1005.0471v1 [math.CO] 4 May 2010

3. Hart, Derrick, Explorations of geometric combinatorics in vector spacesover finite fields, Ph.D., UNIVERSITY OF MISSOURI - COLUMBIA,2008, 70 pages

4. Hart D, Iosevich A, Ubiquity of simplices in subsets of vector spacesover finite fields, ANALYSIS MATHEMATICA Volume: 34 Issue: 1Pages: 29-38 Published: JAN 2008

5. M. S. Payne, D. Coulson, A dense distance 1 excluding set in R3,Austr. Math. Soc. Gaz. 34 (2) (2007), 97–102.

6. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry,2005, 499 pages.

7. P. Erdos, Some combinatorial, geometric, and set theoretic problemsin measure theory, in: Measure Theory, Oberwolfach, 1983, eds. D.Kolzow, D. Maharam-Stone, Springer Lecture Notes in MathematicsVol. 1089, Springer-Verlag, 1984, 321–327.

8. K. J. Falconer, The realization of small distances in plane sets of pos-itive measure, Bull. London Math. Soc. 18(1986), 471–474.

9. K. J. Falconer, J. M. Marstrand, Plane sets of positive density at infin-ity contain all large distances, Bull. London Math. Soc. 18(1986),475–477.

1

Page 2: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

10. J. Bourgain, A Szemeredi-type theorem for sets of positive density inRn, Israel J. Math 54(1986), 307–316. (This paper actually did notgive a citation to my work, although clearly ought to have done.)

11. H. Furstenberg, Y. Katznelson, B. Weiss, Ergodic theory and con-figurations in sets of positive density, in: Mathematics of RamseyTheory, J. Nesetril, V. Rodl, eds., Algorithms and Combinatorics 5,Springer Verlag, 1990, 184–198.

12. H. T. Croft, K. J. Falconer, R. K. Guy, Unsolved Problems in Ge-ometry, Problem Books in Mathematics, Springer-Verlag, 1991.

2./ L. A. Szekely, Measurable chromatic number of geometric graphsand sets without some distances in Euclidean space, Combina-torica 4(1984), 213–218.

References

1. M. S. Payne, Unit distance graphs with ambiguous chromatic number,Electronic J. Combinatorics 16 (2009) pp. 7.

2. F. M. de Oliveira Filho, F. Vallentin, Fourier analysis, linear program-ming and densities of distance avoiding sets in Rn

3. M. S. Payne, D. Coulson, A dense distance 1 excluding set in R3,Austr. Math. Soc. Gaz. 34 (2) (2007), 97–102.

4. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry,2005, 499 pages.

5. L. Lovasz and K. Vesztergombi, Geometric representations of graphs,in: Paul Erdos and his Mathematics II, Bolyai Studies 11, Springer-Verlag, 2002, 471–498.

6. P. Erdos, Some combinatorial and metric problems in geometry, in:Intuitive Geometry, Siofok, 1985, Coll. Math. Soc. J. Bolyai48(1987), 167–177.

7. H. T. Croft, K. J. Falconer, R. K. Guy, Unsolved Problems in Ge-ometry, Problem Books in Mathematics, Springer-Verlag, 1991.

8. L. Babai, P. Frankl, Linear Algebra Methods in Combinatorics,Part 1, Preliminary Version, July 1988, Department of Computer Sci-ence, The University of Chicago. (Also Preliminary Version 2, Septem-ber 1992).

9. R. B. Eggleton, 3 unsolved problems in graph theory, Ars Combina-toria 23A(1987), 105–121.

10. A. Raigorodskii, Borsuk’s problem and the chromatic number of cer-tain metric spaces, Russ. Math. Surv. 56 (1) (2001) 103–109.

11. Raigorodskii, A.M. Borsuk’s problem and the chromatic numbers ofmetric spaces (2007) Electronic Notes in Discrete Mathematics, 28,pp. 273-280.

3./ L. A. Szekely, On the number of homogeneous subgraphs of agraph, Combinatorica 4(1984), 363–372.

2

Page 3: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. David Conlon, On the Ramsey Multiplicity of Complete Graphs, arXiv:0711.4999v1[math.CO] 30 Nov 2007

2. J. Cutler, B. Montagh,Unavoidable subgraphs of colored graphs, DIS-CRETE MATHEMATICS Volume: 308 Issue: 19 Pages: 4396-4413Published: OCT 6 2008

3. A. Thomason, The simplest case of Ramsey’s theorem, in: Paul Erdosand his Mathematics II, Bolyai Studies 11, Springer-Verlag, 2002, 667–695.

4. A. Thomason, Random graphs, strongly regular graphs and pseudo-random graphs, in: Surveys in Combinatorics, LMS Lecture Notes123, C.U.P., Cambridge, 1987, 173–195.

4./ L. A. Szekely, On two concepts of discrepancy in a class of com-binatorial games, in: Finite and Infinite Sets, Coll. Math. Soc.Janos Bolyai 37(1985), 679–683.

References

1. AS Fraenkel, Combinatorial games: selected bibliography with a suc-cinct gourmet introduction, the electronic journal of combinatorics(2009), #DS2

2. J. Beck, Inevitable randomness in discrete mathematics, UniversityLecture Notes Series 49, AMS, 2009.

3. Andras Csernenszky, The PickerChooser diameter game, TheoreticalComputer Science Volume 411, Issues 40-42, 6 September 2010, Pages3757-3762

4. J. Beck, Surplus of Graphs and the Lovsz Local Lemma, BuildingBridges Bolyai Society Mathematical Studies, 2008, Volume 19, 47-102, DOI: 10.1007/978-3-540-85221-6 2

5. Balogh J, Martin R, Pluhar A, The Diameter Game, RANDOM STRUC-TURES & ALGORITHMS 35 (2009) 3 369–389.

6. Feldheim ON, Krivelevich M, Winning Fast in Sparse Graph Construc-tion Games, COMBINATORICS PROBABILITY & COMPUTINGVolume: 17 Issue: 6 Pages: 781-791 Published: NOV 2008

7. J. Beck, Combinatorial Games: Tic-Tac-Toe Theory, Cambridge Uni-versity Press, 2008, 746 pages.

8. Alon N, Krivelevich M, Spencer J, et al. Discrepancy games ELEC-TRONIC JOURNAL OF COMBINATORICS 12 (1): Art. No. R51SEP 29 2005

9. Frieze A, Krivelevich M, Pikhurko O, et al. The game of JumbleGCOMBINATORICS PROBABILITY & COMPUTING 14 (5-6): 783-793 SEP-NOV 2005

3

Page 4: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

10. J. Beck, Deterministic graph games and a probabilistic intuition, Com-binatorics, Probability and Computing 3(1994), 13–26.

11. J. Beck, Achievement games and the probabilistic method, Combi-natorics, Paul Erdos is Eighty (Volume 1), Keszthely, Hungary,1993, eds. D. Miklos, V. T. Sos, T. Szonyi, Bolyai Society Mathemat-ical Studies 1, 51–78.

12. J. Beck, Games, randomness, and algorithms, in: The Mathematicsof Paul Erdos vol. I, eds. R. L. Graham and J. Nesetril, Algorithmsand Combinatorics 13, Springer-Verlag, 1997, 280–310.

5./ L. A. Szekely, A note on common origin of cubic binomial identi-ties, a generalisation of Suranyi’s proof on Le Jen Shoo’s formula,J. Comb. Theory Ser. A 40(1985), 171–174.

References

1. Kadell KWJ Telescoping partial fractions decompositions, the little q-Jacobi functions of complex order, and the nonterminating q-Saalschutzsum RAMANUJAN JOURNAL 13 (1-3): 449-469 JUN 2007

2. Eric W. Weisstein, CRC Concise Encyclopedia of Mathematics, page2927.

3. Eric W. Weisstein. ”Szekely Identity.” From MathWorld–A WolframWeb Resource.http://mathworld.wolfram.com/SzekelyIdentity.html

4. Jiang Zeng, Pfaff-Schaalschutz revisited, J. Comb. Theory Ser. A51(1989), 141–143.

5. V. Strehl, Binomial identities—combinatorial and algorithmic aspects,Disc. Math. 136(1994), 309–346.

6. R. A. Proctor, D. C. Wilson, Interpretation of a basic hypergeomet-ric identity with Lie characters and Young tableaux, Disc. Math.137(1995), 297–302.

6./ L. A. Szekely, Holiday numbers: sequences resembling the Stir-ling numbers of second kind, Acta Sci. Math. (Szeged) 48(1985),459–467.

References

1. Wang, Yi; Yeh, Yeong-Nan Polynomials with real zeros and Po’lyafrequency sequences. J. Combin. Theory Ser. A 109 (2005), no. 1,63–74

2. Klazar M, Luca F On some arithmetic properties of polynomial expres-sions involving Stirling numbers of the second kind ACTA ARITH 107(4): 357-372 2003

3. H. K. Hwang, Asymptotics of Poisson approximation to random dis-crete distributions: An analytic approach Adv. Appl. Probability,31 (2) 1999, 448–491

4

Page 5: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

7./ A. Bogmer and L. A. Szekely, Asymptotic formula for the numberof solutions of a diophantic system, Annales Univ. Sci. Bud.Eotvos 28(1985), 203–215.

References

1. I. Joo, On the number of partitions of N into terms of 1, 2, ..., n, re-peating a term at most n times, Annales Univ. Sci. Bud. Eotvos28(1985), 217–227.

2. G. O. H. Katona, Ramanujan’s work in the theory of partitions, J.Indian Inst. Sci. (1987), 33–38.

8./ L. A. Szekely and N. C. Wormald, Generating functions for theFrobenius problem with 2 or 3 generators, Math. Chronicle15(1986), 49–57.

References

1. David Einstein, Daniel Lichtblau, Adam Strzebonski, Stan WagonFROBENIUS NUMBERS BY LATTICE POINT ENUMERATIONINTEGERS: ELECTRONIC JOURNAL OF COMBINATORIAL NUM-BER THEORY 7 (2007), #A15

2. Aicardi F, Fel LG, Gaps in nonsymmetric numerical semigroups, IS-RAEL JOURNAL OF MATHEMATICS 175(1)(2010) 85–112

3. Holroyd AE, Partition identities and the coin exchange problem JOUR-NAL OF COMBINATORIAL THEORY SERIES A Volume: 115 Is-sue: 6 Pages: 1096-1101 Published: AUG 2008

4. K Woods, Rational generating functions and lattice point sets, Ph. D.Thesis, University of Michigan, 2004

5. Leonid G. Fel, Frobenius problem for semigroups S(d1, d2, d3), 2006,Functional Analysis and Other Mathematics Volume 1, Number 2,119-157, DOI: 10.1007/s11853-007-0009-5

6. LG Fel, Analytic Representations in the 3-dim Frobenius Problemarxiv.orgLG Fel - Arxiv preprint math/0507370, 2005 - arxiv.org

7. Denham G Short generating functions for some semigroup algebrasELECTRON J COMB 10 (1): Art. No. R36 2003

8. A. Barvinok, J. E. Pommersheim, An algorithmic theory of latticepoints in polyhedra, New Perspectives in Geometric CombinatoricsMSRI Publications 38, 1999, 91–147.

9. Barvinok, A; Woods, K, Short rational generating functions for latticepoint problems, JOURNAL OF THE AMERICAN MATHEMATI-CAL SOCIETY; 2003; v.16, no.4, p.957-979.

9./ L. A. Szekely, The analytic behaviour of the holiday numbers,Acta Sci. Math. (Szeged) 51(1987), 365–369.

5

Page 6: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Wang, Yi; Yeh, Yeong-Nan Polynomials with real zeros and Po’lyafrequency sequences. J. Combin. Theory Ser. A 109 (2005), no. 1,63–74

2. Klazar, Martin; Luca, Florian On some arithmetic properties of poly-nomial expressions involving Stirling numbers of the second kind. ActaArith. 107 (2003), no. 4, 357–372.

3. H. K. Hwang, Asymptotics of Poisson approximation to random dis-crete distributions: An analytic approach Adv. Appl. Probability,31 (2) 1999, 448–49

10./ P. Erdos, I. Joo and L. A. Szekely, Remarks on infinite series,Studia Sci. Math. Hung. 22(1987) (1-4), 395–400.

References

1. M. Szegedy, G. Tardos, On the decomposition of infinite series intomonotone decreasing parts, Studia Sci. Math. Hung. 23(1988),81–84.

2. M. Horvath, Answer to a problem of Joo, Studia Sci. Math. Hung.23(1988), 245–250.

11./ L. A. Szekely, Inclusion-exclusion formulae without higher terms,Ars Comb. 23B(1987), 7–20.

References

1. D. A. Grable, Hypergraphs and sharpened sieve inequalities, DiscreteMath. 132 (1994)(1-3), 75–82.

2. D. de Caen, A lower bound on the probability of a union, DiscreteMath. 169(1997), no. 1-3, 217–220.

12./ L. A. Szekely and N. C. Wormald, Bounds on the measurablechromatic number of Rn, Discrete Math. 75(1989), 343–372.(Also published as: Bounds on the measurable chromatic numberof Rn, in: Graph Theory and Combinatorics 1988, Proceedingsof the Cambridge Combinatorial Conference in Honour of PaulErdos, ed. B. Bollobas, Annals of Discrete Mathematics 43,North-Holland, 1989, 343–372.)

References

1. M. S. Payne, D. Coulson, A dense distance 1 excluding set in R3,Austr. Math. Soc. Gaz. 34 (2) (2007), 97–102.

2. C. Bachoc, G. Nebe, F. M. de Oliveira Filho, F. Vallentin, Lowerbounds for measurable chromatic numbers, GEOMETRIC AND FUNC-TIONAL ANALYSIS 19 (2009) Issue: 3 Pages: 645-661.

6

Page 7: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

3. F. M. de Oliveira Filho, F. Vallentin, Fourier analysis, linear program-ming and densities of distance avoiding sets in Rn

4. page 254, CRC Handbook of Discrete and Computational Geometry,(E.Goodman, J. O’Rourke, eds.), CRC Press, 1997.

5. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry,2005, 499 pages.

6. R. Radoicic, G. Toth, A note on the chromatic number of R3, Discreteand Computational Geometry—The Goodman–Pollack Festschrift(Algebra and Combinatorics 25), Springer-Verlag, 2003.

7. O. Nechustan, On the space chromatic number, Discrete Math. 256(1-2) (2002), 499–507

8. T. R. Jensen and B. Toft, Graph Coloring Problems, Wiley-Interscience,1995.

9. V. Klee, S. Wagon, Old and New Unsolved Problems in Plane Ge-ometry and Number Theory, MAA Dolciani Expositions No. 11,1991, Providence, RI.

10. H. T. Croft, K. J. Falconer, R. K. Guy, Unsolved Problems in Ge-ometry, Problem Books in Mathematics, Springer-Verlag, 1991.

11. L. Babai, P. Frankl, Linear Algebra Methods in Combinatorics,Part 1, Preliminary Version, July 1988, Department of Computer Sci-ence, The University of Chicago. (Also Preliminary Version 2, Septem-ber 1992).

12. K. Cantwell, Edge-Ramsey theory, Discrete Comput. Geom. 15(1996)(3), 341–352.

13. K. Cantwell, Finite Euclidean Ramsey theory, J. Combin. Theory A73(1996), 273–285.

14. D. Coulson, An 18-colouring of 3-space omitting distance one, DiscreteMath. 170(1997), 241–247.

13./ P. L. Erdos and L. A. Szekely, Applications of antilexicographicorder I: An enumerative theory of trees, Adv. Appl. Math.10(1989), 488–496

References

1. Jacob Post, COMBINATORICS OF ARC DIAGRAMS, FERRERSFILLINGS, YOUNG TABLEAUX AND LATTICE PATHS, Master’sthesis in Computing Science, 2001, Simon Fraser University.

2. B. Vance, Counting ordered trees by permuting their parts, Amer.Math. Monthly 2006 113 (4): 329-335

3. Donald E. Knuth, The Art of Computer Programming, Vol. 4, Sec-tions 7.2.1.5: Generating All Partitions, Exercise 10, Addison–Wesley,2005.

7

Page 8: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

4. C. Semple and M. Steel, Phylogenetics, Oxford Lecture Series in Math-ematics and its Applications 24, Oxford University Press, 2003

5. Akos Toroczkai, On the topological classification of binary trees usingthe Horton-Strahler index, Phys. Rev. E 6501 (1): 6130-+ Part 2JAN 2002.

6. P. Hilton, J. Pedersen, Two recurrence relations for Stirling factors,Bull. Belg. Math. Soc.-Sim. 6 (4) (1999), 615–623.

7. P. W. Diaconis, and S. P. Holmes, Matchings and phylogenetic trees,Proc. Natl. Acad. Sci. USA 95(25) (1998), 14600-14602.

8. W. Y. Chen, A general bijective algorithm for trees, Proc. Natl.Acad. Sci. USA 87(1990), 9635–9639.

9. W. Y. C. Chen, On the combinatorics of plethysm, Ph. D. Thesis, M.I. T., Cambridge, Ma., 1991.

10. M. A. Steel, The complexity of reconstructing trees from qualitativecharacters and subtrees, J. Classification 9(1992), 91–116.

11. P. L. Erdos, A new bijection on rooted forests, Discrete Math. 111(1993), 179–188.

12. R. P. Stanley, Enumerative Combinatorics, Vol. 2, Cambridge Uni-versity Press, 1999.

13. M. A. Steel, Decompositions of leaf-coloured binary trees, Adv. Appl.Math. 14(1993), 1–24.

14. R. Ehrenborg, M. Mendez, Schroder parenthesizations and chordates,J. Comb. Theory Ser A 67(1994), 127–139.

15. M. Hendy, P. Hilton, J. Pedersen, Stirling factors and phylogenetictrees, Journees Mathematiques & Informatique 5(1994), 110–122.

16. T. Bier, Remarks on the algebra of calculus, manuscript.

14./ T. D. Porter and L. A. Szekely, Generating functions for a prob-lem of Riordan, J. Comb. Math. Comb. Comput. 6(1989),195–198.

References

1. T. D. Porter, Some results in combinatorial analysis and graph theory,Ph. D. Thesis, University of New Mexico, Albuquerque, NM, 1990.

15./ M. Carter, M. Hendy, D. Penny, L. A. Szekely and N. C. Wormald,On the distribution of length of evolutionary trees, SIAM J. Dis-crete Math. 3(1990), 38–47.

8

Page 9: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. M. Steel, The Penny Ante: Mathematical biology or biological math-ematics? New Zealand Science Review Vol 66 (1) 2009 12–13.

2. Quantifying the potential utility of phylogenetic characters Author(s):Cotton JA, Wilkinson M Source: TAXON Volume: 57 Issue: 1 Pages:131-136 Published: FEB 2008

3. D. Cieslik, Shortest Connectivity, An Introduction with Applicationsin Phylogeny, Springer, 2005.

4. Semple C, Steel M Unicyclic networks: Compatibility and enumerationIEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGYAND BIOINFORMATIOCS 3 (1): 84-91 JAN-MAR 2006

5. D Bryant, The Splits in the Neighborhood of a Tree, Annals of Com-binatorics 8 (2004) 1-11

6. T Dezulian, M Steel, Phylogenetic closure operations and homoplasy-free evolution, Proceedings of the 2004 International Federation ofClassification Societies, Springer- Verlag (in press)

7. Arias JS, Miranda-Esquivel DR Profile Parsimony (PP): an analysisunder Implied Weights (IW) CLADISTICS 20 (1): 56-63 FEB 2004

8. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

9. C. Semple and M. Steel, Phylogenetics, Oxford Lecture Series in Math-ematics and its Applications 24, Oxford University Press, 2003

10. Dorit S. Hochbaum, Anu Pathria, Path Costs in Evolutionary TreeReconstruction (1997) Journal of Computational Biology

11. Dan Faith, Syst. Biol.12. K. Hewitt, Blocks as a tool for learning: Historical and contemporary

perspectives, Young Children 56 (1) (2001).

13. M. A. Steel, Distribution on bicoloured binary trees arising from theprinciple of parsimony, Discrete Appl. Math. 41(1993), 245–261.

14. C. Semple, M. Steel, Tree reconstruction from multistate characters,Adv. Appl. Math. 28 (2002), 169–184.

15. M. A. Steel, Distributions on bicoloured evolutionary trees, Ph. D.Thesis, Massey University, Palmerston North, New Zealand, 1989.

16. M. A. Steel, The complexity of reconstructing trees from qualitativecharacters and subtrees, J. Classification 9(1992), 91–116.

17. M. A. Steel, Decompositions of leaf-coloured binary trees, Adv. Appl.Math. 14(1993), 1–24.

18. M. A. Steel, M. D. Hendy, D. Penny, The significance of the length ofthe shortest tree, J. Classification 9(1992), 71–90.

19. D. Penny, M. D. Hendy, M. A. Steel, Testing the theory of descent, in:Phylogenetic analysis of DNA sequences, eds. M. M. Miyamoto,Oxford Univversity Press, Oxford, 1991, 155–183.

9

Page 10: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

20. J. B. Slowinski, Unordered versus ordered characters, Syst. Biol.42(1993) (2), 155–165.

21. P. A. Goloboff, Homoplasy and the choice among cladograms, Cladis-tics 7 (1991) (3), 215–232.

22. W. P. Maddison, M. Slatkin, Null models for the number of evolution-ary steps in a character on a phylogenetic tree, Evolution 45 (1991)(5) 1184-1197.

23. J. W. Moon, M. A. Steel, A limiting theorem for parsimoniously bi-coloured trees, Appl. Math. Letters 6(4)(1993), 5–8.

24. P. L. Erdos, A new bijection on rooted forests, Discrete Math. 111(1993),179–188.

25. H. H. Bock Probabilistic models in cluster analysis, Comput. Stat.Data An. 23 (1996)(1) 5–28.

26. A. M. Hamel, M. A. Steel, The length of a leaf colouration on a randombinary tree, SIAM Discrete Math. 10 (1997), no. 3, 359–372.

27. M. A. Steel, L. Goldstein, and M. S. Waterman, A central limit theo-rem for parsimony length of trees, Adv. Appl. Probability, 28(1996),1051–1071.

28. D. S. Hochbaum, A. Pathria, Path costs in evolutionary tree recon-struction, J. Comput. Biol. 4(1997) (2), 163–175.

29. E. Matisoo-Smith, R. M. Roberts, G. J. Irwin, et al., Patterns ofprehistoric human mobility in Polynesia indicated by mtDNA fromthe Pacific rat, Proc. Natl. Acad. Sci. USA 95 (25), 15145–15150.

30. L. J. Collins, V. Moulton, D. Penny, Use of RNA secondary structurefor studying the evolution of RNase P and RNase MRP, J. Mol. Evol.51 (2000), 194–204.

16./ T. D. Porter and L. A. Szekely, On a matrix discrepancy prob-lem, Congr. Num. 73(1990), 239–248.

References

1. Baogang Xua, Juan Yana, and Xingxing Yu, A note on balanced bi-partitions, Discrete Mathematics Volume 310, Issue 20, 28 October2010, Pages 2613-2617

2. Jie Maa and Xingxing Yu, Bounds for pairs in partitions of graphs,Discrete Mathematics Volume 310, Issues 15-16, 28 August 2010, Pages2069-2081

3. Rui Li, Baogang Xu, Biased Judicious Partition of Graphs

4. Baogang Xu, Juan Yan, Xingxing Yu, Balanced judicious bipartitionsof graphs, Journal of Graph Theory Volume 63, Issue 3, pages 210225,March 2010

5. T. D. Porter, Some results in combinatorial analysis and graph theory,Ph. D. Thesis, University of New Mexico, Albuquerque, NM, 1990.

10

Page 11: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

6. Bollobas, B.; Scott, A. D. Problems and results on judicious parti-tions. Random structures and algorithms (Poznan, 2001). RandomStructures Algorithms 21 (2002), no. 3-4, 414–430.

7. T. D. Porter, Graph partitions, J. Comb. Math. Comb. Comput.15(1994), 111–118.

8. T. D. Porter, Minimal partitions of a graph, Ars Combinatoria 53(1999), 181–186.

9. T. D. Porter, and Bing Yang, Graph partitions II, J. Comb. Math.Comb. Comput. 37(2001), 149–158.

17./ A. A. Kooshes, B. M. E. Moret and L. A. Szekely, Improvedbounds on the prison yard problem, Congr. Num. 76(1990),145–149.

References

1. Z. Furedi, D. Kleitman, The prison yard problem, Combinatorica14(1994), 287–300.

2. A. A. Kooshesh, Structuring techniques for path and visibility prob-lems, Ph. D. Thesis, University of New Mexico, Albuquerque, NM,1992.

18./ L. H. Clark, J. I. McCanna, R. C. Entringer and L. A. Szekely,Extremal problems for local properties of graphs, AustralasianJ. Comb. 4(1991), 25–31.

References

1. N Alon, A Shapira, On an Extremal Hypergraph Problem of Brown,Erdos and Sos Combinatorica, 26 (6) (2006) 627–645.

2. Mieczyslaw Borowiecki, Elzbieta Sidorowicz, Some extremal problemsof graphs with local constraints, Discrete Mathematics 251 (2002),19–32.

3. Borowiecki, Mieczyslaw; Mihok, Peter On graphs with a local heredi-tary property. Graph theory (Kazimierz Dolny, 1997). Discrete Math.236 (2001), no. 1-3, 53–58.

4. J. I. McCanna, The classification of self-dual graphs and other resultsin graph theory, Ph. D. Thesis, University of New Mexico, Albu-querque, NM, 1990.

5. Akos Seress, Polygonal Graphs, Horizons of Combinatorics Bolyai So-ciety Mathematical Studies, 2008, Volume 17, 179-188, DOI: 10.1007/978-3-540-77200-2 9

6. A. Seress, T. Szabo, Dense graphs with cycle neighbourhoods, J.Comb. Theory Ser. B 63(1995), 281–293.

7. T. Szabo, Extremal problems for graphs and hypergraphs, Ph. D.Thesis, Ohio State University, Columbus, 1996.

11

Page 12: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

19./ K. A. Johnson, R. Grassl, J. I. McCanna and L. A. Szekely,Pascalian rectangles modulo m, Quaest. Math. 14(1991), 383–400.

References

1. Graham N., , Harary F., , Livingston M., , Stout Q. F., (1993/02).”Sub-cube Fault-Tolerance in Hypercubes.” Information and Computation102(2): 280-314.

2. Peyman Nayeri, Charles J. Colbourn and Goran Konjevod, Random-ized Postoptimization of Covering Arrays, Lecture Notes in ComputerScience, 2009, Volume 5874/2009, 408-419, DOI: 10.1007/978-3-642-10217-2 40

3. J. I. McCanna, The classification of self-dual graphs and other resultsin graph theory, Ph. D. Thesis, University of New Mexico, Albu-querque, NM, 1990.

20./ L. A. Szekely, L. H. Clark and R. C. Entringer, An inequalityfor degree sequences, Discrete Math. 103(1992), 293–300.

References

1. Antal Ivanyi, Reconstruction of complete interval tournaments. II.Acta Univ. Sapientiae, Mathematica, 2, 1 (2010) 4771.

2. SN Qiao, On The Zagreb Index Of Quasi-Tree Graphs, Applied Math-ematics E-Notes, 10(2010), 147-150. Available free at mirror sites ofhttp://www.math.nthu.edu.tw

3. S Zhang, W Wang, TCE Cheng, Bicyclic graphs with the first threesmallest and largest values of the first general Zagreb index, Com-munications in Mathematical and in Computer Chemistry / MATCH2006, vol. 56, (3), pp. 579–592

4. Guo YL, Du YJ, Wang Y, BIPARTITE GRAPHS WITH EXTREMEVALUES OF THE FIRST GENERAL ZAGREB INDEX, MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTERCHEMISTRY 63(2) (2010) 469–480.

5. Lo ASL, Triangles in Regular Graphs with Density Below One Half,COMBINATORICS PROBABILITY & COMPUTING Volume: 18Issue: 3 Pages: 435-440 Published: MAY 2009

6. : Cheng TCE, Guo YL, Zhang SG, et al., Extreme values of the sum ofsquares of degrees of bipartite graphs, DISCRETE MATHEMATICSVolume: 309 Issue: 6 Pages: 1557-1564 Published: APR 6 2009

7. Yeon Soo Yoon, Ju Kyung Kim, A relationship between bounds on thesum of squares of degrees of a graph, J. Appl. Math. & Computing21 (2006) 233–238.

8. Cioaba SM Sums of powers of the degrees of a graph DISCRETEMATHEMATICS 306 (16): 1959-1964 AUG 28 2006

12

Page 13: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

9. Yu AM, Lu M, Tian F On the spectral radius of graphs LINEARALGEBRA AND ITS APPLICATIONS 387: 41-49 AUG 1 2004

10. Zhang SG, Zhang HL Unicyclic graphs with the first three smallestand largest first general Zagreb index MATCH-COMMUNICATIONSIN MATHEMATICAL AND IN COMPUTER CHEMISTRY 55 (2):427-438 2006

11. Gutman I, Das KC The first Zagreb index 30 years after MATCH-COMMUN MATH CO (50): 83-92 FEB 2004

12. Furedi Z, Kundgen A Moments of graphs in monotone families JOUR-NAL OF GRAPH THEORY 51 (1): 37-48 JAN 2006

13. K. C. Das, Sharp bounds for the sum of the squares of the degrees ofa graph, Kragujevac J. Math.

14. K. C. Das, Maximizing the sum of the squares of the degrees of agraph, DISCRETE MATHEMATICS 285 (1-3): 57-66 AUG 6 2004

15. Y. Caro and R. Yuster, Graphs with large variance, Ars Combinato-ria 57 (2000), 151–162.

16. H. Alzer, An inequality for increasing sequences and its integral ana-logue, Discrete Math. 133(1994), 279–283.

17. D. de Caen, An upper bound on the sum of squares of degrees in agraph, Discrete Math. 185 (1998) (1-3), 245–248.

21./ P. L. Erdos, P. Frankl, D. J. Kleitman, M. E. Saks and L. A.Szekely, Sharpening the LYM inequality, Combinatorica 12(1992),287–293.

References

1. Tran Dan Thu, A generic identity of two set systems

2. Kisvoelcsey A, Weighted cross-intersecting families, DISCRETE MATH-EMATICS Volume: 308 Issue: 11 Pages: 2247-2260 Published: JUN6 2008

3. Tran Dan Thu, An AZ-style identity and Bollobs deficiency, Journal ofCombinatorial Theory, Series A Volume 114, Issue 8, November 2007,Pages 1504-1514

4. A. Kisvolcsey: Antichain problems in finite sets, Ph.D. Thesis, EotvosUniversity, (2003), 1–74.

5. G. W. Peck, Kleitman and combinatorics: a celebration, DiscreteMath. 257 (2002), 193–224.

6. C. Bey, Polynomial LYM inequalities, Combinatorica 25 (1) (2005)19–38.

7. D. J. Kleitman, Extremal problems on hypergraphs, in: ExtremalProblems for Finite Sets, Proc. Conf. held in Visegrad, 1991,Bolyai Soc. Math. Studies 3, 355–374.

13

Page 14: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

22./ F. Shahrokhi and L. A. Szekely, Effective lower bounds for cross-ing number, bisection width and balanced vertex separator interms of symmetry, in: Integer Programming and Combinato-rial Optimization, Proceedings of a Conference held at CarnegieMellon University, May 25-27, 1992, by the Mathematical Pro-gramming Society, eds. E. Balas, G. Cornuejols, R. Kannan,102–113, CMU Press, 1992.

References

1. M. Lomonosov, A. Sebo, On the geodesic-structure of graphs: a poly-hedral approach to metric decomposition, in: Integer Programmingand Combinatorial Optimization, Proceedings of a Conferenceheld at Erice, Italy, April 21-May 1, 1993, by the Mathemati-cal Programming Society, eds. Rinaldi and Wolsey, 221–234.

2. O. Sykora, I. Vrto, On crossing numbers of hypercubes and cube-connected cycles, BIT Comp. Sci. and Num. Math. 33(1993)232–237.

3. O. Sykora, I. Vrto, On VLSI layouts of the star graph and relatednetworks, Integration, the VLSI Journal 17(1994), 83–93.

4. M. Scharbrodt, Die Kreuzungszahl von Graphen, Diplomarbeit, In-stitut fur Informatik der Universitat zu Koln, 1994.

5. A. Liebers, Methods for planarizing graphs — a survey and annotatedbibliography, Konstanzer Schriften in Mathematik und Informatik12 (1996).

6. Liebers, A. Planarizing graphs - A survey and annotated bibliography(2001) Journal of Graph Algorithms and Applications, 5 (1), pp. 1-74.

23./ P. L. Erdos and L. A. Szekely, Algorithms and min-max the-orems on certain multiway cuts, in: Integer Programming andCombinatorial Optimization, Proceedings of a Conference heldat Carnegie Mellon University, May 25-27, 1992, by the Math-ematical Programming Society, eds. E. Balas, G. Cornuejols, R.Kannan, 334–345, CMU Press, 1992.

References

1. I. Milis: Approximating a Class of Classification Problems in EfficientApproximation and Online Algorithms (Ed. E. Bampis, K. Jansen,C. Kenyon) LNCS 3484 (2006), 213–249.

2. E. Dahlhaus, D. S. Johnson, C. H. Papadimitriou, P. D. Seymour, M.Yannakakis, The complexity of multiterminal cuts, SIAM J. Com-puting 23(1994)(4), 864–894.

24./ L. H. Clark, F. Shahrokhi and L. A. Szekely, A linear-time al-gorithm for graph partition problems, Inform. Process. Letters42(1992), 19–24.

14

Page 15: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Jie Ma, Pei-Lan Yen, Xingxing Yu: On several partitioning problemsof Bollobs and Scott. JCT Ser B 100(2010), 631-649.

2. D. Rautenbach, Z. Szigeti, Simultaneous large cuts, 2004

3. R. D. Dutton, A polynomial graph partitioning problem

4. A. Liebers, Methods for planarizing graphs — a survey and annotatedbibliography, Konstanzer Schriften in Mathematik und Informatik12 (1996).

5. Liebers, A. Planarizing graphs - A survey and annotated bibliography(2001) Journal of Graph Algorithms and Applications, 5 (1), pp. 1-74.

6. T. D. Porter, Some results in combinatorial analysis and graph theory,Ph. D. Thesis, University of New Mexico, Albuquerque, NM, 1990.

7. T. D. Porter, On a bottleneck graph bipartition conjecture of Erdos,Combinatorica 12(1992), 317–321.

8. T. D. Porter, Graph partitions, J. Comb. Math. Comb. Comput.15(1994), 111–118.

9. J. Berry, M. Goldberg, Path optimization and near-greedy analysisfor graph partitioning: an empirical study, Proc. SODA ’95, 1995,223–232.

10. A. Hamacher, Baumzerlegungen unter Nebenbedingungen—Ein Clus-terverfahren zur Losung praktischer Vehicle-Routing-Probleme, Inaugural-Dissertation zur Erlagung des Doktorgrades der Mathematisch- Natur-wissenschaftlichen Fakultat der Universitat zu Koln, Koln, 1997.

11. A. Hamacher, W. Hochstattler, and C. Moll, Tree partitioning underconstraints—clustering for vehicle routing problems, Discrete Appl.Math. 99 (1–3) (2000), 55–69.

12. S. Bylka, A. Idzik, Z. Tuza, Maximum cuts: improvements and localalgorithmic consequences of the Edwards-Erdos inequality, DiscreteMath. 194(1999), 39–58.

13. Jonathan W. Berry, Mark K. Goldberg, Path Optimization for GraphPartitioning Problems, Discrete Applied Mathematics 90 (1-3), pp.27-50.

25./ D. de Caen and L. A. Szekely, The maximum size of 4- and 6-cycle free bipartite graphs on m, n vertices, in: Graphs, Sets andNumbers, Proceedings of the Conference Dedicated to the 60th

Birthdays of A. Hajnal and Vera T. Sos, Budapest, 1991, eds.G. Halasz, L. Lovasz, D. Miklos, T. Szonyi, Coll. Math. Soc.Janos Bolyai 60(1992), 135–142.

15

Page 16: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Stefan Neuwirth, Aspects quantitatifs de linconditionnalite, Habilita-tion Thesis, Universite de Franche-Comte, 2008

2. Peter Damaschke, Ranking hypotheses to minimize the search cost inprobabilistic inference models, Discrete Applied Mathematics Volume157, Issue 6, 28 March 2009, 1218-1228.

3. E Gyori, Triangle-Free Hypergraphs, Combinatorics, Probability andComputing (2006) 15, 185-191.

4. O Milenkovic, D Leyba, N Kashyap, Shortened Array Codes of LargeGirth Arxiv preprint cs.DM/0504016, 2005 - arxiv.org

5. Z Furedi, A Naor, J Verstraete, On the Turan Number for the HexagonAdv. Math. 203 (2006), no. 2, 476–496.

6. Van Dam ER The combinatories of Dom de Caen DESIGNS CODESAND CRYPTOGRAPHY 34 (2-3): 137-148 FEB-MAR 2005

7. F Lazebnik, AJ Woldar, General properties of some families of graphsdefined by systems of equations, Journal of Graph Theory, 2001 (38),65-86.

8. K. E. Mellinger, D. Mubayi, A new construction of extremal bipartitegraphs from finite geometries Journal of Graph Theory, 49 (2005), no.1, 1–10.

9. A. Naor and J. Verstraete, A note on bipartite graphs without 2k-cycles, Combinatorics, Probability and Computing 14 (2005) 845–849.

10. M. Simonovits, Some of my favourite Erdos Theorems, and relatedresults, theories, in: Paul Erdos and his Mathematics II, Bolyai Studies11, Springer-Verlag, 2002, 565–636..

11. J. A. Bondy, Extremal problems of Paul Erdos on circuits in graphs,in: Paul Erdos and his Mathematics II, Bolyai Studies 11, Springer-Verlag, 2002, 135–156.

12. S. Neuwirth, The size of bipartite graphs with girth eight,

13. F. Lazebnik, V. A. Ustimenko, A. J. Woldar, New constructions ofbipartite graphs on m,n vertices with many edges, and without smallcycles, J. Combin. Theory Ser. B 61(1994), 111–117.

14. G. N. Sarkozy, Cycles in bipartite graphs and an application in numbertheory, J. Graph Theory 19(1995) (3), 323–331.

15. E. Gyori, C6-free bipartite graphs and product representation of squares,Discrete Math. 165/166(1997), 371–375.

16. M. Simonovits, Paul Erdos’ influence on extremal graph theory, in:The Mathematics of Paul Erdos vol. II, eds. R. L. Graham andJ. Nesetril, Algorithms and Combinatorics 14, Springer-Verlag, 1997,148–193.

16

Page 17: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

17. P. Erdos, R. J. Faudree, C. C. Rousseau, and R. H. Schelp, The numberof cycle lengths in graphs of given minimum degree and girth, DiscreteMath. 200 (1999), 55–60.

26./ M. A. Steel, M. D. Hendy, L. A. Szekely and P. L. Erdos, Spectralanalysis and a closest tree method for genetic sequences, Appl.Math. Letters 5(1992)(6), 63–67.

References

1. CR Marshall, Molecular approaches to echinoderm phytogeny, in: Echin-oderms through time: proceedings of the eighth , 1994 - CRC

2. MARTA CASANELLAS AND JESUS FERNANDEZ-SANCHEZ, REL-EVANT PHYLOGENETIC INVARIANTS OF EVOLUTIONARY MOD-ELS, arXiv:0912.1957v1 [math.AG] 10 Dec 2009

3. Bryant D, : Hadamard Phylogenetic Methods and the n-taxon Process,BULLETIN OF MATHEMATICAL BIOLOGY Volume: 71 Issue: 2Pages: 339-351 Published: FEB 2009

4. J. Stoye: Divide-and-conquer multiple sequence alignment, Ph.D. The-sis Report 97-02 University of Bielefeld (1997), 1–144.

5. SPECTRUM a program for spectral analysis, at

(taxonomy.zoology.gla.ac.uk/mac/spectrum/spectrum.html)

6. FA Matsen and SN Evans, A matrix algebra approach to tree shape

7. B. Chor, M. D. Hendy, S. Snir, Maximum likelihood Jukes-Cantortriplets: Analytic solutions, Mol. Biol. Evol. 23 (3) 2006.

8. D.H. Huson - D. Bryant: Application of phylogenetic networks in evo-lutionary studies, Molecular Biology And Evolution 23 (2006), 254–267.

9. MD Hendy, S Snir, Hadamard Conjugation for the Kimura 3ST Model:Combinatorial proof using path sets IEEE-ACM TRANSACTIONSON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS Vol-ume: 5 Issue: 3 Pages: 461-471 Published: JUL-SEP 2008

10. M.D. Hendy: Hadamard conjugation: an analytical tool for phyloge-netics, in Mathematics of evolution & phylogeny (ed. O. Gascuel)Oxford Univ. Press (2004), 143–177.

11. D. Bryant: Extending tree models to split networks, Chapter 17, inAlgebraic Statistics for Computational Biology (Ed. L. Pachter andB. Sturmfels) in press Cambridge Univ. Press (2005), 331–346.

12. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

13. A. M. Paterson, L. J. Wallis, G. P. Wallis, Preliminary molecular anal-ysis of Pelecanoides georgicus (Procellariiformes : Pelecanoididae) onWhenua Hou (Codfish Island): implications for its taxonomic status,New Zealand J. Zool. 27 (4) 415–423.

14. M. A. Steel, M. D. Hendy, D. Penny, Parsimony can be consistent!Syst. Biol. 42(1993), 581–587.

17

Page 18: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

15. M. D. Hendy, D. Penny, M. A. Steel, Discrete Fourier spectral analysisfor evolution, Proc. Natl. Acad. Sci. USA 91(1994), 3339–3343.

16. M. Steel, M. D. Hendy, D. Penny, Invertible models of sequence evolu-tion, Preprint 93/02, School of Mathematics, Massey University, sub-mitted to Mathematical Biosciences.

17. M. D. Hendy, M. A. Charleston, Hadamard conjugatio: a versatile toolfor modelling nucleotid sequence evolution, New Zealand J. Botany31(1993), 231–237.

18. M. A. Steel, The maximum likelihood point for a phylogenetic tree isnot unique, Syst. Biol 43(4)(1994), 560–564.

19. V. Ferretti, D. Sankoff, A remarkable non-linear invariant for evolutionwith heterogeneous rates, 134(1996), Math. Bioscience 71–83.

20. M. Steel, M. D. Hendy, D. Penny, Reconstructing evolutionary treesfrom nucleotide pattern probabilities, Universitat Bielefeld, Forschung-schwerpunkt Strukturbildungprozesse, Materialen XCIV, 1995.

21. V. Ferretti, D. Sankoff, The empirical discovery of phylogenetic invari-ants, Adv. Appl. Prob. 25(1993), 290–302.

22. V. Ferretti, B. F. Lang, D. Sankoff, Skewed base composition, asym-metric transition matrices, and phylogenetic invariants, J. Computa-tional Biology 1(1994), 77–92.

23. P. J. Waddell, D. Penny, M. D. Hendy, G. Arnold, The sampling dis-tributions and covariance matrix of phylogenetic spectra, Mol. Biol.Evol. 11(1994), 630–642.

24. P. J. Waddell, D. Penny, T. Moore, Extending Hadamard conjugationto model sequence evolution with variable rates across sites, Inf. andMath. Sci. Reports Series B 96/11, Massey University.

25. P. J. Waddell, D. Penny, T. Moore, Hadamard conjugations and mod-eling sequence evolution with unequal rates across sites, Mol. Phylo-genet. Evol 8(1997)(1) 33–50.

26. P. J. Waddell, Statistical Methods of Phylogenetic Analysis, IncludingHadamard Conjugations, LogDet Transforms, and Maximum Likeli-hood. PhD thesis, Massey University, New Zealand. (1996)

27. H. J. Bandelt, Combination of data in phylogenetic analysis, PlantSyst. Evol. (1995) Suppl 9. 355–361.

28. D. A. Morrison, Phylogenetic tree-building, Int. J. Parasitology26(1996)(6), 589–617.

29. D. Penny, M. Hendy, P. Lockhart, M. A. Steel, Corrected parsimony,minimum evolution and Hadamard conjugation, Syst. Biol. 45(1996)(4),596–606.

30. M. Steel, M. D. Hendy, D. Penny, Reconstructing phylogenies fromnucleotide pattern probabilities: a survey and some new results, Disc.Appl. Math. 88 (1998) 367–396.

18

Page 19: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

31. M. Steel, P. J. Waddell, Approximating likelihoods under low but vari-able rates across sites, Appl. Math. Letters 12 (6)(1999) 13–19.

27./ L. A. Szekely, P. L. Erdos and M. A. Steel, The combinatorics ofevolutionary trees—a survey, in: Actes du Seminaire, SeminaireLotharingien de Combinatoire, 28e Session, 15–18 mars: 1992,Saint-Nabor, Ottrott, J. Zeng, ed., Publication de l’Institute deRecherche Mathematique Avancee, Universite Louis Pasteur, Stras-bourg, 1992, 129–143.

References

1. Websters Quotations, Facts and Phrases “reconstructing”

2. G.L. McColm: An introduction to random trees, J. Languages andComputation 2 (2002), 1–25. Research on Language and Compu-tation 1 (2003), 203–226.

28./ P. L. Erdos and L. A. Szekely, Evolutionary trees: An integermulticommodity max-flow–min-cut theorem, Adv. Appl. Math.13(1992), 375–389.

References

1. Xin Xiao; Li Shuguang; Colored Multiway Cuts in Trees of Rings, In-ternational Forum on Information Technology and Applications, 2009.IFITA ’09. Issue Date: 15-17 May 2009 On page(s): 236 - 238

2. Lajos Soukup, Infinite Combinatorics: From Finite to Infinite, Hori-zons of Combinatorics Bolyai Society Mathematical Studies, 2008, Vol-ume 17, 189-213, DOI: 10.1007/978-3-540-77200-2 10

3. Xin Xiao; Li Shuguang; Colored Multiway Cuts in Generalized TreeNetworks, Information Engineering, 2009. ICIE ’09. WASE Interna-tional Conference on Issue Date: 10-11 July 2009, 299 - 301

4. Jennifer F. Hoyal Cuthill, Simon J. Braddy and Philip C. J. Donoghue,A formula for maximum possible steps in multistate characters: isolat-ing matrix parameter effects on measure of evolutionary convergence,Cladistics 26 (2010) 98–102.

5. M.A. Steel: Some statistical aspects of the maximum parsimony method,In Molecular Systematics and Evolution: Theory and Practice(Series: Experientia Supplementum Vol. 92) (Ed. R. DeSalle, G.Giribet, W. Wheeler). Birkhauser (2002), 125–140.

6. Guo, J., Huffner, F., Kenar, E., Niedermeier, R., Uhlmann, J. Com-plexity and exact algorithms for multicut (2006) Lecture Notes in Com-puter Science (including subseries Lecture Notes in Artificial Intelli-gence and Lecture Notes in Bioinformatics), 3831 LNCS, pp. 303-312.

7. Jiong Guo - F. Huffner - E. Kenar -R. Niedermeier - J. Uhlmann:Complexity and exact algorithms for multicut in interval and boundedtreewidth graphs, Eur. J. Oper. Res. (2007) (186) 542–553.

19

Page 20: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

doi:10.1016/j.ejor.2007.02.014

8. Guo J, Huffner F, Kenar E, et al. Complexity and exact algorithmsfor vertex multicut in interval and bounded treewidth graphs EURO-PEAN JOURNAL OF OPERATIONAL RESEARCH 186 (2): 542-553 APR 16 2007

9. Alfieri, A., Nicosia, G., Pacifici, A., Exact algorithms for a discretemetric labeling problem, Discrete Optimization 3 (3), pp. 181-1942006.

10. Guo J, Huffner F, Kenar E, et al. Complexity and exact algorithmsfor multicut LECTURE NOTES IN COMPUTER SCIENCE 3831:303-312 2006

11. Nicosia, G., A. Pacifici (2004), Exact algorithms for a discrete metriclabeling problem. In Proc. CTW04 Workshop on Graphs andCombinatorial Optimization, (L. Liberti, F. Maffioli eds.) Elec.Notes in Discr. Math. 17 (2004), 196–200.

12. C. Semple and M. Steel, Phylogenetics, Oxford Lecture Series in Math-ematics and its Applications 24, Oxford University Press, 2003

13. E. Dahlhaus, D. S. Johnson, C. H. Papadimitriou, P. D. Seymour,M. Yannakakis, The complexity of multiway cuts, 24th ACM STOC(1992), 241–251.

14. M. A. Steel, Decompositions of leaf-coloured binary trees, Adv. Appl.Math. 14(1993), 1–24.

15. D. Penny, P. J. Lockhart, M. A. Steel, M. D. Hendy, The role ofmodels in reconstructing evolutionary trees, in: Models in PhylogenyReconstruction, eds. R. W. Scotland, D. J. Siebert, D. M. Williams,Oxford University Press, 1994, 211–230.

16. E. Dahlhaus, D. S. Johnson, C. H. Papadimitriou, P. D. Seymour, M.Yannakakis, The complexity of multiterminal cuts, SIAM J. Com-puting 23(1994)(4), 864–894.

17. M. Steel, M. Charleston, Five surprising properties of parsimoniouslycoloured trees, Bull. Math. Biol. 57(2)(1995), 367–375.

18. H.S. Zullo: Feasible flows in multicommodity graphs, Ph.D. ThesisUniversity of Colorado at Denver, (1995) 1–66.

19. J. Kleinberg - E. Tardos: Approximation algorithms for classificationproblem with pairwise relationships: metric labeling and Markov ran-dom fields, 40th IEEE FOCS’99 (1999), 14–23.

20. A. Gupta - E. Tardos: A constant factor approximation algorithmfor a class of classification problems, STOC 2000, Portland, Oregon,USA, (2000) 652–658.

21. J. Kleinberg - E. Tardos: Approximation algorithms for classificationproblem with pairwise relationships: metric labelling and Markov ran-dom fields, J. ACM 49 (2002), 616–639.

20

Page 21: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

29./ L. H. Clark, R. C. Entringer, P. Erdos, H. Sun and L. A. Szekely,Extremal problems for the Bondy-Chvatal closure of a graph,in: ”Graphs, Matrices, and Designs: Festschrift in Honor ofNorman J. Pullman”, ed. R. S. Rees, Marcel Dekker, Inc., N.Y., 1993, 73–83.

References

1. Spinrad, Jeremy P, A note on computing graph closures. 6th Interna-tional Conference on Graph Theory. Discrete Math. 276 (2004), no.1-3, 327–329.

30./ M. A. Steel, L. A. Szekely, P. L. Erdos and P. Waddell, A com-plete family of phylogenetic invariants for any number of taxa un-der the Kimure 3ST model, New Zealand J. of Botany 31(1993),289–296.

References

1. Alan R. Lemmon, Jeremy M. Brown, Kathrin Stanger-Hall and EmilyMoriarty Lemmon, The Effect of Ambiguous Data on PhylogeneticEstimates Obtained by Maximum Likelihood and Bayesian Inference,Syst Biol (2009) 58 (1): 130-145. doi: 10.1093/sysbio/syp017

2. DOUGLAS J. EMLEN, JENNIFER MARANGELO, BERNARD BALL,AND CLIFFORD W. CUNNINGHAM, DIVERSITY IN THE WEAPONSOF SEXUAL SELECTION: HORN EVOLUTION IN THE BEETLEGENUS ONTHOPHAGUS (COLEOPTERA: SCARABAEIDAE), Evo-lution, 59(5), 2005, pp. 10601084

3. Lemmon AR, Brown JM, Stanger-Hall K, et al., The Effect of Am-biguous Data on Phylogenetic Estimates Obtained by Maximum Like-lihood and Bayesian Inference, SYSTEMATIC BIOLOGY Volume: 58Issue: 1 Pages: 130-145 Published: FEB 2009

4. Allman ES, Rhodes JA, Molecular phylogenetics from an algebraicviewpoint Source: STATISTICA SINICA Volume: 17 Issue: 4 Pages:1299-1316 Published: OCT 2007

5. Heath TA, Hedtke SM, Hillis DM, Taxon sampling and the accuracy ofphylogenetic analyses Source: JOURNAL OF SYSTEMATICS ANDEVOLUTION Volume: 46 Issue: 3 Pages: 239-257 Published: MAY2008

6. A.A. Mignault: Molecular Phylogenetics In The Family Sphingidae(Lepidoptera: Bombycoidea) Ms.C. Thesis,University of Maryland,College Park (2004), 1–164.

7. J. G. Sumner, Entanglement, invariants and phylogenetics, Ph.D. The-sis, University of Tasmania, 2006.

8. JG Sumner, MA Charleston, LS Jermiin, PD Jarvis, Markov invari-ants, plethysms, and phylogenetics, JOURNAL OF THEORETICALBIOLOGY Volume: 253 Issue: 3 Pages: 601-615 Published: AUG 72008 XXX

21

Page 22: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

9. N Eriksson, Simulation studies of algebraic invariants for phylogeny

10. M Casanellas, J Fernandez-Sanchez Geometry of the Kimura 3-parametermodel ADVANCES IN APPLIED MATHEMATICS Volume: 41 Issue:3 Pages: 265-292 Published: SEP 2008

11. M Casanellas, J Fernandez-Sanchez, Performance of a New InvariantsMethod on Homogeneous and Nonhomogeneous Quartet Trees, Molec-ular Biology and Evolution, 24 Issue: 1 Pages: 288-293 Published:JAN 2007

12. D.M. Hillis: Phylogenetics and the study of HIV, in The Evolutionof HIV (Ed. K.A. Crandall) John Hopkins University Press (1999),105–121.

13. S.M. Sullivant: Toric ideals in algebraic statistics, UC Berkeley Ph.D.Thesis (2005), 1–137.

14. S.L. Pereira: Filogenia e evolucao molecular em cracidae (aves), Ph.D.thesis, Instituto De Biociencias Universidade De Sao Paolo - Brasil,(2000), 1–187.

15. K.M. Pickett - G.L. Tolman - W.C. Wheeler - J.W. Wenzel: Parsimonyovercomes statistical inconsistency with the addition of more data fromthe same gene, Cladistics 21 (2005), 438–445.

16. PJ Waddell, Measuring the Fit of Sequence Data to PhylogeneticModel: Allowing for Missing Data, Molecular Biology and Evolution,2004 Mar;22(3):395-401.

17. Emlen, Douglas J., Marangelo, Jennifer, Ball, Bernard, Cunningham,Clifford W., DIVERSITY IN THE WEAPONS OF SEXUAL SELEC-TION: HORN EVOLUTION IN THE BEETLE GENUS ONTHOPH-AGUS (COLEOPTERA: SCARABAEIDAE), Evolution Volume: 59(2005) Issue: 5 Pages: 1060-1084

18. D Sankoff, M Blanchette, Phylogenetic invariants for metazoan mito-chondrial genome evolution, Genome Inform Ser Workshop GenomeInform. 1998;9:22-31.

19. J Adachi, M Hasegawa, G Kitagawa - 1996 MOLPHY version 2.3:programs for molecular phylogenetics based on maximum likelihoodComp. Sci Monographs, N.96 Inst. Stat. Math. Tokyo (1996),1–150.

http://bioinfo.uah.edu/csm96.pdf

20. Molphy: ProtML, NucML phylogeny programs (by J. Adachi - M.Hasegawa)

http://bioweb.pasteur.fr/seqanal/interfaces/prot-nucml.html

21. Ziheng Yang: PAML: Phylogenetic analysis with maximum likelihood,PAML User’s Guide, (2004), 1–68.http://abacus.gene.ucl.ac.uk/software/paml.html

22. M.D. Hendy: Hademard conjugation: an analytical tool for phyloge-netics, in Mathematics of evolution & phylogeny (ed. O. Gascuel)Oxford Univ. Press (2004), 143–177.

22

Page 23: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

23. Lemmon AR, Moriarty EC The importance of proper model assump-tion in Bayesian phylogenetics SYSTEMATIC BIOLOGY 53 (2): 265-277 APR 2004

24. N. Eriksson, K. Ranestad, B. Sturmfels, S. Sullivant: Phylogeneticalgebraic geometry, Projective Varieties With Unexpected Properties:A Volume 2005

25. N. Eriksson Toric ideals of homogeneous phylogenetic models Inter-national Conference on Symbolic and Algebraic Computation, IS-SAC (2004), 149–154.

26. Elizabeth S. Allman and John A. Rhodes, Phylogenetic invariants forstationary base composition JOURNAL OF SYMBOLIC COMPUTA-TION 41 (2): 138-150 FEB 2006

27. Bernd Sturmfels and Seth Sullivant, Toric ideals of phylogenetic invari-ants JOURNAL OF COMPUTATIONAL BIOLOGY 12 (4): 457-481MAY 2005

28. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

29. Elizabeth S. Allman and John A. Rhodes, Phylogenetic invariants forthe general Markov model of sequence mutation, Mathematical Bio-sciences, 186, (2003) (2), 113–144.

30. J. Kim, Slicing hyperdimensional oranges: The geometry of phyloge-netic estimation, Mol. Phylogenet. Evol. 17 (1)(2000), 58–75.

31. R. Ota, P. J. Waddell, M. Hasegawa, et al., Appropriate likelihoodratio tests and marginal distributions for evolutionary tree models withconstraints on parameters, Mol. Biol. Evol. 17 (5) (2000), 798–803.

32. D. Sankoff and M. Blanchette, Phylogenetic invariants for genome re-arrangements, J. Comput. Biol. 6 (3-4) (1999), 431–435.

33. D. Sankoff and M. Blanchette, Probability models for genome rear-rangement and linear invariants for phylogenetic inference, RECOMB’99Lyon, France (1999), 302–309.

34. M. Steel, M. D. Hendy, D. Penny, Invertible models of sequence evolu-tion, Preprint 93/02, School of Mathematics, Massey University, sub-mitted to Mathematical Biosciences.

35. M. D. Hendy, M. A. Charleston, Hadamard conjugatio: a versatile toolfor modelling nucleotid sequence evolution, New Zealand J. Botany31(1993), 231–237.

36. M. D. Hendy, D. Penny, M. A. Steel, Discrete Fourier spectral analysisfor evolution, Proc. Natl. Acad. Sci. USA 91(1994), 3339–3343.

37. M. A. Steel, Y. X. Fu, Classifying and counting linear phylogeneticinvariants for the Jukes–Cantor model, J. Comp. Biol. 2(1995)(4),39–47.

38. V. Ferretti, D. Sankoff, A remarkable non-linear invariant for evolutionwith heterogeneous rates, 134(1996), Math. Bioscience 71–83.

23

Page 24: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

39. V. Ferretti, D. Sankoff, Phylogenetic invariants for more general evo-lutionary models, J. Theor. Biology 173(1995), 147–162.

40. X. Y. Fu, Linear invariants under Jukes and Cantors one-parametermodels, J. Theor. Biol. 173 (1995) (4), 339–352.

41. M. D. Hendy, D. Penny, Complete families of linear invariants forsome stochastic models of sequence evolution, with and without themolecular clock assumption, J. Comput. Biol. 3 (1996), 19–31.

42. D. Penny, M. Hendy, P. Lockhart, M. A. Steel, Corrected parsimony,minimum evolution and Hadamard conjugation, Syst. Biol. 45(1996)(4),596–606.

43. P. J. Waddell, D. Penny, T. Moore, Hadamard conjugations and mod-eling sequence evolution with unequal rates across sites, Mol. Phylo-genet. Evol 8(1997)(1) 33–50.

44. M. Steel, M. D. Hendy, D. Penny, Reconstructing evolutionary treesfrom nucleotide pattern probabilities, Universitat Bielefeld, Forschung-schwerpunkt Strukturbildungprozesse, Materialen XCIV, 1995.

45. D. L. Swofford, G. J. Olsen, P. J. Waddell, D. M. Hillis, PhylogeneticInference, in: Molecular Systematics, D. M. Hillis, C. Moritz, B. K.Mable, eds., 2nd edition, Sinauer Associates, Inc., Sunderland, Ma.,1996.

46. M. Steel, Reconstructing evolutionary models under a variety of Markov-style models, Proceedings of Phylogeny Workshop held at Prince-ton University, February 6–8, 1995, Host: Simon Tavare, DIMACSTechnical Report 95–48, October 1995, 51–54.

47. P. J. Waddell, D. Penny, Evolutionary trees of apes and humans fromDNA sequences, Chapter 3 in: Handbook of Symbolic Evolution,eds. A. J. Lock and C. R. Peters, Oxford University Press, Oxford, p.53–73.

48. P. J. Waddell, D. Penny, T. Moore, Extending Hadamard conjugationto model sequence evolution with variable rates across sites, Inf. andMath. Sci. Reports Series B 96/11, Massey University.

49. P. J. Waddell, Statistical Methods of Phylogenetic Analysis, IncludingHadamard Conjugations, LogDet Transforms, and Maximum Likeli-hood. PhD thesis, Massey University, New Zealand. (1996)

50. J. B. Whitfield, Molecular and morphological data suggest a single ori-gin of the polydnaviruses among braconid wasps, Naturwissenschaften84 (1997) (11), 502–507.

51. P. J. Waddell, M. A. Steel, General time-reversible distances with un-equal rates across sites: Mixing Gamma and inverse Gaussian distri-butions with invariant sites, Mol. Phylogenet. Evol. 8 (1997) (3),398–414.

52. M. E. Siddall, A. G. Kluge, Probabilism and phylogenetic inference,Cladistics 13 (1997) (4), 313–336.

24

Page 25: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

53. M. Steel, M. D. Hendy, D. Penny, Reconstructing phylogenies fromnucleotide pattern probabilities: a survey and some new results, Disc.Appl. Math. 88 (1998) 367–396.

54. T. R. Hagedorn, Determining the structure and number of phyloge-netic invariants, Adv. Appl. Math 24 (2000) 1–21.

55. T. R. Hagedorn, L. F. Landweber, Phylogenetic invariants and geom-etry, J. Theor. Biology 205 (3) (2000), 365–376.

56. S. N. Evans, X. W. Zhou, Constructing and counting phylogeneticinvariants, J. Comput. Biol. 5 (4)(1998), 713–724.

57. M. Steel, P. J. Waddell, Approximating likelihoods under low but vari-able rates across sites, Appl. Math. Letters 12 (6)(1999) 13–19.

58. T.R. Hagedorn: Invariants for the general model, Currents in Com-putational Molecular Biology, RECOMB’01, Montreal, Canada, postersection (ed. N. El-Mobrouk, T. Lengauer, D. Sankoff) (2001), 207–208.

31./ P. L. Erdos and L. A. Szekely, Counting bichromatic evolutionarytrees, Discrete Appl. Math. 47(1993), 1–8.

References

1. A. Meir - J. Moon - M.A. Steel: A limiting theorem on 2-coloredtrivalent trees. Congressus Numerantium 150 (2001), 43–63.

2. C. Semple and M. Steel, Phylogenetics, Oxford Lecture Series in Math-ematics and its Applications 24, Oxford University Press, 2003

3. M. A. Steel, Decompositions of leaf-coloured binary trees, Adv. Appl.Math. 14(1993), 1–24.

4. C. Tuffley: Bounding probabilities in a Markovian model of characterevolution, Research Report 132 University of Canterbury, Christchurch,New Zeeland, November (1995)

5. C. Tuffley and M. Steel, Links between maximum likelihood and max-imum parsimony under a simple model of site substitution, Bull.Math. Biol. 59 (1997)(3), 581–607.

32./ D. de Caen and L. A. Szekely, On a problem of Erdos and Lovasz,Ars Comb. 35A(1993), 187–192.

References

1. M. Simonovits, Some of my favourite Erdos Theorems, and relatedresults, theories, in: Paul Erdos and his Mathematics II, Bolyai Studies11, Springer-Verlag, 565–636.

2. Zoltan Furedi, Andre Kundgen, Turan problems for integer-weightedgraphs, J. Graph Theory 40 (2002), 195–225.

33./ L. A. Szekely, M. A. Steel, and P. L. Erdos, Fourier calculus onevolutionary trees, Adv. Appl. Math. 14(1993), 200–216.

25

Page 26: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Matsen FA, : Fourier Transform Inequalities for Phylogenetic Trees,IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGYAND BIOINFORMATICS Volume: 6 Issue: 1 Pages: 89-95 Published:JAN-MAR 2009

2. Bryant D, Hadamard Phylogenetic Methods and the n-taxon Process,BULLETIN OF MATHEMATICAL BIOLOGY Volume: 71 Issue: 2Pages: 339-351 Published: FEB 2009

3. Sullivant S Toric fiber products JOURNAL OF ALGEBRA 316 (2):560-577 OCT 15 2007

4. W. Buczynska - J.A. Wisniewski: On geometry of binary symmetricmodels of phylogenetic trees, J. European Math. Soc. 9 (3) (2007),609–635

5. E.S. Allman - J.A. Rhodes: Phylogenetic ideals and varieties for thegeneral Markov model, Adv. Appl. Math. 40 (2008) (2), 127–148.

6. Pachter L, Sturmfels B The mathematics of phylogenomics SIAM RE-VIEW 49 (1): 3-31 MAR 2007

7. S.M. Sullivant: Toric ideals in algebraic statistics, UC Berkeley Ph.D.Thesis (2005), 1–137.

8. S. Sullivant: Topic fiber products, arXiv:math.AC/0602052 v1 (2006),1–19.

9. Chor B, Hendy MD, Snir S Maximum likelihood Jukes-Cantor triplets:Analytic solutions MOLECULAR BIOLOGY AND EVOLUTION 23(3): 626-632 MAR 2006

10. E.S. Allman - J.A. Rhodes: The identifiability of tree topology for phy-logenetic models, including covarion and mixture models, JOURNALOF COMPUTATIONAL BIOLOGY 13 (5): 1101-1113 JUN 2006

11. M.D. Hendy - S. Snir: Hadamard conjugation for the Kimura 3STmodel: Combinatorial proof using path sets IEEE-ACM TRANSAC-TIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMAT-ICS Volume: 5 Issue: 3 Pages: 461-471 Published: JUL-SEP 2008

12. M.D. Hendy: Hademard conjugation: an analytical tool for phyloge-netics, in Mathematics of evolution & phylogeny (ed. O. Gascuel)Oxford Univ. Press (2004), 143–177.

13. M. Casanellas - L.D. Garcia - S. Sullivant: Catalog of small trees,Chapter 15, in Algebraic Statistics for Computational Biology(Ed. L. Pachter and B. Sturmfels) in press Cambridge Univ. Press(2005) 298–311.

14. M. Casanellas - S. Sullivant: The Strand Symmetric Model, Chap-ter 16, in Algebraic Statistics for Computational Biology (Ed. L.Pachter and B. Sturmfels) in press Cambridge Univ. Press (2005),312–330.

26

Page 27: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

15. D. Bryant: Extending tree models to split networks, Chapter 17, inAlgebraic Statistics for Computational Biology (Ed. L. Pachter andB. Sturmfels) in press Cambridge Univ. Press (2005), 331–346.

16. Bashford JS, Jarvis PD, Sumner JG, et al. U(1) x U(1) x U(1) sym-metry of the Kimura 3ST model and phylogenetic branching processesJ PHYS A-MATH GEN 37 (8): L81-L89 FEB 27 2004

17. C. Semple and M. Steel, Phylogenetics, Oxford Lecture Series in Math-ematics and its Applications 24, Oxford University Press, 2003

18. David Sankoff, Mathieu Blanchette, Comparative Genomics via Phy-logenetic Invariants for Jukes-Cantor Semigroups (1999) Proceedingsof the International Conference on Stochastic ...

19. M. Vingron - H-P. Lenhof - P. Mutzel, Computational Molecular Biol-ogy, in M. Dell’Amico, F. Maffioli, S. Montello, Annotated Bibliogra-phies in Combinatorial Optimization, Wiley, 1999, 445–471.

20. D. Sankoff and M. Blanchette, Phylogenetic invariants for genome re-arrangements, J. Comput. Biol. 6 (3-4) (1999), 431–435.

21. D. Sankoff - M. Blanchette: Probability models for genomec invariants,Adv. Appl. Prob. 25(1993), 290–302.

22. V. Ferretti, B. F. Lang, D. Sankoff, Skewed base composition, asym-metric transition matrices, and phylogenetic invariants, J. Computa-tional Biology 1(1994), 77–92.

23. M. D. Hendy, D. Penny, M. A. Steel, Discrete Fourier spectral analysisfor evolution, Proc. Natl. Acad. Sci. USA 91(1994), 3339–3343.

24. V. Ferretti, D. Sankoff, Phylogenetic invariants for more general evo-lutionary models, J. Theor. Biology 173(1995), 147–162.

25. V. Ferretti, D. Sankoff, A remarkable non-linear invariant for evolutionwith heterogeneous rates, 134(1996), Math. Bioscience 71–83.

26. D. Penny, M. Hendy, P. Lockhart, M. A. Steel, Corrected parsimony,minimum evolution and Hadamard conjugation, Syst. Biol. 45(1996)(4),596–606.

27. M. Steel, M. D. Hendy, D. Penny, Invertible models of sequence evolu-tion, Preprint 93/02, School of Mathematics, Massey University, sub-mitted to Mathematical Biosciences.

28. M. Steel, M. D. Hendy, D. Penny, Reconstructing evolutionary treesfrom nucleotide pattern probabilities, Universitat Bielefeld, Forschung-schwerpunkt Strukturbildungprozesse, Materialen XCIV, 1995.

29. D. L. Swofford, G. J. Olsen, P. J. Waddell, D. M. Hillis, PhylogeneticInference, in: Molecular Systematics, D. M. Hillis, C. Moritz, B. K.Mable, eds., 2nd edition, Sinauer Associates, Inc., Sunderland, Ma.,1996.

30. A. W. M. Dress, D. H. Huson and V. Moulton, Analyzing and visual-izing sequence and distance data using SplitsTree, Discrete AppliedMathematics, 71(1996), 95–109.

27

Page 28: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

31. P. J. Waddell, D. Penny, T. Moore, Extending Hadamard conjugationto model sequence evolution with variable rates across sites, Inf. andMath. Sci. Reports Series B 96/11, Massey University.

32. P. J. Waddell, D. Penny, T. Moore, Hadamard conjugations and mod-eling sequence evolution with unequal rates across sites, Mol. Phylo-genet. Evol 8(1997)(1) 33–50.

33. P. J. Waddell, Statistical Methods of Phylogenetic Analysis, IncludingHadamard Conjugations, LogDet Transforms, and Maximum Likeli-hood. PhD thesis, Massey University, New Zealand. (1996)

34. D. H. Huson, Analyzing Evolutionary Data with SplitsTree2: A Pro-gram for Analyzing and Visualizing Evolutionary Data, ftp::ftp.uni-bielefeld.de/pub/math/splits (1997)

35. M. Steel, M. D. Hendy, D. Penny, Reconstructing phylogenies fromnucleotide pattern probabilities: a survey and some new results, Disc.Appl. Math. 88 (1998) 367–396.

36. S. N. Evans, X. W. Zhou, Constructing and counting phylogeneticinvariants, J. Comput. Biol. 5 (4)(1998), 713–724.

34./ L. A. Szekely, P. L. Erdos, M. A. Steel and D. Penny, A Fourierinversion formula for evolutionary trees, Appl. Math. Letters6(1993) (2), 13–17.

References

1. Elizabeth S. Allman, Sonia Petrovic, John A. Rhodes, Seth Sullivant,Identifiability of 2-tree Mixtures for Group-based Models, ” IEEE/ACMTransactions on Computational Biology and Bioinformatics, 20 Aug.2010. IEEE computer Society Digital Library. IEEE Computer Soci-ety, http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.79

2. Goodall, Andrew, Combinatorics, Complexity, and Chance, January2007 , pp. 103-130(28), 7. FOURIER ANALYSIS ON FINITE ABELIANGROUPS: SOME GRAPHICAL APPLICATIONS.

3. Bryant D, : Hadamard Phylogenetic Methods and the n-taxon Process,BULLETIN OF MATHEMATICAL BIOLOGY Volume: 71 Issue: 2Pages: 339-351 Published: FEB 2009

4. P.D. Jarvis - J.D. Bashford - J.G. Sumner: Path integral formula-tion and Feynman rules for phylogenetic branching models, Journal ofPhysics A: Mathematical and General 38 (44), pp. 9621-9647

5. B. Chor, M. D. Hendy, S. Snir, Maximum likelihood Jukes-Cantortriplets: Analytic solutions, Mol. Biol. Evol. 23 (3) 2006.

6. P.D. Jarvis - J.D. Bashford - J.G. Sumner: Path integral formulationof phylogenetic branching processes, J. Phys. A: Math. Gen. 38(2005) 9621–9647.

28

Page 29: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

7. M.D. Hendy - S. Snir: Hadamard conjugation for the Kimura 3STmodel: Combinatorial proof using path sets Source: IEEE-ACM TRANS-ACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFOR-MATICS Volume: 5 Issue: 3 Pages: 461-471 Published: JUL-SEP2008

8. M.D. Hendy: Hademard conjugation: an analytical tool for phyloge-netics, in Mathematics of evolution & phylogeny (ed. O. Gascuel)Oxford Univ. Press (2004), 143–177.

9. P.D. Jarvis - J.D. Bashford - J.G. Sumner: Path integral formulation ofphylogenetic branching processes, preprint arXiv:q-bio.PE/0411047v1 27 Nov (2004), 1–21.

10. P. D. Jarvis, J. D. Bashford, Quantum field theory and phylogeneticbranching J PHYS A-MATH GEN 34 (49): L703-L707 DEC 14 2001.

11. D. Penny, M. D. Hendy, M. A. Steel, Progress with methods for con-structing evolutionary trees, Trends in Ecology & Evolution March1992 Vol 7, No. 3, 73–79.

12. M. Steel, M. D. Hendy, D. Penny, Invertible models of sequence evolu-tion, Preprint 93/02, School of Mathematics, Massey University, sub-mitted to Math. Biosciences.

13. D. Sankoff, Analytical approaches to genomic evolution, Biochimie75 (1993) (5), 409–413.

14. M. A. Steel, Y. X. Fu, Classifying and counting linear phylogeneticinvariants for the Jukes–Cantor model, J. Comp. Biol. 2(1995)(4),39–47.

15. M. Steel, M. D. Hendy, D. Penny, Reconstructing evolutionary treesfrom nucleotide pattern probabilities, Universitat Bielefeld, Forschung-schwerpunkt Strukturbildungprozesse, Materialen XCIV, 1995.

16. C. Tuffley, Trees and Ps and Things that Sneeze: Markov ProcessModels of Site Substitution, Master of Science in Mathematics Thesis,University of Canterbury, 1997.

17. M. Steel, M. D. Hendy, D. Penny, Reconstructing phylogenies fromnucleotide pattern probabilities: a survey and some new results, Disc.Appl. Math. 88 (1998) 367–396.

35./ F. Shahrokhi and L. A. Szekely, Concurrent flows and packetrouting in Cayley graphs, in: Graph-Theoretic Concepts in Com-puter Science Proc. 19th Intnl. Workshop WG’93, ed. J. vanLeeuwen, Lecture Notes in Computer Science Vol. 790, SpringerVerlag, Berlin, 1994, 327–338. (Also published as: Integral uni-form concurrent flows and all pairs packet routing, Congr. Num.97(1993), 3–16.)

29

Page 30: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. S. R. Ohring, F. Sarkar, S. K. Das, D. H. Hohndei, Cayley graph con-nected cycles: A new class of fixed-degree interconnection networks,28th Hawaii International Conference on System Sciences (HICSS’95)p. 479.

2. E Arraiz, A Mart?n, O Meza, M Ortega, Metaheuristics for computingthe forwarding index of a graph, International Transactions in Opera-tional Research Volume 12 Issue 3 Page 299 - May 2005

3. Marie-Claude Heydemann - Bertrand Ducourthial, Cayley Graphs andInterconnection Networks

4. C. Serafino, G. DiStefano, M. Flammini, Low-congested interval rout-ing schemes for hypercubelike networks, Networks 36 (2000), no. 3,191–201.

5. M.-C. Heydemann, Cayley graphs and interconnection networks, in:Algebraic Methods and Applications, eds. G. Hahn and G. Sabidussi,NATO ASI Series C Vol. 497, Kluwer, 1997, 167–224.

36./ P. L. Erdos and L. A. Szekely, On weighted multiway cuts intrees, Math. Programming, 65(1994), 93–105.

References

1. Navodit Misra, Guy Blelloch, R. Ravi and Russell Schwartz, Gener-alized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny, Research in Computational Molecular Biology Lec-ture Notes in Computer Science, 2010, Volume 6044/2010, 369-383,DOI: 10.1007/978-3-642-12683-3 24

2. Xin Xiao; Li Shuguang; Colored Multiway Cuts in Trees of Rings, In-ternational Forum on Information Technology and Applications, 2009.IFITA ’09. Issue Date: 15-17 May 2009 On page(s): 236 - 238

3. Xiang Xiao, Jingli Sun, ”Empirical Study on the Relationship betweenSalaries of Corporate Top Managers,” icie, vol. 2, pp.285-288, 2009WASE International Conference on Information Engineering, 2009

4. Weng Suxiang Jin Yonsheng, Deeply Analysis in Mobile Clients’ Con-sumptive Behavior Based on Data Mining Technology, 2009 Interna-tional Forum on Information Technology and Applications, Chengdu,China May 15-May 17 ISBN: 978-0-7695-3600-2

5. Xin Xiao; Li Shuguang; Colored Multiway Cuts in Generalized TreeNetworks, Information Engineering, 2009. ICIE ’09. WASE Interna-tional Conference on Issue Date: 10-11 July 2009, 299 - 301

6. Wittler, Roland Phylogeny-based analysis of gene clusters, Ph.D. The-sis, Universitat Bielefeld, 2010.

7. Pouly M, NENOK - A SOFTWARE ARCHITECTURE FOR GENERICINFERENCE, INTERNATIONAL JOURNAL ON ARTIFICIAL IN-TELLIGENCE TOOLS 19(1)(2010) 65–99

30

Page 31: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

8. Kalpakis K, Tang SL, Maximum lifetime continuous query processingin wireless sensor networks, AD HOC NETWORKS 8 (7)(2010) 723–741

9. J. Stoye, R. Wittler: A Unified Approach for Reconstructing An-cient Gene Clusters, IEEE-ACM TRANSACTIONS ON COMPUTA-TIONAL BIOLOGY AND BIOINFORMATICS Volume: 6 Issue: 3Pages: 387-400 Published: JUL-SEP 2009

10. Cedric BENTZ, Resolution exacte et approchee de problemes de multi-flot entier et de multicoupe: algorithmes et complexite, Ph. D. Thesis,2006,

11. Giribet G, Wheeler WC The case for sensitivity: a response to Grantand Kluge CLADISTICS 23 (3): 294-296 JUN 2007

12. Nagamochi H Algorithms for the minimum partitioning problems ingraphs ELECTRONICS AND COMMUNICATIONS IN JAPAN PARTIII-FUNDAMENTAL ELECTRONIC SCIENCE 90 (10): 63-78 2007

13. Alfieri, A., Nicosia, G., Pacifici, A., Exact algorithms for a discretemetric labeling problem, Discrete Optimization 3 (3), pp. 181-194,2006.

14. I. Milis: Approximating a Class of Classification Problems in EfficientApproximation and Online Algorithms (Ed. E. Bampis, K. Jansen,C. Kenyon) LNCS 3484 (2006), 213–249.

15. M. Pouly and J. Kohlas. Minimizing Communication Costs of Dis-tributed Local Computation. Tech. Report, Department of Infor-matics, University of Fribourg TR 05-20 (2005), 1–27.

16. C BENTZ, C COSTA, L LETOCART, F ROUPIN A BIBLIOGRA-PHY ON MULTICUT AND INTEGER MULTIFLOW PROBLEMSRapport technique CEDRIC No 654 (2004)

17. Nicosia, G., A. Pacifici (2004), Exact algorithms for a discrete metriclabeling problem. In Proc. CTW04 Workshop on Graphs andCombinatorial Optimization, (L. Liberti, F. Maffioli eds.) Elec.Notes in Discr. Math. 17 (2004), 196–200.

18. M-C. Costa - A. Billionnet: Multiway cut and integer flow problemsin trees, Elec. Notes Disc. Math. 17 (2004), 105–109.

19. C. Semple and M. Steel, Phylogenetics, Oxford Lecture Series in Math-ematics and its Applications 24, Oxford University Press, 2003

20. M-C. Costa - L. Letocart: Polynomial algorithms for multiterminal cutand flow problems in trees, in Proc. ECCO XV, (Lugano, Switzer-land) (Editor: Luca Maria Gambardella) (2002) 1–23.

21. M-C. Costa - L. Letocart - F. Roupin: Minimal multicut and maximalinteger multiflow: a survey - Proc. ECCO XIV (Bonn, Germany)(2001), also in European J. Operation Research (2004), 1–15.

22. M. Laurent: Max-cut problems, in M. Dell’Amico, F. Maffioli, S. Mon-tello, Annotated Bibliographies in Combinatorial Optimization,Wiley, 1999, 241–259

31

Page 32: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

23. E. Dahlhaus, D. S. Johnson, C. H. Papadimitriou, P. D. Seymour,M. Yannakakis, The complexity of multiway cuts, 24th ACM STOC(1992), 241–251.

24. D. Bertsimas, C. Teo, R. Vohra, Nonlinear formulations and improvedrandomized algorithms for multicut problems, in: Integer Program-ming and Combinatorial Optimization, 4th International IPCOConference, Copenhagen, Denmark, May 1995, Proceedings, eds.E. Balas and J. Clausen, Lecture Notes in Computer Science Vol. 920,Springer-Verlag, 29–39.

25. D. Bertsimas, C. Teo, R. Vohra, Analysis of LP relaxations for multi-way and multicut problems, Networks 34 (1999), 102–114.

26. C. Tuffley, Bounding probabilities in a Markovian model of characterevolution, Research Report No. 132, November 1995, University ofCanterbury, Christchurch, New Zealand.

27. W. Hasan, R. Motwani: Coloring away communication in parallelquery optimization, Proc. 21st VLDB Conf. Zurich, Swizerland,(1995) 239–250.

28. W. Hasan - R. Motwani: Coloring away communication in paral-lel query optimization, in Readings in Database Systems (MorganKaufmann Series in Data Management Systems, 3rd Ed) (Ed.M. Stonebraker and J.M. Hellerstein) Morgan-Kaufmann Publishers,(1998), 448-460.

29. W. Hasan: Optimization of SQL queries for parallel machines, Ph.D.Thesis Stanford University (1995) 1–122.

30. C. Tuffley and M. Steel, Links between maximum likelihood and max-imum parsimony under a simple model of site substitution, Bull.Math. Biol. 59 (1997)(3), 581–607.

31. G. Calinescu, H. Karloff, Y. Rabani, An impoved approximation algo-rithm for multiway cut, ACM STOC ’98, Dallas Texas USA (1998)48–52.

32. G. Calinescu, H. Karloff, An impoved approximation algorithm formultiway cut, J. Comp. Syst. Sci. 60 (3)(2000), 564–574.

33. Gruia Calinescu, Howard Karloff, Yuval Rabani, Multiway Cut (1998)

37./ F. Shahrokhi and L. A. Szekely, The complexity of the bottleneckgraph bipartition problem, J. Comb. Math. Comb. Comput.15(1994), 221–226.

References

1. Rui Li, Baogang Xu, Biased Judicious Partition of Graphs

2. Jie Ma Xingxing Yu, Partitioning 3-uniform hypergraphs

3. Baogang Xua, Juan Yana, Xingxing Yu, A note on balanced biparti-tions, Discrete Mathematics Volume 310, Issue 20, 28 October 2010,Pages 2613-2617

32

Page 33: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

4. Jie Ma, Pei-Lan Yen, Xingxing Yu, On several partition problems ofBollobas and Scott, Journal of Combinatorial Theory, Series B, 2010.

5. Jie Ma, Xingxing Yu, Bounds for pairs in partitions of graphs DiscreteMathematics, 2010.

6. Jie Ma Pei-Lan Yen, Xingxing Yu, Judicious partitions of hypergraphswith edge size at most 3, submitted

7. B. Xu, X. Yu, On a bipartition problem of Bollobas and Scott, Com-binatorica 29 (2009) 595–618.

8. T. D. Porter, and Bing Yang, Graph partitions II, J. Comb. Math.Comb. Comput. 37(2001), 149–158.

9. T. D. Porter, Graph partitions, J. Comb. Math. Comb. Comput.15(1994), 111–118.

10. T. D. Porter, Minimal partitions of a graph, Ars Combinatoria 53(1999), 181–186.

11. B. Bollobas, A. D. Scott, Exact bounds for judicious partitions ofgraphs, Combinatorica 19 (1999) (4), 473–486.

12. B. Bollobas, A. D. Scott, Problems and results on judicious partitions,Random Structures and Algorithms, Volume 21 , Issue 3-4 (October2002) 414 - 430.

38./ P. L. Erdos, A. Seress and L. A. Szekely, On intersecting chainsin Boolean algebras, Combinatorics, Probability, and Computing,3(1994), 57–62.

References

1. Karen Meagher, Covering arrays on graphs: qualitative independencegraphs and extremal set partition theory, arXiv:math/0701553

2. F. Brunk, Intersection problems in combinatorics, Ph.D. Thesis, St.Andrews University, 2008.

3. Rudolf Ahlswede,Vladimir Blinovsky, Lectures on advances in combi-natorics, Springer-Verlag, 2008

4. R. Ahlswede: Advances on extremal problems in number theory andcombinatorics, in European Congress of Mathematics, Barcelona,2000 Vol. 1, Progress in Mathematics 201 (2001), 147–175.

5. R. Ahlswede, N. Cai, Incomparability and intersection properties ofBoolean interval lattices and chain posets, Europ. J. Combinatorics17(1996), 667–687.

6. Eva Czabarka, Intersecting chains in finite vector spaces, Combina-torics, Probability and Computing, 8 (1999), 509–5282.

7. Eva Czabarka, Shifting technique in finite vector spaces, Ph.D. Thesis,University of South Carolina, Columbia, 1998.

39./ M. A. Steel, L. A. Szekely and M. D. Hendy, Reconstructing treeswhen sequence sites evolve at variable rates, J. ComputationalBiology 1(1994)(2), 153–163.

33

Page 34: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Luay Nakhleh, Phylogenetic Networks, Ph.D. Dissertation, Universityof Texas Austin 2004.

2. Elizabeth S. Allman, Mark T. Holder and John A. Rhodes, Estimatingtrees from filtered data: Identifiability of models for morphologicalphylogenetics Journal of Theoretical Biology Volume 263, Issue 1, 7March 2010, Pages 108-119

3. M.A. Steel, A basic limitation on inferring phylogenies by pairwisesequence comparisons , Journal of Theoretical Biology Volume 256,Issue 3, 7 February 2009, Pages 467-472

4. Allman ES, Rhodes JA, Molecular phylogenetics from an algebraicviewpoint Source: STATISTICA SINICA Volume: 17 Issue: 4 Pages:1299-1316 Published: OCT 2007

5. PJ Waddell, R Ota, D Penny, Measuring fit of sequence data to phylo-genetic model: Gain of power using marginal tests, Journal of molec-ular evolution, 2009 vol. 69, Number 4, 289-299,

6. IB Rogozin, VN Babenko, YI Wolf, EV Koonin, Dollo parsimony andreconstruction of genome evolution Chapter 11 in - Parsimony, phy-logeny, and genomics by V. A. Albert, Oxford University Press, 2005.

7. Frederick A. Matsen, Elchanan Mossel and Mike Steel, Mixed-up Trees:the Structure of Phylogenetic Mixtures, Bulletin of Mathematical Bi-ology Volume 70, Number 4, 1115-1139.

8. Elizabeth S. Allman, Cecile Ane, and John A. Rhodes, Identifiabilityof a Markovian model of molecular evolution with Gamma-distributedrates, Adv. in Appl. Probab. Volume 40, Number 1 (2008), 229-249.

9. James S. Farris, Parsimony and explanatory power, Cladistics 24(2008)Issue 5, pages 825847

10. E Susko, On the distributions of bootstrap support and posterior dis-tributions for a star tree, Syst Biol (2008) 57 (4): 602-612.

11. V Knoop, K Muller, Gene und Stammbaume: ein Handbuch zurmolekularen Phylogenetik, Spektrum Akademischer Verlag, 2. Au-flage, 2009.

12. M.A. Steel: Some statistical aspects of the maximum parsimony method,In Molecular Systematics and Evolution: Theory and Practice(Series: Experientia Supplementum Vol. 92) (Ed. R. DeSalle, G.Giribet, W. Wheeler). Birkhauser (2002), 125–140.

13. Warren John Ewens, Gregory Grant, Statistical Methods in Bioinfor-matics: An Introduction, - Science - 2001 - 476 pages.

14. S Aris-Brosou - Power of phylogenetic tests, Systematic Biology, 2003

15. WT White, SF Hills, R Gaddam, BR Holland, D Penny Treenesstriangles: visualizing the loss of phylogenetic signal. Molecular Biologyand Evolution 0737-4038 vol: 24 (9) 2007 p:2029 -39

34

Page 35: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

16. JGM Thewissen, SI Madar, ST Hussain, A Weiner, PL - ParametricPhylogenetics? Systematic Biology 1063-5157 vol: 49 (4) 2000 p:817

17. Daniel Stefankovic, Pitfalls of heterogeneous processes for phylogeneticreconstruction. Systematic Biology 1063-5157 vol: 56 (1) 2007 p:113-24

18. Ronald W. DeBry, Identifying Conflicting Signal in a Multigene Analy-sis Reveals a Highly Resolved Tree: The Phylogeny of Rodentia (Mam-malia), Systematic Biology, 52(5)(2003) 604-617

19. Penny, D., McComish, B.J., Charleston, M.A., Hendy, M.D. Math-ematical elegance with biochemical realism: The covarion model ofmolecular evolution (2001) Journal of Molecular Evolution, 53 (6), pp.711-723.

20. DeBry, R.W. Identifying Conflicting Signal in a Multigene AnalysisReveals a Highly Resolved Tree: The Phylogeny of Rodentia (Mam-malia) (2003) Systematic Biology, 52 (5), pp. 604-617.

21. Kosiol, C., Bofkin, L., Whelan, S. Phylogenetics by likelihood: Evo-lutionary modeling as a tool for understanding the genome (2006)Journal of Biomedical Informatics, 39 (1 SPEC. ISS.), pp. 51-61.

22. Elliott Sober, Instrumentalism, Parsimony, and the Akaike FrameworkPhilosophy of Science, volume 69 (2002), pages S112-S123

23. D Bryant, N Galtier, MA Poursat Likelihood calculation in molecularphylogenetics, Mathematics of Evolution and Phylogeny. Oxford; NewYork: 2004.

24. ES Allman, JA Rhodes The identifiability of tree topology for phylo-genetic models, including covarion and mixture models

25. RH Mihaescu, D Adkins, C Daskalakis, C Hill, A A Polynomial TimeAlgorithm for Phylogenetic Tree Reconstruction from Logarithmic-Sized Data

26. S. Schulmeister, Inconsistency of Maximum Parsimony Revisited, Syst.Biol. 53(4):521-528, 2004

27. NV Grishin, A Novel Approach to Phylogeny Reconstruction from Pro-tein Sequences, Journal of Molecular Evolution Volume 48, Number 3March 1999 264 - 273

28. J FAIVOVICH, CFB HADDAD, PCA GARCIA, DR FROST, JACAMPBELL, WC WHEELER Systematic Review of the Frog Fam-ily Hylidae, with special reference to Hylaniae: Phylogenetic Analysisand Taxonomic Revision, Bulletin of the American Museum of NaturalHistory, 2005, 240 pages.

29. P. Goloboff, Parsimony, likelihood, and simplicity, Cladistics Volume19 Page 91 - April 2003

30. RW DeBry, Identifying Conflicting Signal in a Multigene AnalysisReveals a Highly Resolved Tree: The Phylogeny of Rodentia (Mam-malia), Systematic Biology Volume 52, Number 5 / October 2003

35

Page 36: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

31. JG Sumner, PD Jarvis, Using the tangle: a consistent constructionof phylogenetic distance matrices for quartets 2006 Mathematical Bio-sciences 204 (1), pp. 49-67

32. ES Allman, JA Rhodes, Quartets and Parameter Recovery for theGeneral Markov Model of Sequence Mutation, Applied MathematicsResearch eXpress 2004, No. 4

33. Allman ES, Rhodes JA Phylogenetic ideals and varieties for the generalMarkov model, ADVANCES IN APPLIED MATHEMATICS Volume:40 Issue: 2 Pages: 127-148 Published: FEB 2008

34. Lusy Nakleh, Phylogenetic Networks, Ph. D. Thesis, Rice University,2004, 289 pages.

35. E Sober, Instrumentalism, Parsimony, and the Akaike Framework,Philosophy of Science, 69 (September 2002) pp. S112-S123.

36. ES Allman, Phylogenetic Invariants: Recent Progress and New Direc-tions, 67 pages.

37. X Gu, WH Li, Estimation of evolutionary distances under stationaryand nonstationary models of nucleotide substitution, PNAS Vol. 95,Issue 11, 5899-5905, May 26, 1998 This paper was presented at the col-loquium ”Computational Biomolecular Science,” organized by RussellDoolittle, J. Andrew McCammon, and Peter G. Wolynes, held Septem-ber 11-13, 1997, sponsored by the National Academy of Sciences at theArnold and Mabel Beckman Center in Irvine, CA.

38. R Tarrio, F Rodriguez-Trelles, FJ Ayala, Shared Nucleotide Compo-sition Biases Among Species and Their Impact on Phylogenetic Re-constructions of the Drosophilidae, Molecular Biology and Evolution18:1464-1473 (2001)

39. Bob Mau, Michael A. Newton, and Bret Larget, Bayesian phyogeneticinference via Markov chain Monte Carlo methods, University of Wis-consin - Madison, Department of Statistics preprint.

40. Stefankovic, D., Vigoda, E. Phylogeny of mixture models: Robust-ness of maximum likelihood and non-identifiable distributions (2007)Journal of Computational Biology, 14 (2), pp. 156-189.

41. D. Stefankovic, E. Vigoda, Phylogeny of mixture models: maximumlikelihood, ambiguity, and linear tests

42. E.S. Allman - J.A. Rhodes: The identifiability of tree topology forphylogenetic models, including covarion and mixture models, arXiv:r-bio.PE/0511009v1 (2005). 1–20.

43. E. Mossel, E. Vigoda, Phylogenetic MCMC algorithms are misleadingon mixtures of trees, Science Vol 309, 30 September 2005, 2207-2209.

44. Siddall ME Success of parsimony in the four-taxon case: Long-branchrepulsion by likelihood in the Farris Zone CLADISTICS 14: (3) 209-220 SEP 1998

36

Page 37: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

45. James S. Rogers, Maximum Likelihood Estimation of PhylogeneticTrees Is Consistent When Substitution Rates Vary According to theInvariable Sites plus Gamma Distribution, Systematic Biology, Volume50, Number 5 / September 1, 20 Pages: 713-722

46. S. Aris-Brosou, Least and most powerful phylogenetic tests to elucidatethe origin of the seed plants in presence of conflicting signals undermisspecified modes, Syst. Biol. 2003 52 (6), pp. 781-793.

47. S. N. Evans and T. Warnow, Unidentifiable divergence times in rates-across-sites models, IEEE Transactions on Computational Biologyand Bioinformatics 1 (2004) 130–135.

48. Elizabeth S. Allman and John A. Rhodes, Phylogenetic invariants forstationary base composition

49. Elizabeth S. Allman and John A. Rhodes, Quartets and parameterrecovery for the general Markov model of sequence mutation, AppliedMathematics Research Express 2004:4 (2004) 107-131.

50. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

51. C. Semple and M. Steel, Phylogenetics, Oxford Lecture Series in Math-ematics and its Applications 24, Oxford University Press, 2003

52. M. J. Sanderson, and J. Kim, Parametric phylogenetics? SystematicBiology, 49(4) (2000), 817-829.

53. E. Mossel, Phase transitions in phylogeny, T AM MATH SOC 356 (6):2379-2404 2004

54. Junhyong Kim, Tandy Warnow, Tutorial on Phylogenetic Tree Es-timation in ISMB’99, 7th Conf. Intell. Systems for MolecularBiology, August 6-10, Heidelberg, Germany Tutorial Section, (1999),1–29.

55. J. S. Farris, Likelihood and inconsistency, Cladistics 15 (1999), 199–204.

56. M. Steel, D. Penny, Parsimony, likelihood and the role of models inmolecular phylogenetics, Mol. Biol. Evol. 17 (2000), 839–850.

57. M. Steel, M. D. Hendy, D. Penny, Reconstructing evolutionary treesfrom nucleotide pattern probabilities, Universitat Bielefeld, Forschung-schwerpunkt Strukturbildungprozesse, Materialen XCIV, 1995.

58. Junhyong Kim, General inconsistency conditions for maximum parsi-mony: effects of branch edges and increasing number of taxa, Syst.Biol. 45(3)(1996), 363–374.

59. J. T. Chang, Inconsistency of evolutionary tree topology reconstruc-tion methods when substitution rates vary accross characters, Math.Biosci. 134 (1996), 189–215.

60. M. Steel, A. Cooper, D. Penny, Confidence intervals for divergencetime of two clades, Syst. Biol. 45(2)(1996), 127–134.

61. C. Tuffley, M. Steel, Modelling the covarion hypothesis of nucleotidesubstitution, Math. Biosci. 147 (1998), 63–91.

37

Page 38: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

62. M. Steel, Reconstructing evolutionary models under a variety of Markov-style models, Proceedings of Phylogeny Workshop held at Prince-ton University, F ebruary 6–8, 1995, Host: Simon Tavare, DIMACSTechnical Report 95–48, October 1995, 51–54.

63. A. de Queiroz, M. J. Donoghue, J. Kim, Separate versus combinedanalysis of phylogenetic evidence, Annual Review of Ecology andSystematics 26 (1995), 657–681.

64. K. Rice, T. Warnow, Parsimony is hard to beat, COCOON’97. (Com-puting and Combinatorics, Third Annual International Confer-ence), Shanghai, August 20-22, 1997, Tao Jiang and D.T. Lee, (Eds.).Lecture Notes in Computer Science Vol. 1276, Springer-Verlag 124–133.

65. P. J. Waddell, D. Penny, T. Moore, Extending Hadamard conjugationto model sequence evolution with variable rates across sites, Inf. andMath. Sci. Reports Series B 96/11, Massey University.

66. P. J. Waddell, D. Penny, T. Moore, Hadamard conjugations and mod-eling sequence evolution with unequal rates across sites, Mol. Phylo-genet. Evol 8(1997)(1) 33–50.

67. C. Tuffley, Trees and Ps ans Things that Sneeze: Markov ProcessModels of Site Substitution, Master of Science in Mathematics Thesis,University of Canterbury, 1997.

68. Junhyong Kim, Large-scale phylogenies and measuring the perfor-mance of phylogenetic estimators, Syst. Biol. 47(1) (1998), 43–60.

69. T. Warnow, Some combinatorial optimization problems in phyloge-netics, in: Graph Theory and Combinatorial Biology, L. Lovaszet. al., eds. Bolyai Society Mathematical Studies 7, Janos BolyaiMathematical Society, Budapest, 1999, 363–413.

70. E. Baake, What can and what cannot be inferred from pairwise se-quence comparison? Math. Biosci. 154 (1998), 1–21.

71. E. Baake, and Arndt von Haeseler, Distance measures in terms ofsubstitution processes, Theor. Population Biology 55 (1999) 166–175.

72. M. Steel, M. D. Hendy, D. Penny, Reconstructing phylogenies fromnucleotide pattern probabilities: a survey and some new results, Disc.Appl. Math. 88 (1998) 367–396.

73. M. Bonet, M. Steel, T. Warnow, S. Yooseph, Better methods for solv-ing parsimony and compatibility, J. Comp. Biol. 5(3) (1998), 391–407.

74. T. R. Hagedorn, Determining the structure and number of phyloge-netic invariants, Adv. Appl. Math 24 (2000) 1–21.

75. D. Huson, S. Nettles, T. Warnow, Obtaining highly accurate topol-ogy estimates of evolutionary trees from very short sequences, RE-COMB’99 Lyon, France (1999), 198–207.

38

Page 39: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

76. J. S. Farris, Likelihood and inconsistency, Cladistics 15 (1999), 199–204.

40./ N. Graham, R. C. Entringer and L. A. Szekely, New tricks for oldtrees: maps and the pigeonhole principle, Amer. Math. Monthly101(1994), 664–667.

References

1. Charles Wells, A Handbook of Mathematical Discourse, pp. 558, 2002.

2. Zhang F, Yan WG, : Enumerating spanning trees of graphs with aninvolution J. COMBINATORIAL THEORY SERIES A Volume: 116Issue: 3 Pages: 650-662 Published: APR 2009

3. Che ZY On k-pairable graphs from trees CZECHOSLOVAK MATH-EMATICAL JOURNAL 57 (1): 377-386 2007

4. H. Y. Gao,, Minimum tree-cycle-length of the tori,

5. D Christofides, Pair Lengths of Product Graphs, Discrete Math. 306(2006) 2111–2114.

6. Zhibo Chen, On k-pairable graphs, DISCRETE MATHEMATICS 287(1-3): 11-15 OCT 28 2004

7. K. B. Reid, The latency center of a tree,

8. D. B. West, Introductions to Graph Theory, Prentice-Hall, 1996.

9. T. D. Porter, The distance of a spanning tree, submitted to UtilitasMathematica.

10. K. B. Reid, The k-ball l-path branch weight centroid, Discrete Appl.Math. 80(1997)(2-3) 239–246.

11. K. B. Reid, Balance vertices in trees, Networks 34 (4) (1999), 264–271.

41./ R. C. Entringer, A. Meir, J. W. Moon and L. A. Szekely, Onthe Wiener index of trees from certain families, Australasian J.Comb., 10(1994), 211–224.

References

1. Computing the Szeged index of third and fourth dendrimer nanostars,Micro & Nano Letters, IET 2 (2007)(4)107 - 110

2. Deng H.-Y., The trees on n ≥ 9 vertices with the first to seventeenthgreatest Wiener indices are chemical trees, Communications in Math-ematical and in Computer Chemistry / MATCH 2007, vol. 57, br. 2,str. 393-402

3. Thomas Jansen, Madeleine Theile Stability in the self-organized evolu-tion of networks, GECCO ’07 Proceedings of the 9th annual conferenceon Genetic and evolutionary computation

39

Page 40: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

4. Tamur Ali Khan, Ralph Neininger, Tail Bounds for the Wiener Indexof Random Trees, DMTCS Proceedings, 2007 Conference on Analysisof Algorithms, AofA 07

5. H. Deng, WIENER INDEX OF TORI TP,Q[C4, C8] COVERED BYC4 AND C8, MATCH, 56(2006)(2) 357–374.

6. S. Wagner, Graph-theoretical enumeration and digital expansions: ananalytic approach, Ph.D. Thesis, Graz, 2006.

7. W Du, X Li, Y Shi, Algorithms and extremal problem on Wienerpolarity index, MATCH Commun. Math. Comput. Chem. v62

8. Ali Iranmanesh,Yaser Alizadeh, and Bahman Taherkhani, Computingthe Szeged and PI Indices of VC5C7[p,q] and HC5C7[p,q] Nanotubes,Int J Mol Sci. 2008 February; 9(2): 131144.

9. S. Wagner, H. Wang, On the parity of the Wiener index, EuropeanJournal of Combinatorics Volume 30, Issue 4, May 2009, Pages 996-1004

10. Dobrynin, A.A., Branchings in trees and the calculation of the Wienerindex of a tree, 2000 Match 41, pp. 119-134

11. Morris, K., Panholzer, A., Prodinger, H., On some parameters in heapordered trees , Combinatorics Probability and Computing 13 (4-5),pp. 677-696

12. Duncan J. Watts, Small Worlds: The Dynamics of Networks betweenOrder and Randomness, Princeton University Press, Princeton andOxford, 1999.

13. S. Wagner, Correlation of graph-theoretical indices SIAM JOURNALON DISCRETE MATHEMATICS 21 (1): 33-46 2007

14. S. Wagner, Some asymptotic results on the number of matchings ofrandom graphs and trees

15. S. Wagner, Subset counting in trees, Ars Combinatoria, to appear

16. S. Wagner, On the average Wiener index of trees, Australasian J.Comb. 2007.

17. S. Wagner, On the average Wiener index of trees II:Degree-restrictedtrees. Chemical trees.

18. A. Meir, J. W. Moon, On centroid branches of trees from certain fam-ilies, Discrete Math. 250 (2002), 153–170.

19. Yih-En Andrew Ban, Sergei Bespamyatnikh, Nabil H. Mustafa, On aconjecture of Wiener indices in combinatorial chemistry, Algorithmica,40(2):99-118, 2004.

20. Yih-En Andrew Ban, Sergei Bespamyatnikh, Nabil H. Mustafa, On aconjecture of Wiener indices in combinatorial chemistry, Proc. of theNinth International Computing and Combinatorics Conference CO-COON, 2003, LNCS 2697, pp. 509-518.

21. R. Entringer, Distance in graphs: trees, J. Comb. Math. Comb.Comput. 24 (1997), 65–84.

40

Page 41: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

22. K. MORRIS, A PANHOLZER, H PRODINGER, On Some Parametersin Heap Ordered Trees, Combinatorics, Probability and Computing(2004) 13, 677-696.

23. Svante Janson, The Wiener Index Of Simply Generated Random Trees,Random Structures and Algorithms, 22, No.4, 337-358 (2003).

24. Ralph Neininger, Wiener index of random trees Combinatorics, Prob-ability & Computing, 2002 11 (6), pp. 587-597.

25. L. H. Clark, A. Meir, and J. Moon, On the Steiner distance of treesfrom certain families, Australasian J. Comb. 20 (1999), 47–68.

42./ F. Shahrokhi and L. A. Szekely, On canonical concurrent flows,crossing number and graph expansion, Combinatorics, Probabil-ity, and Computing 3 (1994), 523–543.

References

1. Meinolf Sellmann, Reduction Techniques in Constraint Programmingand Combinatorial Optimization, Ph.D. Thesis, Universitat PaderbornFachbereich Mathematik/Informatik, 2002.

2. Vida Dujmovic, Ken-ichi Kawarabayashi, Bojan Mohar, David R. Wood,Improved upper bounds on the crossing number, SCG ’08 Proceedingsof the twenty-fourth annual symposium on Computational geometry,2008.

3. D BOKAL, G FIJAVZ, DR WOOD -THE MINOR CROSSING NUM-BER OF GRAPHS WITH AN EXCLUDED MINOR ELECTRONICJOURNAL OF COMBINATORICS Volume: 15 Issue: 1 Article Num-ber: R4 Published: JAN 1 2008

4. DR Wood, JA Telle, Planar Decompositions and the Crossing Numberof Graphs with an Excluded Minor New York J. Math 13(2007), 117–146.

5. D. Bokal, Structural Approach to the Crossing Number of Graphs,Doctoral Thesis, University of Ljubljana, 2006.

6. Marie-Claude Heydemann - Bertrand Ducourthial, Cayley Graphs andInterconnection Networks

7. Norbert Sensen, Lower Bounds and Exact Algorithms for the GraphPartitioning Problem using Multicommodity Flows, Lecture Notes inComputer Science Volume 2161 / 2001 p. 391.

8. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

9. J. P. Tillich, Edge isoperimetric inequalities for product graphs, Dis-crete Math 213 (2000), 291–320.

10. S. L. Bezrukov, Edge isoperimetric problems on graphs, in: GraphTheory and Combinatorial Biology, L. Lovasz et. al., eds. BolyaiSociety Mathematical Studies 7, Janos Bolyai Mathematical Society,Budapest, 1999, 157–198.

41

Page 42: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

11. P. Sole, J. P. Tillich, On the dual distance and the gap of a binarycode Discrete Math. 192(1998)(1-3) 333–336.

12. M.-C. Heydemann, Cayley graphs and interconnection networks, in:Algebraic Methods and Applications, eds. G. Hahn and G. Sabidussi,NATO ASI Series C Vol. 497, Kluwer, 1997, 167–224.

13. A. Liebers, Methods for planarizing graphs — a survey and annotatedbibliography, Konstanzer Schriften in Mathematik und Informatik12 (1996).

14. Liebers, A. Planarizing graphs - A survey and annotated bibliography(2001) Journal of Graph Algorithms and Applications, 5 (1), pp. 1-74.

43./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, Improvedbounds for the crossing numbers on surfaces of genus g, in:Graph-Theoretic Concepts in Computer Science Proc. 19th Intnl.Workshop WG’93, ed. J. van Leeuwen, Lecture Notes in Com-puter Science Vol. 790, Springer Verlag, Berlin, 1994, 388–395.

References

1. W Winterbach, The crossing number of a graph in the plane, MSc (Ap-plied Mathematics: Graph Theory) Thesis, University of Stellenbosch,2004.

2. P. Ruzicka, On efficiency of path systems induced by routing and com-munication schemes, Computing and Informatics 20 (2) (2001), 181–205.

3. A. Liebers, Methods for planarizing graphs — a survey and annotatedbibliography, Konstanzer Schriften in Mathematik und Informatik12 (1996).

4. Liebers, A. Planarizing graphs - A survey and annotated bibliography(2001) Journal of Graph Algorithms and Applications, 5 (1), pp. 1-74.

44./ F. Shahrokhi, L. A. Szekely and I. Vrto, Crossing numbers ofgraphs, lower bound techniques and algorithms: a survey, Proc.of Graph Drawing ’94 held at DIMACS, Princeton Lecture Notesin Computer Science Vol. 894, Springer Verlag, Berlin, 1995,131–142.

References

1. C Gutwenger, P Mutzel, R Weiskircher, Inserting an edge into a planargraph, Algorithmica (2005) 41: 289-308.

2. C Gutwenger, P Mutzel, R Weiskircher, Inserting an edge into a pla-nar graph, Symposium on Discrete Algorithms Proceedings of thetwelfth annual ACM-SIAM symposium on Discrete algorithms Wash-ington, D.C., United States Pages: 246 - 255 Year of Publication: 2001ISBN:0-89871-490-7

42

Page 43: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

3. W Winterbach, The crossing number of a graph in the plane, MSc (Ap-plied Mathematics: Graph Theory) Thesis, University of Stellenbosch,2004.

4. R. B. Richter, G. Salazar, A survey of good crossing number theoremsand questions,

5. Cyril Gavoille, Nicolas Hanusse, Compact Routing Tables for Graphsof Bounded Genus (1999) 26th International Colloquium on Automata,Languages and Programming (ICALP)

6. G. di Battista, P. Eades, R. Tamassia, I. G. Tollis, Graph Drawing(Algorithms for the visualization of graphs) Prentice Hall, 1999.

7. P. Bose, F. Gomez, P. Ramos, et al. Drawing nice projections ofobjects in space, Lecture Notes in Computer Science Vol. 1027, 1996,52–63.

8. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

9. R. Tamassia, Advances in the theory and practice of graph drawing,Technical Report, 1999 Theoretical Computer Science 217 (2), pp. 235-254

10. Tamassia, R., Graph Drawing, Chapter 44., in: CRC Handbook ofDiscrete and Computational Geometry, (E.Goodman, J. O’Rourke,eds.), CRC Press, 1997.

11. Redouane, Y., Communication in interconnection networks and gen-eralized degree in graphs, PhD. Thesis, Laboratoire de Recherche enInformatique, Paris-Orsay, 1997.

12. M. Junger, E. K. Lee, P. Mutzel, T. Odenthal, A polyhedral ap-proach to the multi-layer crossing minimization problem, in: Proc.5th Intl. Symposium Graph Drawing, Lecture Notes in ComputerScience 1353, Springer Verlag, Berlin, 1997, 13–24.

13. A. Liebers, Methods for planarizing graphs — a survey and annotatedbibliography, Konstanzer Schriften in Mathematik und Informatik12 (1996).

14. Liebers, A. Planarizing graphs - A survey and annotated bibliography(2001) Journal of Graph Algorithms and Applications, 5 (1), pp. 1-74.

15. J. Kratochvıl, Crossing number of abstract topological graphs, Proc.6th Intl. Symposium on Graphs Drawing, Lecture Notes in Com-puter Science, Springer Verlag, Berlin, 1998.

16. R. Tammasia, Graph drawing, in Handbook of Discrete and Compu-tational Geometry, ed. Goodman and O’Rourke, CRC press, 1997.

45./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, Book em-beddings and crossing numbers, in: Graph-Theoretic Conceptsin Computer Science Proc. 20th Intnl. Workshop WG’94, ed.J. van Leeuwen, Lecture Notes in Computer Science Vol. 903,

43

Page 44: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

Springer Verlag, Berlin, 1995, 256–268 (Also published as: Bookembeddings and crossing numbers, J. Graph Theory 21(1996)(4),413–424.)

References

1. LETICIA RODRIGUES BUENO, Sobre reducao de cruzamentos dearestas em desenho linear, Master Thesis, 2005, Maringa, PR.

2. Rong-Long Wang and Zheng Tang, A Parallel Algorithm for Fixed Lin-ear Crossing Number Problem, IJCSNS International Journal of Com-puter Science and Network Security, VOL.6 No.11, November 2006

3. Bansal, R.; Srivastava, K.; Shweta; Varshney, K.; Sharma, N.; Anevolutionary algorithm for the 2-page crossing number problem, vo-lutionary Computation, 2008. CEC 2008. (IEEE World Congress onComputational Intelligence). IEEE Congress on Issue Date: 1-6 June2008 On page(s): 1095 - 1102 Location: Hong Kong Print ISBN: 978-1-4244-1822-0

4. Hongmei. He, Ondrej. Sykora, A Hopfield Neural Network Model forthe Outerplanar Drawing Problem, IAENG International Journal ofComputer Science, 32:4, IJCS 32 4 17

5. H He, AM Salagean, E Ma”kinen, One- and two-page crossing num-bers for some types of graphs, INTERNATIONAL JOURNAL OFCOMPUTER MATHEMATICS 87(8)(2010) 1667–1679

6. A. Riskin, On the outerplanar crossing numbers of complete multipar-tite graphs, ArXiv:math/0605264v1

7. R. Cimikowski, B. Mumey, Approximating the fixed linear crossingnumber, (2007) Discrete Applied Mathematics, 155 (17), pp. 2202-2210.

8. H He, O Sy’kora, AM Salagean, I Vrt’o, Heuristic crossing minimisa-tion algorithms for the two-page drawing problem

9. He, O Sy’kora, A Salagean, Various island-based parallel genetic al-gorithms for the 2-page drawing problem Proceedings of the 24thIASTED international conference on ..., 2006

10. H He, O Sy’kora, AM Salagean, E Ma”kinen, Parallelisation of geneticalgorithms for the 2-page crossing number problem JOURNAL OFPARALLEL AND DISTRIBUTED COMPUTING 67 (2): 229-241FEB 2007

11. He HM, Sykora O, Makinen E An improved neural network model forthe two-page crossing number problem IEEE TRANSACTIONS ONNEURAL NETWORKS 17 (6): 1642-1646 NOV 2006

12. He HM, Sykora O, Makinen E Genetic algorithms for the 2-page bookdrawing problem of graphs JOURNAL OF HEURISTICS 13 (1): 77-93FEB 2007

44

Page 45: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

13. Wang, R.-L., Okazaki, K., Artificial neural network for minimum cross-ing number problem, 2005 International Conference on Machine Learn-ing and Cybernetics, ICMLC 2005, pp. 4201-4204

14. A Riskin, The circulark-partite crossing number ofKm,n, Arxiv preprintmath.CO/0605235, 2006

15. Wang RL, Okazaki K Solving the minimum crossing number problemusing an improved artificial neural network LECTURE NOTES INARTIFICIAL INTELLIGENCE 3930: 797-803 2006

16. Cimikowski R An analysis of some linear graph layout heuristics JOUR-NAL OF HEURISTICS 12 (3): 143-153 MAY 2006

17. Wang RL, Okazaki K An efficient parallel algorithm for the minimumcrossing number problem NEUROCOMPUTING 67: 411-416 AUG2005

18. Michael Baur, Ulrik Brandes, Crossing reduction in circular layouts.In: Proceedings of the 30th International Workshop on Graph-TheoreticConcepts in Computer Science (WG’04), Lecture Notes in ComputerScience, pages 332-343. Springer-Verlag, 2004

19. W Winterbach, The crossing number of a graph in the plane, MSc (Ap-plied Mathematics: Graph Theory) Thesis, University of Stellenbosch,2004.

20. Fulek R, He HM, Sykora O, et al. Outerplanar crossing, numbers of3-row meshes, Halin graphs and complete p-partite graphs LECTURENOTES IN COMPUTER SCIENCE 3381: 376-379 2005

21. Kolman P, Matousek J Crossing number, pair-crossing number, andexpansion JOURNAL OF COMBINATORIAL THEORY SERIES B92 (1): 99-113 SEP 2004

22. Hongmei He and O. Sykora, New circular drawing algorithms,

23. Wang RL, Xu XS, Tang Z A near-optimum parallel algorithm for agraph layout problem IEICE T FUND ELECTR E87A (2): 495-501FEB 2004

24. R. Cimikowski, B. Mumey, Approximating the fixed linear crossingnumber, Discrete Applied Mathematics, 122 (2002), no. 1-3,

25. A. Riskin, On the outerplanar crossing numbers of Km,n, BulletinICA 39 (2003), 7–15.

26. Dujmovic V, Wood DR On linear layouts of graphs DISCRETE MATH-EMATICS AND THEORETICAL COMPUTER SCIENCE 6 (2): 339-357 2004

27. R. Cimikowski, Algorithms for the fixed linear crossing number prob-lem Disc. Appl. Math. 122 (2002) (1-3), 93–115.

28. H. Harborth, Special numbers of crossings for complete graphs DiscreteMath. 244 (1-3) (2002) 95–102.

45

Page 46: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

29. D. Bergstrand, A. Woo, The outer crossing number of a graph: a newparameter with results for Km,n, Technical Report, Rollins College,1997.

30. A. Liebers, Methods for planarizing graphs — a survey and annotatedbibliography, Konstanzer Schriften in Mathematik und Informatik12 (1996).

31. Liebers, A. Planarizing graphs - A survey and annotated bibliography(2001) Journal of Graph Algorithms and Applications, 5 (1), pp. 1-74.

32. L. Stacho, I. Vrto, Bisection width of transposition graphs, DiscreteAppl. Math. 84 (1998), 221–235.

46./ D. J. Kleitman, R. C. Entringer and L. A. Szekely, A noteon spanning trees with minimum average distance, Bull. Inst.Comb. Appl. 17(1996), 71–78.

References

1. Bang Ye Wu, KunMao Chao, Chuan Yi Tang, On the Optimum Re-quirement Graph Problem, Proc. of the 19th Workshop on Combina-torial Mathematics and Computation Theory

2. Kenta Ozeki and Tomoki Yamashita, Spanning Trees: A Survey, Graphsand Combinatorics DOI: 10.1007/s00373-010-0973-2

3. Maurice Tchuente, Paulin Melatagia Yonta, Jean-Michel Nlong andYves Denneulin, On the Minimum Average Distance Spanning Tree ofthe Hypercube, Acta Applicandae Mathematicae Volume 102, Num-bers 2-3, 219-236, DOI: 10.1007/s10440-008-9215-5

4. Vojtech Balint, The non-approximability of bicriteria network designproblems, Journal of Discrete Algorithms Volume 1, Issues 3-4, June2003, Pages 339-355

5. Peter Dankelmann, Roger Entringer, Average distance, minimum de-gree, and spanning trees, Journal of Graph Theory Volume 33, Issue1, pages 113, January 2000

6. Wu, B.Y., On the intercluster distance of a tree metric, (2006) Theo-retical Computer Science, 369 (1-3), pp. 136-141.

7. A. A Dobrynin, R. Entringer, I. Gutman, Wiener index of trees: The-ory and applications, Acta Appl. Math. 66 (3) (2001), 211–249.

8. Dahlhaus E, Dankelmann P, Goddard W, et al. MAD trees anddistance-hereditary graphs DISCRETE APPL MATH 131 (1): 151-167 SEP 6 2003

9. BY Wu, KM Chao, CY Tang, Light graphs with small routing cost,Networks Volume 39, Issue 3 , Pages 130 - 138

10. I Broere, MJ Doring, P Dankelmann, The average distance in weightedgraphs

11. BY Wu, KM Chao, CY Tang, On the Optimum Requirement GraphProblem

46

Page 47: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

12. P Dankelmann, A note on MAD spanning trees J. Combin. Math.Combin. Comput, 2000

13. P. Dankelmann, G. Dlamini, H. C. Swart, Upper bounds on distancemeasures in K2,l-free graphs,

14. G. W. Peck, Kleitman and combinatorics: a celebration, DiscreteMath. 257 (2002), 193–224.

15. R. Entringer, Distance in graphs: trees, J. Comb. Math. Comb.Comput. 24 (1997), 65–84.

16. T. D. Porter, A bound involving the centroid and the Wiener index ofa tree, Utilitas Math. 53 (1998), 141–146.

17. P. Dankelmann, R. Entringer, Average distance, minimum degree, andspanning trees, J. Graph Theory 33 (2000), 1–13.

47./ C. Barefoot, L. H. Clark, R. C. Entringer, T. D. Porter, L. A.Szekely and Zs. Tuza, Minimal l-cycle saturated graphs, DiscreteMath. 150(1996), 31–48.

References

1. Tom Bohman, Maria Fonoberova, Oleg Pikhurko, The Saturation Func-tion of Complete Partite Graphs, J. of Combinatorics, 2010.

2. Paul Wenger, Three Existence Problems in Extremal Graph Theory,Ph.D. Thesis, University of Illinois at Urbana-Champaign, 2010.

3. Yehuda Ashkenazi, Path Saturated Graphs

4. Chen YC, Minimum C-5-Saturated Graphs, JOURNAL OF GRAPHTHEORY Volume: 61 Issue: 2 Pages: 111-126 Published: JUN 2009

5. Gould R, Luczak T, Schmitt J Constructive upper bounds for cycle-saturated graphs of minimum size ELECTRONIC JOURNAL OFCOMBINATORICS 13 (1): Art. No. R29 MAR 31 2006

6. Pikhurko O., Results and open problems on minimum saturated hy-pergraphs ARS COMBINATORIA 72: 111-127 JUL 2004

7. Y. Ashkenazi, C3-saturated graphs, Discrete Math 297 (2005), no. 1-3,152–158.

8. D. Bryant, and Hung-Lin Fu, C4-saturated bipartite graphs, DiscreteMath. 259 (1-3) (2002), 263-268.

9. T. D. Porter, Some results in combinatorial analysis and graph theory,Ph. D. Thesis, University of New Mexico, Albuquerque, NM, 1990.

48./ F. Shahrokhi and L. A. Szekely, Uniform concurrent multicom-modity flow in product graphs, Proceedings of the Twenty-seventhSoutheastern International Conference on Combinatorics, GraphTheory and Computing (Baton Rouge, LA, 1996), Congr. Nu-merantium 122 (1996), 67–89.

47

Page 48: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. P. Bonsma, Matching-cuts and Leafy Trees in Graphs 2006

2. P. Bonsma, Sparsest cut and concurrent flows in product graphs, Dis-crete Appl. Math. 2004, 136 (2-3), pp. 173-182

49./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, The cross-ing number of a graph on a compact 2-manifold, Adv. Math.123(1996), 105–119.

References

1. Vida Dujmovic, Ken-ichi Kawarabayashi, Bojan Mohar, David R. Wood,Improved upper bounds on the crossing number, SCG ’08 Proceedingsof the twenty-fourth annual symposium on Computational geometry,2008.

2. PAUL C. KETTLER, A CONSTRUCTIVE PROOF OF THE HIRSCHCONJECTURE, manuscript 2009.

3. Biswal P, Lee JR, Rao S, Eigenvalue Bounds, Spectral Partitioning,and Metrical Deformations via Flows, JOURNAL OF THE ACM57(3)2010

4. The minor crosssing number of graphs with an excluded minor Au-thor(s): Bokal D, Fijavz G, Wood DR Source: ELECTRONIC JOUR-NAL OF COMBINATORICS Volume: 15 Issue: 1 Article Number:R4 Published: JAN 1 2008

5. DR Wood, JA Telle, Planar Decompositions and the Crossing Numberof Graphs with an Excluded Minor New York J. Math 13(2007), 117–146.

6. D. Bokal, Structural Approach to the Crossing Number of Graphs,Doctoral Thesis, University of Ljubljana, 2006.

7. Drago Bokal, On the crossing numbers of Cartesian products withtrees, Journal of Graph Theory, 2007.

8. O. Sykora, I. Vrto, On VLSI layouts of the star graph and relatednetworks, Integration, the VLSI Journal 17(1994), 83–93.

9. M. Scharbrodt, Die Kreuzungszahl von Graphen, Diplomarbeit, In-stitut fur Informatik der Universitat zu Koln, 1994.

10. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

11. R. K. Guy, A quarter century of Monthly unsolved problems, 1969-1993, American Mathematical Monthly 100 (1993), 945–949.

50./ C. A. Barefoot, R. C. Entringer, and L. A. Szekely, Extremalvalues for ratios of distances in trees, Discrete Appl. Math.80(1997), 37–56.

48

Page 49: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Dong HW, Guo XF, Character of Graphs with Extremal Balaban In-dex, MATCH-COMMUNICATIONS IN MATHEMATICAL AND INCOMPUTER CHEMISTRY 63(3)(2010) 799–812.

2. Du WX, Li XL, Shi YT, Algorithms and Extremal Problem on WienerPolarity Index, MATCH-COMMUNICATIONS IN MATHEMATICALAND IN COMPUTER CHEMISTRY Volume: 62 Issue: 1 Pages: 235-244 Published: 2009

3. P Dankelmann, SA Durban, Average Distance and Generalised Pack-ing in Graphs, DISCRETE MATHEMATICS 310(17-18)(2010) 2334–2344.

4. Dahlhaus E, Dankelmann P, Ravi R A linear-time algorithm to com-pute a MAD tree of an interval graph INFORM PROCESS LETT 89(5): 255-259 MAR 16 2004

5. Dahlhaus E, Dankelmann P, Goddard W, et al. MAD trees anddistance-hereditary graphs DISCRETE APPL MATH 131 (1): 151-167 SEP 6 2003

6. Wuchty S, Stadler PF Centers of complex networks J THEOR BIOL223 (1): 45-53 JUL 7 2003

7. F Jelen, Superdominance Order and Distance of Trees, Ph. D. Thesis2002, Bonn University.

8. A. A. Dobrynin, R. Entringer, I. Gutman, Wiener index of trees: The-ory and applications, Acta Appl. Math. 66 (3) (2001), 211–249.

9. R. Entringer, Distance in graphs: trees, J. Comb. Math. Comb.Comput. 24 (1997), 65–84.

10. T. D. Porter, A bound involving the centroid and the Wiener index ofa tree, Utilitas Math. 53 (1998), 141–146.

51./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, Drawingsof graphs on surfaces with few crossings, Algorithmica 16 (1996)118–131.

References

1. S Smorodinsky, M. Sharir, On k-Sets in Three Dimensions, Relations,1999.

2. Chimani, Markus, Computing crossing numbers, Ph.D. Thesis, TUDortmund, 2009.

3. Vida Dujmovic, Ken-ichi Kawarabayashi, Bojan Mohar, David R. Wood,Improved upper bounds on the crossing number, SCG ’08 Proceedingsof the twenty-fourth annual symposium on Computational geometry,2008.

4. Daniel NΘ Coore, Botanical ComputingΘ A Developmental Approachto Generating Interconnect Topologies on an Amorphous Computer,PhD Thesis, MIT, 1999.

49

Page 50: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

5. The minor crosssing number of graphs with an excluded minor Au-thor(s): Bokal D, Fijavz G, Wood DR Source: ELECTRONIC JOUR-NAL OF COMBINATORICS Volume: 15 Issue: 1 Article Number:R4 Published: JAN 1 2008

6. DR Wood, JA Telle, Planar Decompositions and the Crossing Numberof Graphs with an Excluded Minor New York J. Math 13(2007), 117–146.

7. S Lok, S Feiner, A Survey of Automated Layout Techniques for Infor-mation Presentations, Proceedings of SmartGraphics, 2001

8. R. Cimikowski, I. Vrto, Improved bounds for the crossing number ofthe mesh of trees Journal of Interconnection Networks, 2003 -

9. W Winterbach, The crossing number of a graph in the plane, MSc (Ap-plied Mathematics: Graph Theory) Thesis, University of Stellenbosch,2004.

10. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

52./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, The crossingnumbers of meshes, Proc. Symposium on Graph Drawing ’95,ed. F. J. Brandenburg, Lecture Notes in Computer Science 1027,Springer Verlag, Berlin, 463–471.

References

1. W Winterbach, The crossing number of a graph in the plane, MSc (Ap-plied Mathematics: Graph Theory) Thesis, University of Stellenbosch,2004.

2. A. Liebers, Methods for planarizing graphs — a survey and annotatedbibliography, Konstanzer Schriften in Mathematik und Informatik12 (1996).

3. Liebers, A. Planarizing graphs - A survey and annotated bibliography(2001) Journal of Graph Algorithms and Applications, 5 (1), pp. 1-74.

4. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

5. G. Salazar, Crossing numbers of certain families of graphs, Ph.D.Thesis, Dept. Math. and Statistics, Carleton Uni., Ottawa, 1997.

6. G. Salazar, G., A lower bound on the crossing number of Cm × Cn,Technical Report, IICO-UASLP, San Luis Potosi, 1998.

53./ L. A. Szekely, Crossing numbers and hard Erdos problems indiscrete geometry, Combinatorics, Probability, and Computing6(1997), 353–358.

50

Page 51: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. S Backman, E Croot, M Hamel, D Hart, Sum-product inequalitieswith perturbation, - Arxiv preprint arXiv:0907.0175, 2009

2. I. Barany, Applications of graph and hypergraph theory in geome-try, in: Combinatorial and Computational Geometry, eds. Jacob E.Goodman,Jnos Pach,Emo Welzl, MSRI Publications Vol. 52, 2005,pp. 31–48.

3. CY Shen, Algebraic methods in sum-product phenomena, Arxiv preprintarXiv:0911.2627, 2009

4. Shengjun Pan, On the crossing numbers of complete graphs, Ph.D.Thesis, University of Waterloo, 2006.

5. Ryan Schwartz Jozsef Solymosi, arXiv:1008.3671v1 [math.CO] 22 Aug2010 Frank de Zeeuw, Rational Distances with Rational Angles,

6. B. Reed, Computing Crossing Number in Linear Time, STOC’07, 2007- ACM Press.

7. JA Bondy and USR Murty, Graph Theory, Springer, 2008.

8. David CharltonΛ, Erik D. DemaineΛ, Martin L. DemaineΛ Vida Du-jmovi´c, Pat Morin, Ryuhei Uehara, Ghost Chimneys, CCCG 2010,Winnipeg MB, August 9-11, 2010

9. Steven Stivek, The distances determined by a finite point set

10. E. Borenstein, Additive stucture, rich lines, and exponential set-expansion,Ph.D. Thesis, Georgia Institute of Technology, 2009.

11. Adrian Dumitrescu, On distinct distances among points in general po-sition and other related problems Periodica Mathematica Hungarica,Volume 57, Number 2 / December, 2008 Pages 165-176

12. Gyorgy Elekes, Micha Sharir, Incidences in Three Dimensions and Dis-tinct Distances in the PlaneΛ, Proceedings of the 2010 annual sympo-sium

13. J Matousek, The number of unit distances is almost linear for mostnorms, Advances in Mathematics, 2010

14. S. Pettie, On Nonlinear Forbidden 0-1 Matrix Problems:A refutation ofa Fredi-Hajnal conjecture, Proceedings 21st ACM-SIAM Symposiumon Discrete , 2010

15. PAUL H. KOESTER, SZEMER´EDI-TROTTER INCIDENCE THE-OREM AND APPLICATIONS

16. Terence Tao, Structure and Randomness: pages from year one of amathematical blog, American Mathematical Society, 2000 pp. xii+301.

17. Cooper J, Walters M, Iterated Point-Line Configurations Grow Doubly-Exponentially, DISCRETE & COMPUTATIONAL GEOMETRY 43(3)(2010)554–562

51

Page 52: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

18. Steinerberger S, A note on the number of different inner productsgenerated by a finite set of vectors, DISCRETE MATHEMATICS310(5)(2010) 1112–1117.

19. Pach J, Solymosi J, Tardos G, Crossing Numbers of Imbalanced Graphs,JOURNAL OF GRAPH THEORY 64(1)(2010) 12–21.

20. Elekes G, Density version of a theorem of Beck and Szemeredi-Trotterin combinatorial geometry, to appear in Annales Univ. Sci. Bud.Eotvos.

21. Elekes G, Simonovits M, Szabo E, A Combinatorial Distinction Be-tween Unit Circles and Straight Lines: How Many Coincidences Canthey Have? COMBINATORICS PROBABILITY & COMPUTING 18(2009) Issue: 5 691-705

22. Elekes, G, On the structure of sets with many k-term arithmetic pro-gressions, ACTA ARITHMETICA 138 (2009) Issue: 2 145–164.

23. Fox J, Pach J, Toth CD, A bipartite strengthening of the CrossingLemma, JOURNAL OF COMBINATORIAL THEORY SERIES B100 (2010) Issue: 1 23-35.

24. Sui Yung Cheung, De probabilistische methode, Bachelorscriptie, 2008,Universitat van Amsterdam.

25. Carmi, Paz; Dujmovic, Vida; Morin, Pat; Wood, David R. Distinctdistances in graph drawings. Electron. J. Combin. 15 (2008), no. 1,Research Paper 107, 23 pp.

26. Pach J, Toth G, : Degenerate Crossing Numbers, DISCRETE & COM-PUTATIONAL GEOMETRY Volume: 41 Issue: 3 Pages: 376-384Published: APR 2009

27. Dumitrescu A, Sharir M, Toth CD, Extremal problems on triangleareas in two and three dimensions, JOURNAL OF COMBINATO-RIAL THEORY SERIES A Volume: 116 Issue: 7 Pages: 1177-1198Published: OCT 2009

28. J. Pach and M. Sharir, Combinatorial Geometry and its AlgorithmicApplications, The Alcala Lectures, Mathematical Surveys and Mono-graphs, Vol. 152, Providence, Rhode Island, 2009, American Mathe-matical Society, VIII+235 pages.

29. Noga Alon, Joel Spencer, The probabilistic method, John Wiley andSons, Second Edition, 2004.

30. The minor crosssing number of graphs with an excluded minor Au-thor(s): Bokal D, Fijavz G, Wood DR Source: ELECTRONIC JOUR-NAL OF COMBINATORICS Volume: 15 Issue: 1 Article Number:R4 Published: JAN 1 2008

31. K. J. Swanepoel, UNIT DISTANCES AND DIAMETERS IN EU-CLIDEAN SPACES Discrete Comput. Geom. 41 (2009) 1-27.

32. R. Radoicic, New Results in Erdos-type Combinatorics, Ph.D. Thesis,MIT, 2004.

52

Page 53: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

33. M. Sharir, Arrangements in Geometry: Recent Advances and Chal-lenges LNCS 4698, Springer 2007, 12-16.

34. Bokal D, Fijavz G, Wood DR, The minor crosssing number of graphswith an excluded minor,ELECTRONIC JOURNAL OF COMBINA-TORICS Volume: 15 Issue: 1 Article Number: R4 P ublished: JAN 12008

35. J. Solymosi, C.D. Toth, On a question of Bourgain about geomet-ric incidences COMBINATORICS PROBABILITY & COMPUTINGVolume: 17 Issue: 4 Pages: 619-625 Published: JUL 2008

36. PK Agarwal, R Apfelbaum, G Purdy, M Sharir, Similar simplices in ad-dimensional point set Proceedings of the twenty-third annual sym-posium on , 2007.

37. S. Chaudhuri, Distance sets and the Erdos problem, B. Tech. ProjectReport, April 2005.Indian Institute of Technology.

38. A Dumitrescu, CD Toth, Extremal problems on triangle areas in twoand three dimensions eprint arXiv: 0710.4109, 2007 - arxiv.org

39. A Dumitrescu, CD Toth, Distinct triangle areas in a planar point setProc. 12th Conf. on Integer Programming and Combinat. Opt -Springer

40. B. Bollobas, The Art of Mathematics Coffee Time in Memphis, 2006,Cambridge University Press.

41. DR Wood, JA Telle, Planar Decompositions and the Crossing Numberof Graphs with an Excluded Minor New York J. Math 13(2007), 117–146.

42. Terence Tao, Van H. Vu, Additive Combinatorics, (Cambridge Studiesin Advanced Mathematics 105) 2003.

43. Julia Garibaldi and Alex Iosevich, The Erdos Distance Problem: Lec-ture Notes (15 pages)

44. Matousek, J., Sharir, M., Smorodinsky, S., Wagner, U., K-sets in fourdimensions, Discrete and Computational Geometry 35 (2), pp. 177-191

45. Pach, J., Toth, G., Degenerate crossing numbers, 2006 Proceedings ofthe Annual Symposium on Computational Geometry 2006, pp. 255-258.

46. Terence Tao, Van Vu, Entropy methods

47. P. K. Agarwal, B. Aronov, M. Sharir, On the complexity of many facesin arrangements of pseudosegments and of circles, in: B. Aronov, S.Basu, J. Pach, M. Sharir, eds., Discrete and Computational geometryThe Goodman-Pollack Festschrift, Springer, 2003, 1–25.

48. Akutsu T Algorithms for point set matching with k-differences IN-TERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTERSCIENCE 17 (4): 903-917 AUG 2006

53

Page 54: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

49. Bishnu A, Das S, Nandy SC, et al. Simple algorithms for partial pointset pattern matching under rigid motion PATTERN RECOGNITION39 (9): 1662-1671 SEP 2006

50. D. Bokal, Structural Approach to the Crossing Number of Graphs,Doctoral Thesis, University of Ljubljana, 2006.

51. S. Abolfathe, Incidence problems in plane and higher dimensions

52. Wikipedia, http://en.wikipedia.org/wiki/Crossing number

53. Prospects in Mathematics, ed. by Hugo Rossi, 1998, page 162

54. A. Pluhar, The Recycled Kaplansky’s Game, Acta Cybernetica, 2004

55. K Kawarabayashi, B Reed - Computing crossing number in linear time,Proceedings of the thirty-ninth annual ACM symposium on , 2007.

56. Matousek J, Sharir M, Smorodinsky S, et al. K-sets in four dimen-sions DISCRETE & COMPUTATIONAL GEOMETRY 35 (2): 177-191 FEB 2006

57. Wolf Prize in Mathematics edited by Shiing-Shen Chern, FriedrichHirzebruch, World Scientific, 2001.

58. P. Brass, J. Pach, Problems and results on geometric patterns, in:Graph Theory and Combinatorial Optimization, eds. D. Avis et al.,(GERAD 25th Anniversary Series) Spronger Verlag, New York, 2005,17–36.

59. J Solymosi Ramsey-type resultson planar geometric objects, Ph.D.Thesis, ETHZ.

60. J. Matousek, Lectures on Discrete Geometry, Springer-Verlag, 2002.

61. Alon, N., Last, H., Pinchasi, R., Sharir, M. On the Complexity ofArrangements of Circles in the Plane, Discrete Comput Geom 26:465-492 (2001)

62. J. Solymosi, Dense arrangements are locally very dense I SIAM JOUR-NAL ON DISCRETE MATHEMATICS 20 (3): 623-627 2006

63. Michiel Smid, Planar Graphs, Euler’s Formula, Crossing Numbers,Point-Line Incidences, and Unit-Distances, Carleton University.

64. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

65. S. Smorodinsky, Combinatorial Problems in Computational Geometry,Ph. D. Thesis, Tel-Aviv University, 2003.

66. P. K. Agarwal, E. Nevo, J. Pach, R. Pinchasi, M. Sharir, S. Smorodin-sky, Lenses in arrangements of pseudo-circles and their applications,Journal of the ACM, 2004, 51 (2), pp. 139-186

67. A Iosevich, H Jorati, I Laba, Geometric incidence theorems via Fourieranalysis, TRANSACTIONS OF THE AMERICAN MATHEMATI-CAL SOCIETY 361(2009)Issue: 12 6595-6611.

68. I. Laba, FROM HARMONIC ANALYSIS TO ARITHMETIC COM-BINATORICS, Bulletin (new series) of the AMS 45 (1): 77-115 2008

54

Page 55: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

69. G. Elekes, Csaba D. Toth, Incidences of not-too-degenerate hyper-planes, Annual Symposium on Computational Geometry archive Pro-ceedings of the twenty-first annual symposium on Computational ge-ometry table of contents Pisa, Italy SESSION: Combinatorial geome-try table of contents Pages: 16 - 21 Year of Publication: 2005 ISBN:1-58113-991-8

70. Pach J, Radoicic R, Vondrak J Nearly equal distances and Szemeredi’sregularity lemma COMPUTATIONAL GEOMETRY-THEORY ANDAPPLICATIONS 34 (1): 11-19 APR 2006

71. Iosevich A, Konyagin S, Rudnev M, et al. Combinatorial complexityof convex sequences DISCRETE & COMPUTATIONAL GEOMETRY35 (1): 143-158 JAN 2006

72. M.Rudnev, Szemeredi-Trotter theorem and applications, Post-Graduatelectures in Bristol, 2004.

73. J. Pach, R. Radoicic. J. Vondrak, On the diameter of separated pointsets in R3 with many nearly equal distances EUROPEAN JOURNALOF COMBINATORICS 27 (8): 1321-1332 NOV 2006

74. J. Solymosi, Csaba D. Toth, On distinct distances in homogeneoussets in the Euclidean space Discrete and Computational Geometry, 35(2006) 537-549

75. J. Pach, G. Tardos, Forbidden patterns and unit distances, AnnualSymposium on Computational Geometry archive Proceedings of thetwenty-first annual symposium on Computational geometry table ofcontents Pisa, Italy SESSION: Combinatorial geometry table of con-tents Pages: 1 - 9 Year of Publication: 2005 ISBN:1-58113-991-8

76. J. Pach, G. Tardos, Forbidden paths and cycles in ordered graphs andmatrices ISRAEL JOURNAL OF MATHEMATICS 155: 359-380 2006

77. Mathematics Encyclopedia and Lessons,http://www.mathdaily.com/lessons/Crossing number#Crossing numbers in graph theory

78. Jacob E. Goodman, Pseudoline arrangments in: , Handbook of Dis-crete and Computational Geometry By Jacob E. Goodman, JosephO’Rourke,

79. Agarwal PK, Sharir M Pseudo-line arrangements: Duality, algorithms,and applications SIAM JOURNAL ON COMPUTING 34 (3): 526-5522005

80. E. D. Deamaine, J. S. B. Mitchell, J. O’Rourke, The Open ProblemsProject, pp. 1–69.

81. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry,2005, 499 pages.

82. Akutsu T Algorithms for point set matching with k-differences LEC-TURE NOTES IN COMPUTER SCIENCE 3106: 249-258 2004

83. Stefan Felsner, Geometric Graphs and Arrangements, Some Chap-ters from Combinatorial Geometry, Advanced Lectures in Mathemat-ics, Vieweg & Sohn Verlag, Wiesbaden, 2004.

55

Page 56: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

84. Alex Iosevich, Fourier Analysis and Geometric Combinatorics

85. Thomas Wolff, Recent work connected with the Kakeya problem, pp.43

86. Thomas Wolff, Lectures on Harmonic Analysis, 135 pages,

87. Aronov, B., Pach, J., Sharir, M., Tardos, G., Distinct distances in threeand higher dimensions, Proceedings of the Annual ACM Symposiumon Theory of Computing, pp. 541-546

88. Aronov B, Pach J, Sharir M, et al. Distinct distances in three andhigher dimensions COMB PROBAB COMPUT 13 (3): 283-293 MAY2004

89. Sharir M, Welzl E Point-line incidences in space COMB PROBABCOMPUT 13 (2): 203-220 MAR 2004

90. Sharir M, Welzl E Point-line incidences in space The 18 th AnnualSymposium on Computational Geometry(SCG’02), 2002 pp. 107-111.

91. B. Montaron, An improvement of the crossing number bound, Journalof Graph Theory Volume 50, Issue 1 , (2005) Pages 43 - 54

92. Pach J, Radoicic R, Tardos G, et al. Improving the Crossing Lemmaby finding more crossings in sparse graphs DISCRETE & COMPU-TATIONAL GEOMETRY 36 (4): 527-552 DEC 2006

93. J. Pach, R. Radoicic, G. Tardos, G. Toth, Improving the crossinglemma by finding more crossings in sparse graphs, Annual Symposiumon Computational Geometry archive Proceedings of the twentieth an-nual symposium on Computational geometry table of contents Brook-lyn, New York, USA SESSION: Session 3 table of contents Pages: 68- 75 Year of Publication: 2004 ISBN:1-58113-885-7

94. J. Solymosi, V. Vu, Near optimal bounds for the Erdos distinct dis-tance problem in high dimension, COMBINATORICA Volume: 28Issue: 1 Pages: 113-125 Published: 2008

95. K. J. Swanepoel, P. Valtr, The unit distance problem on spheres, in:Towards a Theory of Geometric Graphs, Contemporary Mathematics342, Amer. Math. Soc. 2004, 273–279,

96. J. Pach, M. Sharir, Geometric incidences, in: Towards a Theory ofGeometric Graphs, Contemporary Mathematics 342, Amer. Math.Soc. 2004, 185–223.

97. J. Pach, Preface, in: Towards a Theory of Geometric Graphs, Con-temporary Mathematics 342, Amer. Math. Soc. 2004, viii–xii.

98. Gavrilov M, Indyk P, Motwani R, et al. Combinatorial and experi-mental methods for approximate point pattern matching ALGORITH-MICA 38 (1): 59-90 JAN 2004

99. Bishnu A, Das S, Nandy SC, et al. An improved algorithm for pointset pattern matching under rigid motion LECT NOTES COMPUTSC 2653: 36-45 2003

56

Page 57: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

100. Noga Alon, Hagit Last, Rom Pinchasi, Micha Sharir, On The Com-plexity of Arrangements of Circles in the Plane, 2001 Discrete andComputanional Geometry 26 (4), pp. 465-492

101. Sharir M The Clarkson-Shor technique revisited and extended COMBPROBAB COMPUT 12 (2): 191-201 MAR 2003

102. Sharir M The Clarkson-Shor technique revisited and extended AnnualSymposium on Computational Geometry archive Proceedings of theseventeenth annual symposium on Computational geometry table ofcontents Medford, Massachusetts, United States Pages: 252 - 256 Yearof Publication: 2001 ISBN:1-58113-357-X

103. R. B. Richter, G. Salazar, A survey of good crossing number theoremsand questions,

104. J. Pach, G. Tardos, Isosceles triangles determined by a planar pointset, Graphs and Combinatorics 18 (4) (2002) 769–779.

105. A. Beygelzimer, S. Radziszowski, On halving line arrangements, Dis-crete Math. 257 (2-3) (2002), 267–283.

106. E. Makai, Jr., J. Pach, and J. Spencer, New results on the distributionof distances determined by separated point sets, in: Paul Erdos andhis Mathematics II, Bolyai Studies 11, Springer-Verlag, 2002, 499–511.

107. L. Lovasz and K. Vesztergombi, Geometric representations of graphs,in: Paul Erdos and his Mathematics II, Bolyai Studies 11, Springer-Verlag, 2002, 471–498.

108. G. Elekes, SUMS versus PRODUCTS in number theory, algebra, andErdos geometry, in: Paul Erdos and his Mathematics II, Bolyai Studies11, Springer-Verlag, 2002, 241–290.

109. B. Aronov, V. Koltun, M. Sharir, Incidences between points and circlesin three and higher dimension, DISCRETE & COMPUTATIONALGEOMETRY 33 (2): 185-206 FEB 2005

110. Aronov, B., Koltun, V., Sharir, M., Incidences between points andcircles in three and higher dimensions, 2002 Proceedings of the AnnualSymposium on Computational Geometry, pp. 116-122

111. M. Sharir, S. Smorodinsky, On generalized geometric graphs and pseu-dolines,

112. M. Sharir, S. Smorodinsky, Extremal configurations and levels in pseu-doline arrangements LECT NOTES COMPUT SC 2748: 127-139 2003

113. G. Tardos, On distinct sums and distinct distances ADV MATH 180(1): 275-289 DEC 1 2003

114. Solymosi J, Tardos G, Toth CD, The k most frequent distances in theplane DISCRETE COMPUT GEOM 28 (4): 639-648 DEC 2002

115. N. Alon, H. Last, R. Pinchasi, et al., On the complexity of arrange-ments of circles in the plane, Discrete and Computational Geometry26(4), 2001, 465–492.

57

Page 58: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

116. Boris Aronov, Micha Sharir, Cutting Circles into Pseudo-segments andImproved Bounds for Incidences, DISCRETE COMPUT GEOM 28(4): 475-490 DEC 2002.

117. Dan Halperin, Arrangements, Handbook of Discrete and Computa-tional Geometry, eds. Jacob E. Goodman and Joseph O’Rourke CRCPress, 1997.

118. Jiri Matousek, Mathematical snapshots from the computational ge-ometry landscape, ICM: Proceedings of the International Congress ofMathematicians

119. Jiri Matousek, Geometric set systems (1998) IEEE Symposium onFoundations of Computer Science

120. Piotr Indyk, Rajeev Motwani, Suresh Venkatasubramanian, GeometricMatching under Noise: Combinatorial Bounds and Algorithms

121. Pankaj K. Agarwal Micha Sharir, On the Number of Congruent Sim-plices in a Point Set, Discrete Comp. Geom. 28 (2002), 123–150.

122. Janos Pach, Micha Sharir, Radial Points in the Plane, Eur. J. Comb22 (6) (2001), 855–863.

123. Pankaj K. Agarwal Micha Sharir, On the Number of Congruent Sim-plices in a Point Set, Annual Symposium on Computational Geometryarchive Proceedings of the seventeenth annual symposium on Compu-tational geometry table of contents Medford, Massachusetts, UnitedStates Pages: 1 - 9 Year of Publication: 2001 ISBN:1-58113-357-X

124. J Solymosi, CD Toth On the distinct distances determined by a planarpoint set, Annual Symposium on Computational Geometry archiveProceedings of the seventeenth annual symposium on Computationalgeometry Medford, Massachusetts, United States Pages: 29 - 32 Yearof Publication: 2001 ISBN:1-58113-357-X

125. P. Brass, Combinatorial geometry problems in pattern matching, DIS-CRETE COMPUT GEOM 28 (4): 495-510 DEC 2002.

126. B. Aronov, T. K. Dey, Polytopes in arrangements, Disc. Comp.Geom. 25 (1) (2001), 51–63.

127. N. Alon, Algebraic and probabilistic methods in discrete mathematics,Geom. Func. Anal. 455–470, Part 2 Sp. Iss. SI2000.

128. J. Solymosi and Cs. D. Toth, Different distances in the plane, Disc.Comp. Geom. 25 (4) (2001), 629–634.

129. J. Solymosi and Cs. D. Toth, The k most frequent distances in theplane, submitted.

130. J. Pach, J. Spencer, and G. Toth, New bounds on crossing numbers,Discrete Comp. Geom. 24 4 (2000), 623–644.

131. G. Elekes, M. B. Nathanson, I. Z. Ruzsa, Convexity and sumsets, J.Number Theory 83 (2) (2000), 194–201.

132. D. B. West, Introductions to Graph Theory, Second Edition, Prentice-Hall, 2001.

58

Page 59: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

133. J. Pach, Crossing numbers, in: Discrete and Computational Geom-etry Japanese Conference JCDCG’98, Tokyo, Japan, December 1998,eds. J. Akiyama, M. Kano, M. Urabe, Lecture Notes in ComputerScience Vol. 1763, 267–273, 2000.

134. MR 99j:11022 (Reviewer: Vsevolod F. Lev) Chen, Yong-Gao On sumsand products of integers. Proc. Amer. Math. Soc. 127 (1999), no. 7,1927–1933. (Reviewer: Vsevolod F. Lev)

135. J. Erickson, Space-time tradeoffs or emptiness queries, SIAM J. Com-put 29 (6) (2000), 1968–1996.

136. Cs. Toth, The complex Szemeredi-Trotter theorem, submitted.

137. G. Elekes, L. Ronyai, A combinatorial problem on polynomials andrational functions, J. Comb. Theory A 89 (2000), 1-20.

138. B. M. Abrego and S. Fernandez-Merchant, On the maximum numberof equilateral triangles, I Discrete and Comp. Geometry 23 (1)(2000), 129–135.

139. J. Pach, Finite point configurations, Chapter 1 in Handbook of Dis-crete and Computational Geometry, ed. Goodman and O’Rourke,CRC press, 1997.

140. J. Pach, Geometric Graph Theory, Chapter 10 in Handbook of Dis-crete and Computational Geometry, ed. Goodman and O’Rourke,CRC press, 1997.

141. J. Pach, J. Spencer, and G. Toth, New bounds on crossing numbers,15th ACM Symposium on Computational Geometry, 1999, 124–133.

142. Suresh Venkatasubramanian, GEOMETRIC SHAPE MATCHING ANDDRUG DESIGN, Ph.D. Thesis, Stanford, 1999.

143. Pach, J., Geometric graph theory. Surveys in combinatorics, 1999(Canterbury), 167–200, London Math. Soc. Lecture Note Ser., 267,Cambridge Univ. Press, Cambridge, 1999.

144. A. Granville, F. Roesler, The set of differences of a given set, Amer.Math. Monthly 106 (4) (1999), 338–344.

145. P. Erdos, On some of my favourite theorems, in: Combinatorics,Paul Erdos is Eighty (Vol. 2) Keszthely, Hungary, 1993, eds. D.Miklos, Vera T. Sos, T. Szonyi, 1996, Bolyai Society MathematicalStudies 2, 97–132.

146. J. Pach, M. Sharir, On the number of incidences between points andcurves, Combinatorics, Probability, and Computing 7 (1998), 121–127.

147. J. Pach, G. Toth, Graphs drawn with few crossings per edge, Proc.Symposium on Graph Drawing ’95, Berkeley, CA, USA, September1996, ed. Stephen North, Lecture Notes in Computer Science 1190,Springer Verlag, Berlin, 345–354.

148. T. K. Dey, and J. Pach, Extremal problems for geometric hypergraphs,Lexture Notes in Computer Science 1178 Springer-Verlag, 1996, 105–114.

59

Page 60: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

149. J. Pach, G. Toth, Graphs drawn with few crossings per edge, Combi-natorica 17(1998)(3), 427–439.

150. T. K. Dey, and J. Pach, Extremal problems for geometric hypergraphs,Disc. Comput. Geom. 19 (1998), 473–484.

151. G. Elekes, On the number of sums and products, Acta Arithm. 81(1997)(4), 365–367.

152. B. Bollobas, To prove and conjecture: Paul Erdos and his mathemat-ics, Amer. Math. Monthly 105(1998) (3), 209–237.

153. L. Babai, Paul Erdos (1913–1996) His influence on the theory of com-puting, 29th ACM Symposium on the Theory of Computing, 383–400, 1997.

154. L. Babai, J. Spencer, Paul Erdos Notices Amer. Math. Soc 45(1998) (1) 64–73.

155. P. Brass, On point sets with many unit distances in few directions,Discrete Comput. Geom. 19(1998)(3), 355–366.

156. T. Dey, Improved bounds for planar k-sets and related problems, Dis-crete Comput. Geom. 19(1998)(3), 373–382.

157. T. Dey, Improved bounds for planar k-sets and related problems, IEEESymposium on Foundations of Computer Science, 1997

158. T. Akutsu, H. Tamaki, T. Tokuyama, Distribution of distances andtriangles in a point set and algorithms for computing the largest com-mon point sets, Discrete Comput. Geom. 20(1998) (3), 307–331.

159. T. Akutsu, H. Tamaki, T. Tokuyama, Distribution of distances and tri-angles in a point set and algorithms for computing the largest commonpoint sets, Annual Symposium on Computational Geometry archiveProceedings of the thirteenth annual symposium on Computationalgeometry, Nice, France Pages: 314 - 323 Year of Publication: 1997ISBN:0-89791-878-9

160. M. Aigner, G. M. Ziegler, Proofs from the Book, Springer-Verlag,1998.

161. B. Bollobas, Paul Erdos and probability theory, Random Structuresand Algorithms 13(3-4) (1998), 521–533.

162. K. J. Swanepoel, Cardinalities of k-distance sets in Minkowski spaces,Discrete Math. 198 (1999), 759–767.

54./ P. L. Erdos, M. A. Steel, L. A. Szekely, and T. J. Warnow,Local quartet splits of a binary tree infer all quartet splits viaone dyadic inference rule, Computers and Artificial Intelligence16(2)(1997), 217–227.

60

Page 61: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. P.M. Huggins, W. Li, D. Haws, T. Friedrich, J. Liu, and R. Yoshida,Bayes estimators for phylogenetic reconstruction, arXiv:0911.0645v2[q-bio.PE] 22 Nov 2009

2. Hamed, Mahe Ben, Wang, Feng, Stuck in the forest: Trees, networksand Chinese dialects, Diachronica, Volume 23, Number 1, 2006 , pp.29-60(32)

3. Alexandre Bouchard-CoteΛ, Percy LiangΛ, Thomas L. Griffiths, DanKleinΛ, A Probabilistic Approach to Diachronic Phonology, Proceed-ings of the 2007 Joint Conference on Empirical Methods in NaturalLanguage Processing and Computational Natural Language Learning,pp. 887896, Prague, June 2007.

4. Huang XQ, Vingron M, Maximum Similarity: A New Formulationof Phylogenetic Reconstruction, JOURNAL OF COMPUTATIONALBIOLOGY Volume: 16 Issue: 7 Pages: 887-896 Published: JUL 2009

5. Kubatko LS, Inference of phylogenetic trees,TUTORIALS IN MATH-EMATICAL BIOSCIENCES IV: EVOLUTION AND ECOLOGY BookSeries: LECTURE NOTES IN MATHEMATICS Volume: 1922 Pages:1-38 Published: 2008

6. Fei Ye - Yan Guo - A. Lawson - Jijun Tang: Improving Tree Searchin Phylogenetic Reconstruction from Genome Rearrangement Data,WEA 2007, C. Demetrescu (Ed.) LNCS 4525 (2007), 352-364.

7. A. Bouchard-Cote - Percy Liang - T.L. Griffiths - D. Klein: A Prob-abilistic Approach to Diachronic Phonology, Conference on Empiri-cal Methods in Natural Language Processing Conference on Compu-tational Natural Language Learning - EMNLP-CoNLL 2007 (2007),1–10.

8. Li, J.-F.- Guo, M.-Z.: Review of phylogenetic tree reconstruction tech-nology, Acta Electronica Sinica 34 (11) (2006), 2047–2052.

9. Gang Wu - Jia-Huai You - Guohui Lin: A lookahead branch-and-bound algorithm for the Maximum Quartet Consistency Problem, Al-gorithms in Bioinf. LNCS 3602 3692 LNBI (2005), 65–76.

10. AWM Dress, PL Erdoes, X-Trees and Weighted Quartet Systems, An-nals of Combinatorics, 7 (2003) 155 - 169.

11. Istvan Miklos: Chapter 13. Bioinformatika, in: Informatikai Algo-ritmusok A. Ivanyi, ed., ELTE Eotvos Kiado, 2004. pp 578, reference120.

12. Tao Liu - Jijun Tang - B.M.E. Moret: Quartet-based phylogeny re-construction from gene orders, COCOON ’05 August 16-19, Kun-ming, Yunnan, Chine (2005), LECTURE NOTES IN COMPUTERSCIENCE 3595: 63-73 2005.

13. Salamin N, Hodkinson TR, Savolainen V Towards building the Treeof Life: A simulation study for all angiosperm genera SYSTEMATICBIOLOGY 54 (2): 183-196 APR 2005

61

Page 62: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

14. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

15. L. A. Salter, Algorithms for Phylogenetic Tree Reconstruction (2000)METMBS’00: PROCEEDINGS OF THE INTERNATIONAL CON-FERENCE ON MATHEMATICS AND ENGINEERING TECHNIQUESIN MEDICINE AND BIOLOGICAL SCIENCES, VOLS I AND II;2000; p.459-465 Conference: International Conference on Mathemat-ics and Engineering Techniques in Medicine and Biological Sciences(METMBS 00); June 26-29, 2000; LAS VEGAS, NEVADA

16. Daniel Huson, Scott Nettles, Laxmi Parida, Tandy Warnow, ShibuYooseph, The Disk-Covering Method for Tree Reconstruction (1998)Proceedings of Proc. “Algorithms and Experiments”, (ALEX‘98),Trento, Italy (1998), 62–75.

17. T. Warnow, B. M. E. Moret, K. St. John: Absolute convergence: truetrees from short sequences, ACM Symp. on Discrete AlgorithmsSODA 2001 (2001), 1–9.

18. S. Bocker, D. Bryant, A. W. M. Dress, M. A. Steel Algorithmic aspectsof tree amalgamation J. Algorithm 37 (2) (2000), 522–537.

55./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, Crossingnumbers: bounds and applications, in: Intuitive Geometry, eds.I. Barany and K. Boroczky, Bolyai Society Mathematical Studies6, Janos Bolyai Mathematical Society, Budapest, 1997, 179–206.

References

1. Ki Sung Park, ESTIMATION OF THE BIPLANAR CROSSING NUM-BERS, Kangweon-Kyungki Math. Jour. 13 (2005), No. 2, pp. 123-126

2. Sergio Cabello, Bojan Mohar, CROSSING AND WEIGHTED CROSS-ING NUMBER OF NEAR-PLANAR GRAPHS, Algorithmica DOI:10.1007/s00453-009-9357-5

3. B Mohar, Do We Really Understand the Crossing Numbers? Mathe-matical Foundations of Computer Science 2010 Lecture Notes in Com-puter Science, 2010, Volume 6281/2010, 38-41, DOI: 10.1007/978-3-642-15155-2 5

4. Mohar, B. On the crossing number of almost planar graphs (2006)Informatica (Ljubljana), 30 (3), pp. 301-303.

5. L.Faria, C.Figueiredo, O.Sykora and I. Vrto, An Improved UpperBound on the Crossing Number of the Hypercube, J. Graph Theory59, Issue 2, pages 145161, October 2008

6. D. Bokal, Structural Approach to the Crossing Number of Graphs,Doctoral Thesis, University of Ljubljana, 2006.

7. J. Fox, Csaba D. Toth, On the decay of crossing numbers, J. Comb.Theory Ser. B, 98(2008) 33–42.

62

Page 63: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

8. Djidjev, H; Vrto, I An improved lower bound for crossing numbersLECTURE NOTES IN COMPUTER SCIENCE; 2002; v.2265, p.96-101 (Conference: 9th International Symposium on Graph Drawing(GD 2001); September 23-26, 2001; VIENNA, AUSTRIA)

9. L Faria, CHM Figueiredo, O Sykora, I Vrt’o, An Improved UpperBound on the Crossing Number of the Hypercube, Proc. 29th Intl.Workshop on Graph-Theoretic Concepts in Computer Science, 230 -236 Volume 2880 / 2003.

10. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

11. H. C. Purchase, Metrics for graph drawing aesthetics, JOURNAL OFVISUAL LANGUAGES AND COMPUTING; OCT 2002; v.13, no.5,p501-516

12. H. N. Djidjev, I. Vrto, Crossing numbers and cutwidth, Journal ofGraph Algorithms and Applications, http://www.cs.brown.edu/publications/jgaa/vol. 7, no. 3, pp. 245-251 (2003)

13. E. de Klerk, J. Maharry, D.V. Pasechnik, R.B. Richter, G. Salazar,Improved bounds for the crossing number of Km,n and Kn, SIAM J.DISCRETE MATH 20 (2006) No. 1, pp. 189-202.

14. R. Cimikowski, I. Vrto, Improved bounds for the crossing number ofthe mesh of trees

15. W Winterbach, The crossing number of a graph in the plane, MSc (Ap-plied Mathematics: Graph Theory) Thesis, University of Stellenbosch,2004.

16. Kolman P, Matousek J Crossing number, pair-crossing number, andexpansion JOURNAL OF COMBINATORIAL THEORY SERIES B92 (1): 99-113 SEP 2004

17. R. Cimikowski, B. Mumey, Approximating the fixed linear crossingnumber, (2007) Discrete Applied Mathematics, 155 (17), pp. 2202-2210.

18. Guy Even Sudipto Guha Baruch Schieber, Improved Approximationsof Crossings in Graph Drawings and VLSI Layout Areas SIAM JOUR-NAL ON COMPUTING; JAN 2 2003; v.32, no.1, p.231-252

19. Sudipto Guha, Nested Graph Dissection and Approximation Algo-rithms ANNU SYMP FOUND COMPUT SCI PROC. pp. 126-135.2000.

20. Godfried T. Toussaint, The Complexity of Computing Nice Viewpointsof Objects in Space (2000) Proc. SPIE Vol. 4117, p. 1-11, VisionGeometry IX, Longin J. Latecki; David M. Mount; Angela Y.

21. J. Pach, G. Toth, Which crossing number is it anyway? J. Comb.Theory Ser B 80 (2) (2000), 225–246.

22. Pach, J., Geometric graph theory. Surveys in combinatorics, 1999(Canterbury), 167–200, London Math. Soc. Lecture Note Ser., 267,Cambridge Univ. Press, Cambridge, 1999.

63

Page 64: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

23. J. Pach, G. Toth, Which crossing number is it anyway? Proc. 39thAnnual Symposium on Foundation of Computer Science, IEEEPress, Baltimore, 1998, 617–626.

24. G. Even, S. Guha, B. Schieber, Improved approximations of crossingsin graph drawings and VLSI layout areas, 30th ACM Symposium onthe Theory of Computer Science, 1998. pp. 296-305. 2000

25. G. Even, S. Guha, B. Schieber, Improved approximations of cross-ings in graph drawings and VLSI layout areas, SIAM JOURNAL ONCOMPUTING; JAN 2 2003; v.32, no.1, p.231-252

56./ R. Ahlswede, N. Alon, P. L. Erdos, M. Ruszinko and L. A.Szekely, Intersecting systems, Combinatorics, Probability, andComputing 6 (2) (1997), 127–137.

References

1. K Meagher, L Moura Erdos-Ko-Rado theorems for uniform set-partitionsystems Electron. J. Combin. 12 (2005), Research Paper 40, 12 pp.(electronic).

2. K. Meagher, COVERING ARRAYS ON GRAPHS: QUALITATIVEINDEPENDENCE GRAPHS AND EXTREMAL SET PARTITIONTHEORY, Ph. D. Thesis, 2005, Waterloo University.

3. C.J. Colbourn - A. Rosa: Triple systems Oxford University Press(1999) p 458.

4. S. Jukna, Extremal combinatorics. With applications in computerscience. Texts in Theoretical Computer Science. An EATCS Series.Springer-Verlag, Berlin, 2001. xviii+375 pp.

5. R. Ahlswede: Advances on extremal problems in number theory andcombinatorics, in European Congress of Mathematics, Barcelona,2000 Vol. 1, Progress in Mathematics 201 (2001), 147–175.

57./ D. de Caen and L. A. Szekely, On dense bipartite graphs ofgirth eight and upper bounds for certain configurations in planarpoint-line systems, J. Combin. Theory Ser. A. 77(1997), 268–278.

References

1. L. Babai, Paul Erdos (1913–1996) His influence on the theory of com-puting, 29th ACM Symposium on the Theory of Computing, 383–400, 1997.

2. J. Solymosi, Dense arrangements are locally very dense I SIAM JOUR-NAL ON DISCRETE MATHEMATICS 20 (3): 623-627 2006

3. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry,2005, 499 pages.

4. Van Dam ER The combinatorics of Dom de Caen DESIGNS CODESAND CRYPTOGRAPHY 34 (2-3): 137-148 FEB-MAR 2005

64

Page 65: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

5. T. Lam, A result on 2k-cycle-free bipartite graphs, submitted

6. J. A. Bondy, Extremal problems of Paul Erdos on circuits in graphs,in: Paul Erdos and his Mathematics II, Bolyai Studies 11, Springer-Verlag, 2002, 135–156.

7. S. Hoory, The size of bipartite graphs with a given girth, J. Comb.TheoryB 86 (2) (2002), 215–220.

8. S. Neuwirth, The size of bipartite graphs with girth eight,

58./ L. H. Clark, J. E. McCanna, L. A. Szekely, A survey of countingbicoloured trees, Bull. Inst. Combin. Appl. 21(1997), 33–45.

References

1. N. Dershowitz and S. Zaks, Up and down young and old, new andeven, manuscript

2. Chunlin Liu, RNA secondary structures and bicoloured ordered trees(2006) Ars Combinatoria, 81, pp. 305-309.

3. Y. Lin, C. Liu, Enumeration for spanning forests of complete bipartitegraphs Ars Combin. 70 (2004), 135–138.

59./ P. L. Erdos and L. A. Szekely, Pseudo-LYM inequalities and AZidentities, Adv. Appl. Math. 19 (1997), pp. 431443.

References

1. Tran Dan Thu, An AZ-style identity and Bollobas deficiency, Journalof Combinatorial Theory, Series A Volume 114, Issue 8, November2007, Pages 1504-1514

60./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, Crossingnumbers of Cm × Cn and other families of curves, Discrete andComp. Geometry 19 (1998), 237–247.

References

1. Zheng WP, Lin XH, Yang YS, et al. On the crossing number of K-msquare P-n GRAPHS AND COMBINATORICS 23 (3): 327-336 JUN2007

2. Klesc M, Kocurova A The crossing numbers of products of 5-vertexgraphs with cycles DISCRETE MATHEMATICS 307 (11-12): 1395-1403 Sp. Iss. SI MAY 28 2007

3. De Mendonca, C.F.X., Xavier, E.F., Stolfi, J., Faria, L., De Figueiredo,C.M.H., The non planar vertex deletion of Cn x Cm, Ars Combinatoria76, pp. 3-28

4. D. Bokal, Structural Approach to the Crossing Number of Graphs,Doctoral Thesis, University of Ljubljana, 2006.

65

Page 66: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

5. Salazar G, Ugalde E An improved bound for the crossing number ofC(m)xC(n): a self-contained proof using mostly combinatorial argu-ments GRAPHS AND COMBINATORICS 20 (2): 247-253 JUN 2004

6. de Mendonca CFX, Xavier EF, Stolfi J, et al. The non planar vertexdeletion of C-n x C-m ARS COMBINATORIA 76: 3-28 JUL 2005

7. A. Riskin, on the nonembeddability and crossing numbers of someKleinical polyhedral maps on the torus Graphs and Combinatorics21 (1): 131-135 MAR 2005

8. D. Mubayi, Intersecting curves in the plane, Graphs and Combina-torics18 (3)(2002) 583–589.

9. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

10. A. Foley, R. Krieger, A. Riskin, and I. Stanton, The crossing numbersof some twisted toroidal graphs, Bull. ICA 36 (2002) 80–88.

11. H. A. Juarez, G. Salazar, Optimal meshes of curves in the Klein bottle,JOURNAL OF COMBINATORIAL THEORY SERIES B; MAY 2003;v.88, no.1, p.185-188.

12. H. A. Juarez, G. Salazar, Drawings of Cm×Cn with one disjoint familyII, J. Comb. Theory 36 (3) (2001), 161–165.

13. L. Y. Glebsky and G. Salazar, The conjecture Cm×Cn is as conjecturedfor all n ≥ m(m+1), JOURNAL OF GRAPH THEORY 47 (1): 53-72SEP 2004

14. E. Garcia-Moreno, G. Salazar, Bounding the crossing number of agraph in terms of the crossing number of a minor with small maximumdegree, J. Graph Theory 36 (3) (2001), 168–173.

15. G. Salazar, A lower bound for the crossing number of Cm × Cn, J.Graph Theory 35 (3) (2000), 222–226.

16. G. Salazar, Small meshes of curves and their role in the analysis ofoptimal meshes, Discrete Math. 263(1-3) (2003),233–246.

61./ F. Shahrokhi, O. Sykora, L. A. Szekely, I. Vrto, Bipartite crossingnumbers of meshes and hypercubes, Proc. 5th Int l. Symposiumon Graph Drawing, Lecture Notes in Computer Science 1353,Springer Verlag, Berlin, 1997, 37–46.

References

1. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

2. S. L. Bezrukov, Edge isoperimetric problems on graphs, Technical Re-port, Dept. of Mathematics and Computer Science, Uni. Paderborn,1997.

62./ P. L. Erdos, A. Frank, and L. A. Szekely, Minimum multiwaycuts in trees, Discrete Appl. Math. 87 (1998), 67–75.

66

Page 67: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Nagamochi H Algorithms for the minimum partitioning problems ingraphs ELECTRONICS AND COMMUNICATIONS IN JAPAN PARTIII-FUNDAMENTAL ELECTRONIC SCIENCE 90 (10): 63-78 2007

2. ALESSIO CAMPISANO, LUCA CITTADINI, GIUSEPPE DI BAT-TISTA, TIZIANA REFICE, CLAUDIO SASSO, Update-driven rootcause analysis in interdomain routing, Universita degli Studi di RomaTre

3. C BENTZ, C COSTA, L LETOCART, F ROUPIN, A BIBLIOGRA-PHY ON MULTICUT AND INTEGER MULTIFLOW PROBLEMS

4. Chandra Chekuri, Anupam Gupta, Amit Kumar, On bidirected relax-ation for the multiway cut problem Disc. Appl. Math 150 (2005),67-79.

63./ Erdos-Ko-Rado and Hilton-Milner type theorems for intersectingchains in posets, Combinatorica, 20(1) (2000) 27–45. (with A.Seress and P. L. Erdos).

References

1. F. Brunk, Intersection problems in combinatorics, Ph.D. Thesis, St.Andrews University, 2008.

2. P.A. Carey - A.P. Godbole: Partial Covering Arrays and a Gener-alized Erdos-Ko-Rado Property, JOURNAL OF COMBINATORIALDESIGNS 18(3) (2010) 155–166.

3. Peter Borg and Fred Holroyd, The Erdos-Ko-Rado properties of var-ious graphs containing singletons, Discrete Mathematics Volume 309,Issue 9, 6 May 2009, Pages 2877-2885

4. Borg P, Holroyd F The Erdos-Ko-Rado properties of set systems de-fined by double partitions, DISCRETE MATHEMATICS Volume: 309Issue: 14 Special Issue: Sp. Iss. SI Pages: 4754-4761 Published: JUL28 2009

5. Holroyd F, Talbot J Graphs with the Erdos-Ko-Rado property DIS-CRETE MATHEMATICS 293 (1-3): 165-176 Sp. Iss. SI APR 6 2005

6. Eva Czabarka, Intersecting chains in finite vector spaces, Combina-torics, Probability and Computing, 8 (1999), 509–528.

7. Eva Czabarka, Shifting technique in finite vector spaces, Ph.D. Thesis,University of South Carolina, Columbia, 1998.

64./ P. L. Erdos, M. A. Steel, L. A. Szekely, and T. J. Warnow, Con-structing big trees from short sequences, ICALP’97, 24th Inter-national Colloquium on Automata, Languages, and Programming(Silver Jubilee of EATCS), Bologna, Italy, July 7th–11th, 1997,Lecture Notes in Computer Science Vol 1256, Springer-Verlag,1997, 827–837.

67

Page 68: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Ionescu T, Polaillon G, Boulanger F, Minimum Tree Cost QuartetPuzzling, JOURNAL OF CLASSIFICATION 27(2)(2010) 136–157

2. M. Tarawneh: A novel quartet-based method for inferring evolution-ary trees from molecular data, Ph.D. Thesis, University of Sidney(2008), 1–151.

3. Short quartet puzzling: A new quartet-based phylogeny reconstructionalgorithm Author(s): Snir S, Warnow T, Rao S Source: JOURNALOF COMPUTATIONAL BIOLOGY Volume: 15 Issue: 1 Pages: 91-103 Published: JAN 2008

4. Gang Wu - M-Y. Kao - Guohui Lin - J-H. You: Reconstructing phy-logenies from noisy quartets in polynomial time with a high successprobability, Algorithms for Mol. Biol. 3:1 (2008), 1–10.

5. Wu G, You JH, Lin GH Quartet-based phylogeny reconstruction withanswer set programming IEEE-ACM TRANSACTIONS ON COM-PUTATIONAL BIOLOGY AND BIOINFORMATICS 4 (1): 139-152JAN-MAR 2007

6. Wu, G., Lin, G., You, J.-H. Quartet based phylogeny reconstructionwith answer set programming (2004) Proceedings - International Con-ference on Tools with Artificial Intelligence, ICTAI, pp. 612-619.

7. P. Kearney, Phylogenetics and the quartet method, in: Current Top-ics in Computational Molecular Biology By Tao (EDT) Jiang, Ying(EDT) Xu, Michael Q. (EDT) Zhang, 2002, 111–134.

8. B.B. Zhou - D. Chu - M. Tarawneh - P. Wang- C. Wang - A. Zamoya- R.P. Brent: Paralell implementation of a quartet-based algorithmfor phylogenetic analysis, Online Proc. Fifth IEEE Workshop onHigh Performance Computational Biology (HICOMB06) (2006),1–8. (to appear in IEEE Bioinf.)

9. B. B. Zhou, M. Tarawneh, D. Chu, P. Wang, C. Wang, A. Zomaya,and R. P. Brent, On a New Quartet-Based Phylogeny ReconstructionAlgorithm, Proceedings ofthe 2006 International Conference on , 2006

10. B.B. Zhou - M. Tarawneh - C. Wang - A. Zamoya - R.P. Brent: A novelquartet-based method for phylogenetic inference, Proc. Fifth IEEESymposium on Bioinformatics and Bioengineering (BIBE05) (2005),32–39.

11. M. Hu - P. Kearney - J.H. Badger: A Collapsing Method for theEfficient Recovery of Optimal Edges in Phylogenetic Trees, Int. J.Artificial Intelligence Tools 14 (2005), 717–731.

12. AWM Dress, PL Erdoes, X-Trees and Weighted Quartet Systems, An-nals of Combinatorics, 7 (2003) 155 - 169.

13. Jonathan Badger, Paul Kearney, Ming Li, John Tsang, Tao Jiang,Selecting the branches for an evolutionary tree: a polynomial timeapproximation scheme, Journal of Algorithms Volume 51 , Issue 1(April 2004) Pages: 1 - 14 Year of Publication: 2004 ISSN:0196-6774

68

Page 69: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

14. G Della Vedova, Multiple Sequence Alignment and Phylogenetic Re-construction: Theory and Methods in Biological Data Analysis, Ph.D.Thesis, Universit‘a degli Studi di Milano.

15. Tao Liu - Jijun Tang - B.M.E. Moret: Quartet-based phylogeny recon-struction from gene orders, COCOON ’05 August 16-19, Kunming,Yunnan, Chine (2005), 237–241.

16. Gang Wu - Guohui Lin - Jia-Huai You: Quartet Based PhylogenyReconstruction with Answer Set Programming, in 16th IEEE Int.Conf. on Tools with Artificial Intelligence (ICTAI’04) (2004),612–619.

17. Gang Wu, Guohui Lin, J. You, and X. Wu. Faster Solution to theMaximum Quartet Consistency Problem with Constrained Program-ming. The 3rd Asia-Pacific Bioinformatics Conference (APBC 2005).January 17-21, 2005, Singapore. Accepted on August 27, 2004.

18. Damon Shing-Min Liu, Che-Hao Wu, An effective approach for con-structing the phylogenetic tree on a grid-based architecture, Proceed-ings - Fourth IEEE Symposium on Bioinformatics and Bioengineering,BIBE 2004, pp. 134-141

19. Gascuel O, McKenzie A Performance analysis of hierarchical clusteringalgorithms J CLASSIF 21 (1): 3-18 2004

20. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

21. Monika Rauch Henzinger, Valerie King, Tandy Warnow, Constructinga Tree from Homeomorphic Subtrees, with Applications to Computa-tional Evolutionary Biology 1999 Algorithmica (New York) 24 (1), pp.1-13

22. D. Pelleg: Algorithms for constructing phylogenies from quartets,Master Thesis, Technion, Haifa, Israel (1998), 1–30.

23. M. Hu: A Collapsing Method for the Efficient Recovery of OptimalEdges in Phylogenetic Trees, Master Thesis, University of Waterloo(2001), 1–106.

24. P. Bonizzoni - G.D. Vedova - G. Mauri: Approximating the maximumisomorphic agreement subtree is hard, Int. J. Found. Comp. Sci 11(2000), 579–590.

25. J.A.A. Nylander: Taxonomic sampling in phylogenetic analysis: Prob-lems and strategies reviewed. Introductory Research Essay No. 1.Department of Systematic Zoology, Evolutionary Biology Centre, Up-psala University. (2001), 1–28.

26. M. Hu - P. Kearney - J.H. Badger: A Collapsing Method for theEfficient Recovery of Optimal Edges in Phylogenetic Trees, 3rd IEEESymposium on Bioinformatics and Bioengineering, March 10-12,2003, Bethesda MD, USA (BIBE’03) 95–106.

27. Vedova, G.D., Wareham, H.T., Optimal algorithms for local vertexquartet cleaning, 2002 Proceedings of the ACM Symposium on AppliedComputing, pp. 173-177

69

Page 70: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

28. Vedova GD, Wareham HT Optimal algorithms for local vertex quartetcleaning BIOINFORMATICS 18 (10): 1297-1304 OCT 2002

29. Haoyong Zhang In, Design, implementation, and analysis of a novelquartet-based phylogenetic reconstruction method, Thesis, (2000) Uni-versity of Waterloo, Department of Computer Science.

30. Tao Jiang - P. Kearney - Ming Li: A polynomial time approximationscheme for inferring evolutionary trees from quartet topologies and itsapplication, submitted (2001), 1–20.SIAM J COMPUT, 2001

31. J.H. Badger - P. Kearney: Picking fruit from the Tree of Life, Proc.16th ACM Symp. Appl. Comp (SAC), Las Vegas, March 11-14,(2001), 61–67.

32. J. Kim - T. Warnow: Tutorial on phylogenetic tree estimation, inISMB’99, 7th Conf. Intell. Systems for Molecular Biology, Au-gust 6-10, Heidelberg, Germany, Tutorial Section, (1999), 1–29.

33. J. Gramm - R. Niedermeier: Minimum quartet inconsistency is fixedparameter tractable, Wilhelm-Schickard-Institute fur InformatikWSI-2001-3 (2001), 1–29.

34. V. Ranwez, O. Gascuel, Quartet based phylogenetic inference: im-provements and limits, Mol. Biol. Evol. 18 (6) 2001, 1103–1116.

35. M. Shpak, G. A. Churchill, The information content of a characterunder a Markov model of evolution, Mol. Phyl. Evol. 17 (2000),231–243.

36. V. Berry - O. Gascuel: Inferring evolutionary trees with strong com-binatorial evidence, Theor. Comp. Sci. 240 (2000), 271–298.

37. M. Csuros: Reconstructing Phylogenies in Markov Models of SequenceEvolution, Ph.D. Thesis Yale University, (2000), 1–232.

38. Haoyong Zhang: Design, implementation and analysis of a novel quartet-based phylogenetic reconstruction method, Thesis for MS in Com-puter Sci. University of Waterloo, Canada (2000) 1–86.

39. V. Berry, D. Bryant, T. Jiang, P. Kearney, Ming Li, T. Wareham,Haoyong Zhang: A practical algorithm for recovering the best sup-ported edges of an evolutionary tree (Extended abstract), ACM Symp.on Discrete Algorithms SODA2000 (2000), 287–296.

40. O. Gascuel, On the optimization principle in phylogenetic analysisand the minimum-evolution criterion, Mol. Biol. Evol. 17(3)(2000),401–405.

41. Susan P. Holmes, Phylogenies: An overview, Statistics and Genetics,(ed. Halloran and Geisser), IMA series, vol 112, Springer Verlag, NY,81–119.

42. D. H. Huson, S. M. Nettles, and T. J. Warnow, Disk-covering, a fast-converging method for phylogenetic tree reconstruction, J. Comp.Biol. 6 (3–4) (1999), 369–386.

70

Page 71: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

43. V. Berry and D. Bryant, Faster reliable phylogenetic analysis, RE-COMB’99 Lyon, France (1999), 59–68.

44. V. Berry, Tao Jiang, P. Kearney, Ming Li, T. Wareham, Quartet clean-ing: improved algorithms and simulations, Algorithms – ESA’99,7th annual European symposium Prague, Chezh Rep. Lect. NotesComp. Sci 1643 (1999), 313–324. (1999).

45. V. Berry, An improved polynomial time algorithm for computing therefined Buneman tree, Preprint CS-RR-342, Warwick University, (1998),1–11. http://www.dcs.warwick.ac.uk/pub/reports/rr/

46. A. Ben-Dor, B. Chor, D. Graur, R. Ophir, D. Pelleg: Constructingphylogenies from quartets: elucidation of Eutherian superordinal rela-tionships, J. Comp. Biol. 5 (1998), 377–390.

47. V. Berry, O. Gascuel, Inferring evolutionary trees with strong com-binatorial evidence, Computing and Combinatorics, Third AnnualInternational Conference, COCOON ’97, Shanghai, China, Au-gust 1997, COCOON’97 Lecture Notes in Computer Science Vol.1276, Springer-Verlag 111–123.

48. K. Rice, T. Warnow, Parsimony is hard to beat, Computing andCombinatorics, Third Annual International Conference, COCOON’97, Shanghai, China, August 1997, COCOON’97 Lecture Notesin Computer Science Vol. 1276, Springer-Verlag 124–133.

49. T. Warnow, Some combinatorial optimization problems in phyloge-netics, in: Graph Theory and Combinatorial Biology, L. Lovaszet. al., eds. Bolyai Society Mathematical Studies 7, Janos BolyaiMathematical Society, Budapest, 1999, 363–413.

50. A. Ambainis, R. Desper, M. Farach, S. Kannan, Nearly tight boundson the learnability of evolution, Proc. 38th IEEE Conference onFoundations of Computer Science (FOCS’97), 1997, 524–533.

51. M. Bonet, M. Steel, T. Warnow, S. Yooseph, Better methods for solv-ing parsimony and compatibility, J. Comp. Biol. 5(3) (1998), 391–407.

52. D. Huson, S. Nettles, K. Rice, T. Warnow, S. Yooseph: Hybrid tree re-construction methods, 2nd Workshop on Algorithmic Engineering(WAE’98), Saarbrucken, Germany (1998),

53. D. Huson, S. Nettles, K. Rice, T. Warnow, S. Yooseph: Hybrid treereconstruction methods, ACM J. Exp. Alg 4 (1998), Articel 5.

54. M. Bonet, M. Steel, T. Warnow, S. Yooseph, Better methods for solv-ing parsimony and compatibility, (extended abstarct) RECOMB 98New York (1998), 40–49.

55. P.E. Kearney: The Ordinal Quartet Method, (extended abstarct) RE-COMB 98 New York (1998), 125-133.

56. B. Chor: From quartets to phylogenetic trees, SOFSEM’98: The-ory and Practice of Informatics, B. Rovan, ed. Lecture Notes inComputer Science 1521, pp. 36–53, Springer-Verlag, 1998.

71

Page 72: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

57. Tao Jiang - P. Kearney - Ming Li: Orchestrating quartets: approxima-tion and data correction, FOCS’98 Proceedings of the 39th AnnualIEEE Symposium on Foundations of Computer Science (1998),

58. V. Berry, Methodes et algorithmes pour reconstruire les arbres del’Evolution, These de Doctorat, Universite de Montpellier II, 1997.

59. V. Berry, O. Gascuel, Reconstructing phylogenies from resolved 4-trees, Rapport de Recherche Universite Montpellier II, R. R. LIRM 97076.

60. D. Huson, S. Nettles, L. Parida, T. Warnow, S. Yooseph, The Disk-Covering Method for Tree Reconstruction, Proceedings of “Algorithmsand Experiments”, (ALEX‘98), Trento, 1998, 62–75.

61. Junhyong Kim, Large-scale phylogenies and measuring the perfor-mance of phylogenetic estimators, Syst. Biol. 47(1) (1998), 43–60.

62. M. Steel, M. D. Hendy, D. Penny, Reconstructing phylogenies fromnucleotide pattern probabilities: a survey and some new results, Disc.Appl. Math. 88 (1998) 367–396.

63. D. Huson, S. Nettles, T. Warnow, Obtaining highly accurate topol-ogy estimates of evolutionary trees from very short sequences, RE-COMB’99 Lyon, France (1999), 198–207.

64. D. Bryant, M. Steel, Fast algorithms for constructing optimal treesfrom quartets, Proc. Tenth Annual ACM-SIAM Symposium onDiscrete Algorithms, Baltimore, Maryland, 1999, 147–155.

65./ P. L. Erdos, M. A. Steel, L. A. Szekely, and T. J. Warnow, Afew logs suffice to build (almost) all trees I, Random Structuresand Algorithms 14(1999)(2) 153–184.

References

1. S Snir, L Pachter, Phylogenetic Profiling of Insertions and Deletionsin Vertebrate Genomes, esearch in Computational Molecular BiologyLecture Notes in Computer Science, 2006, Volume 3909/2006, 265-280,

2. Constantinos Daskalakis and Sebastien Roch, Alignment-Free Phylo-genetic Reconstruction, Research in Computational Molecular BiologyLecture Notes in Computer Science, 2010, Volume 6044/2010, 123-137,

3. RADU MIHAESCU, CAMERON HILL, AND SATISH RAO, FASTPHYLOGENY RECONSTRUCTION THROUGH LEARNING OFANCESTRAL SEQUENCES, arXiv:0812.1587v1 [cs.DS] 8 Dec 2008

4. Mihaescu, Radu Horia, Distance methods for phylogeny reconstruc-tion, Ph.D. Thesis, 2008, University of California, Berkeley.

5. SJ Roch, Markov Models on Trees: Reconstruction and Applications,Ph.D. Thesis, 2007, University of California, Berkeley.

6. Maw-Shang Chang, Chuang-Chieh Lin and Peter Rossmanith, A Prop-erty Tester for Tree-Likeness of Quartet Topologies, Theory of Com-puting Systems DOI: 10.1007/s00224-010-9276-5

72

Page 73: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

7. J Chakerian, S Holmes, Computational Tools for Evaluating Phyloge-netic and Hierarchical Clustering Trees - Arxiv preprint arXiv:1006.1015,2010

8. Myung Jin Choi, Vincent Y. F. Tan, Animashree Anandkumar, AlanS. Willsky, Learning Latent Tree Graphical Models, arXiv:1009.2722v1[stat.ML] 14 Sep 2010

9. Ilan Gronau, Shlomo Moran, and Irad Yavneh, Adaptive DistanceMeasures for Resolving K2P Quartets: Metric Separation versus Stochas-tic Noise, Journal of Computational Biology 2010 doi:10.1089/cmb.2009.0236.

10. Humphries EM, Winker K, Working through polytomies: Auklets re-visited, MOLECULAR PHYLOGENETICS AND EVOLUTION 54(1)(2010)Pages: 88-96

11. Mossel E, Roch S, Incomplete Lineage Sorting: Consistent PhylogenyEstimation from Multiple Loci, IEEE-ACM TRANSACTIONS ONCOMPUTATIONAL BIOLOGY AND BIOINFORMATICS 7(1)(2010)166-171.

12. Gronau I, Moran S, Yavneh I, Towards optimal distance functionsfor stochastic substitution models, JOURNAL OF THEORETICALBIOLOGY 260(2)(2010) Pages: 294-307

13. Roch, S., Toward Extracting All Phylogenetic Information from Ma-trices of Evolutionary Distances, SCIENCE Volume: 327 (2010) Issue:5971 Pages: 1376-1379

14. Bhamidi S, Rajagopal R, Roch S, Network Delay Inference from Ad-ditive Metrics, RANDOM STRUCTURES & ALGORITHMS 37(2)(2010) 176–203

15. Chang MS, Lin CC, Rossmanith P, New Fixed-Parameter Algorithmsfor the Minimum Quartet Inconsistency Problem, THEORY OF COM-PUTING SYSTEMS 47(2)(2010) 342–367

16. Allman ES, Rhodes JA, Trees, Fast and Accurate, SCIENCE 327 Issue:5971 (2010) Pages: 1334-1335

17. Elias I, Lagergren J, Fast neighbor joining, THEORETICAL COM-PUTER SCIENCE Volume: 410 Issue: 21-23 Pages: 1993-2000 Pub-lished: MAY 17 2009

18. Soltis DE, Moore MJ, Burleigh G, et al, Molecular Markers and Con-cepts of Plant Evolutionary Relationships: Progress, Promise, andFuture Prospects, CRITICAL REVIEWS IN PLANT SCIENCES Vol-ume: 28 Issue: 1-2 Pages: 1-15 Published: 2009

19. Mihaescu R, Levy D, Pachter L, Why Neighbor-Joining Works, AL-GORITHMICA Volume: 54 Issue: 1 Pages: 1-24 Published: MAY2009

20. Lacey MR, Calmes J, A Sharp Error Probability Estimate for theReconstruction of Phylogenetic Quartets by the Four-Point Method,JOURNAL OF COMPUTATIONAL BIOLOGY Volume: 16 Issue: 3Pages: 443-456 Published: MAR 2009

73

Page 74: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

21. Willson SJ, Robustness of Topological Supertree Methods for Recon-ciling Dense Incompatible Data, IEEE-ACM TRANSACTIONS ONCOMPUTATIONAL BIOLOGY AND BIOINFORMATICS Volume:6 Issue: 1 Pages: 62-75 Published: JAN-MAR 2009

22. Mossel E, Roch S, Steel M, Shrinkage Effect in Ancestral MaximumLikelihood, IEEE-ACM TRANSACTIONS ON COMPUTATIONALBIOLOGY AND BIOINFORMATICS Volume: 6 Issue: 1 Pages: 126-133 Published: JAN-MAR 2009

23. Steffen Klaere, Tanja Gesell, Arndt von Haeseler, The impact of singlesubstitutions on multiple sequence alignments, Phil. Trans. R. Soc.B Volume: 363 Issue: 1512 Pages: 4041-4047 Published: DEC 27 2008

24. C. Daskalakis - E. Mossel - S. Roch: Evolutionary Trees and the IsingModel on the Bethe Lattice: a Proof of Steels Conjecture, arXiv:math/0509575v2(2008), 1–34.

25. On the hardness of inferring phylogenies from triplet-dissimilaritiesAuthor(s): Gronau I, Moran S Source: THEORETICAL COMPUTERSCIENCE Volume: 389 Issue: 1-2 Pages: 44-55 Published: DEC 102007

26. Short quartet puzzling: A new quartet-based phylogeny reconstructionalgorithm Author(s): Snir S, Warnow T, Rao S Source: JOURNALOF COMPUTATIONAL BIOLOGY Volume: 15 Issue: 1 Pages: 91-103 Published: JAN 2008

27. Gang Wu - M-Y. Kao - Guohui Lin - J-H. You: Reconstructing phy-logenies from noisy quartets in polynomial time with a high successprobability, Algorithms for Mol. Biol. 3:1 (2008), 1–10.

28. C. Daskalakis - E. Mossel - S. Roch: Phylogenies without BranchBounds: Contracting the Short, Pruning the Deep, arXiv:0801.4190v1(2008), 1–19.

29. E. Mossel - S. Roch: Incomplete Lineage Sorting: Consistent Phy-logeny Estimation From Multiple Loci, arXiv:0710.0262v2 (2007),1–14.

30. Grunewald, S., Steel, M., Swenson, M.S. Closure operations in phylo-genetics (2007) Mathematical Biosciences, 208 (2), pp. 521-537.

31. M. R. Lacey, J. T. Tang, A signal-to-noise analysis of phylogeny es-timation by neighbor-joining: insufficiency of polynomial length se-quences, Math. Biosci. 199 (2006) 188-215.

32. Chor B, Hendy M, Penny D Analytic solutions for three taxon MLtrees with variable rates across sites DISCRETE APPLIED MATHE-MATICS 155 (6-7): 750-758 APR 1 2007

33. Maw-Shang Chang - Ling-Ju Hung - Chuang-Chieh Lin - P. Ross-manith A randomized fixed-parameter algorithm for the minimumquartet inconsistency problem, 24th Workshop on Comb. Math.and Comp. Theory CMCT’07 Nantou, Taiwan, April, (2007), 132–138.

74

Page 75: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

34. K. Sjolander: Phylogenetic inference in protein superfamilies: Analysisof SH2 domains, Proceedings ISMB’98 (ed. J. Glasgow et.al) (1998),165–174.

35. Claudine Levasseur, Francois-Joseph Lapointe, Total evidence, aver-age consensus and matrix representation with parsimony: what a dif-ference distances make, Evolutionary Bioinformatics Online 2006: 2249–253.

36. Snir S, Rao S Using max cut to enhance rooted trees consistency IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY ANDBIOINFORMATICS 3 (4): 323-333 OCT-DEC 2006

37. Cryan, M., Goldberg, L.A., Goldberg, P.W., Evolutionary trees canbe learned in polynomial time in the two-state general Markov model, SIAM Journal on Computing 31 (2), pp. 375-397

38. Wu G, You JH, Lin GH A polynomial time algorithm for the minimumquartet inconsistency problem with O(n) quartet errors INFORMA-TION PROCESSING LETTERS 100 (4): 167-171 NOV 30 2006

39. Mossel E, Roch S Learning nonsingular phylogenies and hidden Markovmodels ANNALS OF APPLIED PROBABILITY 16 (2): 583-614 MAY2006

40. T. Warnow: Large-scale phylogenetic reconstruction, in Handbook ofComputational Biology (S. Aluru (editor)), Chapman & Hall, CRCComputer and Information Science Series, (2005), 1–24.

41. D. Adkins - C. Daskalakis - C. Hill - A, Jaffe - R.H. Mihaescu - E.Mossel - S. Rao: MST-based framework for sequence based Tree re-construction, to appear (2005), 1–7.

42. R. Mihaescu - D. Levy - L. Pachter: Why neighbor-joining works,arXiv:cs.DS/0602041 (2006), 1–16.

43. S. Snir - T. Warnow - S. Rao: Quartets MaxCut: A new quartet-basedphylogeny reconstruction algorithm, Bioinformatics (2006), 1–14.

44. U. Roshan: Algorithmic techniques for improving the speed and ac-curacy of phylogenetic methods, Ph.D Thesis, University Texas atAustin (2004) 1–256.

45. S. Bocker: From subtrees to supertrees, Ph.D. Thesis, UniversitatBielefeld (1999) 1–100.

46. Wang LS, Warnow T Reconstructing chromosomal evolution SIAMJOURNAL ON COMPUTING 36 (1): 99-131 2006

47. S. Bhamidi - R. Rajagopal - S. Roch: Network delay infrence fromadditive metrics, arXiv:math.PR/0604367 v1 (2006), 1–19.

48. B.D. Thatte: Invertibility of the TKF model of sequence evolution,Math. Biosci. 200 (2006), 58–75.

49. S. Bocker, Unrooted supertrees: Limitations, traps, and phylogeneticpatchworks; in: Phylogenetic supertrees: the book

75

Page 76: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

50. SN Evans, D Ringe, T Warnow, INFERENCE OF DIVERGENCETIMES AS A STATISTICAL INVERSE PROBLEM, Invited paper,to appear in special volume on Phylogenetic Methods and the Pre-history of Languages Cambridge University Press (2005), 1–19.

51. B Chor, M Hendy, D Penny, Analytic Solutions for Three-Taxon MLMCTrees with Variable Rates Across Sites, LECTURE NOTES IN COM-PUTER SCIENCE, 2001 - Springer volume 2149 p. 204

52. M.R. Lacey - J.T. Chang: A signal-to-noise analysis of phylogeny es-timation by neighbor-joining: Insufficiency of polynomial length se-quences, Math. Biosciences 199 (2006), 188–215.

53. Gang Wu - Jia-Huai You - Guohui Lin: A lookahead branch-and-bound algorithm for the Maximum Quartet Consistency Problem, Al-gorithms in Bioinf. LNCS 3602 (2005), 65–76.

54. M.A. Sanderson: Where have all the clades gone? A systematist’s takeon inferring phylogenies, Evolution 59 (2005) 2056–2058.

55. Xiaomeng Wu - Xiu-Feng Wan - Gang Wu - Dong Xu - Guohui Lin:Phylogenetic analysis using complete signature information pf whole-genomes and clustered neighbor-joining method, 2006 InternationalJournal of Bioinformatics Research and Applications 2 (3), pp. 219-248.

56. M.A. Steel - J. Hein: Reconstructing pedigrees: a combinatorial per-spective, J. Theor. Biol. (2005), 1–16.

57. C. Daskalakis - C. Hill - A. Jaffe - R.H. Mihaescu - E. Mossel - S. Rao:Maximal accurate forests from distance matrices, LECTURE NOTESIN COMPUTER SCIENCE 3909: 281-295 2006

58. R.H. Mihaescu - D. Adkins - C. Daskalakis - C. Hill - A. Jaffe - E.Mossel - S. Roche: A polynomial time algorithm for phylogenetic treereconstruction from logarithmic-size data, to appear (2005), 1–19.

59. S. Snir - A. Rao: Quartet semi-definite programming revisited, sub-mitted (2005), 1–12.

60. E. Mossel, Distorted metric on trees and phylogenetic forests, IEEE/ACMTrans. Comp. Biol. and Bioinf. 4 (1): 108-116 JAN-MAR 2007

61. C. Daskalakis - E. Mossel - S. Roch: Optimal phylogenetic reconstruc-tion, 2006 Proceedings of the Annual ACM Symposium on Theory ofComputing 2006, pp. 159-168

62. Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, TandyWarnow The Performance of Phylogenetic Methods on Trees of BoundedDiameter, Lecture Notes in Computer Science, Springer-Verlag GmbHISSN: 0302-9743 Volume 2149 / 2001 Algorithms in Bioinformatics:First International Workshop, WABI 2001, Aarhus, Denmark, August28-31, 2001, Proceedings Editors: O. Gascuel, B. M. E. Moret (Eds.):p. 214

76

Page 77: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

63. B. M. E. Moret, Tandy Warnow, Reconstructing optimal phylogenetictrees: a challenge in experimental algorithmics, Lecture Notes In Com-puter Science, Experimental algorithmics: from algorithm design torobust and efficient software archive Pages: 163 - 180 Year of Publica-tion: 2002 ISBN:3-540-00346-0

64. E. Mossel - M.A. Steel: How much can evolved characters tell us aboutthe tree that generated them, in Mathematics of Evolution and Phy-logeny (Ed. O. Gascuel) Oxford Univ. Press (2004), 384–412.

65. Tao Liu - Jijun Tang - B.M.E. Moret: Quartet-based phylogeny recon-struction from gene orders, COCOON ’05 August 16-19, Kunming,Yunnan, Chine (2005), 237–241.

66. I. Elias - J. Lagergren: Fast Neighbor Joining, ICALP 2005 LNCS3580 (2005), 1263–1274.

67. A. Rokas, S. B. Carroll, More genes or more taxa? The relative con-tribution of gene number and taxon number to phylogenetic accuracy,Mol. Biol. Evol. 22(5) (2005),1337–1344.

68. E. Mossel - S. Roch: Learning nonsingular phylogenies and hiddenMarkov models, Proceedings of ACM STOC’05 (2005), 366–375.(full version arXiv:cs.LG/0502076 v1 18 Feb 2005) To appear in Annalsof Applied Probability, 2006.

69. U. Roshan - B.M.E. Moret - T.L. Williams - T. Warnow: Performanceof supertree methods on various dataset decompositions, in Phyloge-netic Supertrees: Combining Information to Reveal the Tree ofLife (O.R.P. Bininda-Emonds, editor), Kluwer Academics, (2004),301–328.

70. Gang Wu - Guohui Lin - Jia-Huai You: Quartet Based PhylogenyReconstruction with Answer Set Programming, in 16th IEEE Int.Conf. on Tools with Artificial Intelligence (ICTAI’04) (2004),612–619.

71. Gang Wu, Guohui Lin, J. You, and X. Wu. Faster Solution to theMaximum Quartet Consistency Problem with Constrained Program-ming. The 3rd Asia-Pacific Bioinformatics Conference (APBC 2005).January 17-21, 2005, Singapore. Accepted on August 27, 2004.

72. Gang Wu - Jia-Huai You - Guohui Lin: A lookahead branch-and-boundalgorithm for the Maximum Quartet Consistency Problem, Tech. Re-port TR05-05 University of Alberta (2005), 1–14.

73. F.S. Roberts: Challenges for Discrete Mathematics and TheoreticalComputer Science in the Defense against Bioterrorism, in Bioterror-ism: Mathematical Modeling Applications in Homeland Security(ed. by H. T. Banks and Carlos Castillo-Chavez), Proceeding of DI-MACS and NFS, 2002, SIAM (2003), Chapter 1.

74. Driskell AC, Ane C, Burleigh JG, et al. Prospects for building the treeof life from large sequence databases SCIENCE 306 (5699): 1172-1174NOV 12 2004

77

Page 78: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

75. E. Mossel, M. Steel, How much can evolved characters tell us aboutthe tree that generated them?

76. Piaggio-Talice, Raul; Burleigh, Gordon; Eulenstein, Oliver. 2004.Quartet Supertrees, in Bininda-Emonds, Olaf R.P. (ed), PhylogeneticSupertrees: Combining Information to Reveal the Tree of Life, pp.173-191. Kluwer Academic, Dordrecht, the Netherlands

77. Elizabeth S. Allman and John A. Rhodes, Quartets and parameterrecovery for the general Markov model of sequence mutation, AppliedMathematics Research Express 2004:4 (2004) 107-131.

78. Mossel E, Steel M A phase transition for a random cluster model onphylogenetic trees MATH BIOSCI 187 (2): 189-203 FEB 2004

79. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

80. C. Semple and M. Steel, Phylogenetics, Oxford Lecture Series in Math-ematics and its Applications 24, Oxford University Press, 2003

81. Moret BME, Roshan U, Warnow T Sequence-length requirements forphylogenetic methods LECT NOTES COMPUT SC 2452: 343-3562002

82. Sanderson MJ, Driskell AC The challenge of constructing large phylo-genetic trees TRENDS PLANT SCI 8 (8): 374-379 AUG 2003

83. Sanderson MJ, Driskell AC, Ree RH, et al. Obtaining maximal con-catenated phylogenetic data sets from large sequence databases MOLBIOL EVOL 20 (7): 1036-1042 JUL 2003

84. E. Mossel, On the impossibility of reconstructing ancestral data andphylogenies, J. Comp. Biol. 10 (5): 669-676 2003

85. Lagergren J Combining polynomial running time and fast convergencefor the disk-covering method J COMPUT SYST SCI 65 (3): 481-493NOV 2002

86. M. Csuros: Fast recovery of evolutionary trees with thousands ofnodes, J COMPUT BIOL 9 (2): 277-297 2002

87. L. Nakhleh, U. Roshan, K. St. John, J. Sun, T. Warnow, Designingfast converging phylogenetic methods

88. E. Mossel, Phase transitions in phylogeny, T AM MATH SOC 356 (6):2379-2404 2004

89. Monika Rauch Henzinger, Valerie King, Tandy Warnow, Construct-ing a Tree from Homeomorphic Subtrees, with Applications to Com-putational Evolutionary Biology in Proceedings of the 7th AnnualACM-SIAM Symp. on Discrete Algorithms (SODA ’96) (1996),333–340.

90. M. Csuros: Fast recovery of evolutionary trees with thousands ofnodes, RECOMB’01 Montreal, Canada (2001), 104–113.

91. K. St. John - T. Warnow - B.M.E. Moret - L. Vawter: Performancestudy of phylogenetic methods: (unweighted) quartet methods andNeigbor-joining, J. Algorithms (2002), 173–193..

78

Page 79: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

92. M. Csuros: Reconstructing Phylogenies in Markov Models of SequenceEvolution, Ph.D. Thesis Yale University, (2000), 1–232.

93. M.E. Cryan: Learning and approximation algorithms for problemsmotivated by evolutionary trees, Ph.D. Thesis, University of Warwick(1999), 1–176.

94. D. Huson, S. Nettles, K. Rice, T. Warnow, S. Yooseph: Hybrid treereconstruction methods, ACM J. Exp. Alg 4 (1998), Articel 5.

95. T. Warnow, B. M. E. Moret, K. St. John: Absolute convergence: truetrees from short sequences, ACM Symp. on Discrete AlgorithmsSODA 2001 (2001), 1–9.

96. D. Bryant, M. Steel, Constructing optimal trees from quartets, J.Algorithm 38 (1)(2001), 237–259.

97. M. Csuros, M-Y. Kao, Provably fast and accurate recovery of evolu-tionary trees through harmonic greedy triplets, SIAM J. Computing31 (1) (2001) 306–322.

98. S. Bocker, D. Bryant, A. W. M. Dress, M. A. Steel Algorithmic aspectsof tree amalgamation J. Algorithm 37 (2) (2000), 522–537.

99. B. Chor, M. D. Hendy, B. R. Holland, et al., Mol. Biol. Evol. Multi-ple maxima of likelihood in phylogenetic trees: An analytic approach,17 (2000), 1529–1541.

100. M. Csuros - M-Y Kao: O(n2)-time accurate recovery of large evolu-tionary trees from triplets and quartets, in preparation.

101. M. Steel, D. Penny, Parsimony, likelihood and the role of models inmolecular phylogenetics, Mol. Biol. Evol. 17 (6) (2000) 839–850.

102. Susan P. Holmes, Phylogenies: An overview, Statistics and Genetics,(ed. Halloran and Geisser), IMA series, vol 112, Springer Verlag, NY,81–119.

103. D. H. Huson, S. M. Nettles, and T. J. Warnow, Disk-covering, a fast-converging method for phylogenetic tree reconstruction, J. Comp.Biol. 6 (3–4) (1999), 369–386.

104. V. Berry, Methodes et algorithmes pour reconstruire les arbres del’Evolution, These de Doctorat, Universite de Montpellier II, 1997.

105. T. Warnow, Some combinatorial optimization problems in phyloge-netics, in: Graph Theory and Combinatorial Biology, L. Lovaszet. al., eds. Bolyai Society Mathematical Studies 7, Janos BolyaiMathematical Society, Budapest, 1999, 363–413.

106. M. Cryan, L. A. Goldberg, P. W. Goldberg, Evolutionary trees canbe learned in polynomial time in the two-state general Markov model,FOCS’98 Proceedings of the 39th Annual IEEE Symposium onFoundations of Computer Science, (1998) 436–445.

107. D. Huson, S. Nettles, T. Warnow, Obtaining highly accurate topol-ogy estimates of evolutionary trees from very short sequences, RE-COMB’99 Lyon, France (1999), 198–207.

79

Page 80: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

108. S. Bocker, A. W. M. Dress, M. A. Steel, Patching up X-trees, Annalsof Combinatorics 3 (1999), 1–12.

66./ P. L. Erdos, M. A. Steel, L. A. Szekely, and T. J. Warnow, Afew logs suffice to build (almost) all trees II, Theor. Comp. Sci.221 (1-2)(1999), 77–118.

References

1. Elchanan Mossel and Eric Vigoda, Limitations of Markov Chain MonteCarlo Algorithms for Bayesian Inference of Phylogeny, The Annals ofApplied Probability Vol. 16, No. 4 (Nov., 2006), pp. 2215-2234.

2. Guy Bresler, Elchanan Mossel and Allan Sly, Reconstruction of MarkovRandom Fields from Samples: Some Observations and Algorithms,Lecture Notes in Computer Science, 2008, Volume 5171/2008, 343-356, DOI: 10.1007/978-3-540-85363-3 28.

3. Charles Semple and Mike Steel, Tree Reconstruction via a ClosureOperation on Partial Splits, Lecture Notes in Computer Science, 2001,Volume 2066/2001, 126-134, DOI: 10.1007/3-540-45727-5 11.

4. S. Roch, Sequence Length Requirement of Distance-Based PhylogenyReconstruction: Breaking the Polynomial Barrier, Foundations of Com-puter Science, 2008. FOCS ’08. IEEE 49th Annual IEEE Symposiumon Issue Date: 25-28 Oct. 2008, 729 - 738 Philadelphia, PA.

5. I. Gronau, S. Moran, S. Snir, Fast and reliable reconstruction of phy-logenetic trees with very short edges, SODA ’08 Proceedings of thenineteenth annual ACM-SIAM symposium on Discrete algorithms

6. Sebastien Roch, Phase Transition in Distance-Based Phylogeny Re-construction

7. Daniele Catanzaro, The minimum evolution problem: Overview andclassification, Networks Volume 53, Issue 2, pages 112125, March 2009.

8. Andrej Bogdanov, Elchanan Mossel and Salil Vadhan, The Complexityof Distinguishing Markov Random Fields, Approximation, Random-ization and Combinatorial Optimization. Algorithms and TechniquesLecture Notes in Computer Science, 2008, Volume 5171/2008, 331-342,DOI: 10.1007/978-3-540-85363-3 27

9. Sagi Snir, Λ Raphael Yuster, Reconstructing approximate phylogenetictrees from quartet samples

10. Elchanan Mossel, Sebastien Roch, Allan Sly, On the inference of largephylogenies with long branches: How long is too long? Arxiv preprintarXiv:1001.3480, 2010 - arxiv.org

11. Alexandr AndoniΛ, Mark Braverman, Avinatan Hassidim, Phyloge-netic Reconstruction with Insertions and Deletions,

12. Vincent Ranwez, Methodes efficaces pour reconstruire de grandes phy-logenies suivant le principe du maximum de vraisemblance, UNIVER-SITE DE MONTPELLIER II, Ph.D. Thesis in Informatics, 2002.

80

Page 81: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

13. Steffen Klaere, Tanja Gesell, Arndt von Haeseler, The impact of singlesubstitutions on multiple sequence alignments, Phil. Trans. R. Soc.B

14. G. Hickey - P. Carmi - A. Maheshwari - N. Zeh: NAPX: A PolynomialTime Approximation Scheme for the Noahs Ark Problem Algorithmsin Bioinformatics Lecture Notes in Computer Science, 2008, Volume5251/2008, 76-86,

15. G. Hickey - P. Carmi - A. Maheshwari - N. Zeh: NAPX: An Approxi-mation Algorithm for the Noah’s Ark Problem with Random FeatureLoss, IEEE/ACM Transactions on Bioinformatics and ComputationalBiology http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.37

16. L. van Iersel - J. Keijsper - S. Kelk - L. Stougie - F. Hagen - T.Boekhout: Constructing level-2 phylogenetic networks from triplets,Research in Computational Molecular Biology, RECOMB’08 LNCS4955 (2008), 450–462.

17. L. van Iersel - J. Keijsper - S. Kelk - L. Stougie: Constructing level-2phylogenetic networks from triplets, arXiv:0707.2890v1 [q-bio.PE](2007), 1–24.

18. Short quartet puzzling: A new quartet-based phylogeny reconstructionalgorithm Author(s): Snir S, Warnow T, Rao S Source: JOURNALOF COMPUTATIONAL BIOLOGY Volume: 15 Issue: 1 Pages: 91-103 Published: JAN 2008

19. On the hardness of inferring phylogenies from triplet-dissimilaritiesAuthor(s): Gronau I, Moran S Source: THEORETICAL COMPUTERSCIENCE Volume: 389 Issue: 1-2 Pages: 44-55 Published: DEC 102007

20. C. Daskalakis - E. Mossel - S. Roch: Phylogenies without BranchBounds: Contracting the Short, Pruning the Deep, arXiv:0801.4190v1(2008), 1–19.

21. L. van Iersel - J. Keijsper - S. Kelk - L. Stougie: Constructing level-2phylogenetic networks from triplets, arXiv:0707.2890v1 [q-bio.PE](2007), 1–24.

22. Ming-Yang Kao - Xiang-Yang Li - Weizhao Wang: Average cas anal-ysis for tree labeling schemes, Theor. Comp. Sci (2007), 378 (3) pp.271–291. doi:10.1016/j.tcs.2007.02.066

23. Cryan, M., Goldberg, L.A., Goldberg, P.W., Evolutionary trees canbe learned in polynomial time in the two-state general Markov model, SIAM Journal on Computing 31 (2), pp. 375-397

24. Mossel E, Vigoda E Response to comment on ”Phylogenetic MCMCalgorithms are misleading on mixtures of trees” SCIENCE 312 (5772):doi:10.1126/science.1124180 APR 21 2006

25. Mossel E, Roch S Learning nonsingular phylogenies and hidden Markovmodels ANNALS OF APPLIED PROBABILITY 16 (2): 583-614 MAY2006

81

Page 82: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

26. I. Gronau - S. Moran: Neighbor joining algorithms for inferring phy-logenies via LCA distances JOURNAL OF COMPUTATIONAL BI-OLOGY 14 (1): 1-15 JAN 2007

27. S. Snir - T. Warnow - S. Rao: Quartets MaxCut: A new quartet-basedphylogeny reconstruction algorithm, Bioinformatics (2006), 1–14.

28. T. Warnow: Large-scale phylogenetic reconstruction, in Handbook ofComputational Biology (S. Aluru (editor)), Chapman & Hall, CRCComputer and Information Science Series, (2005), 1–24.

29. D. Adkins - C. Daskalakis - C. Hill - A, Jaffe - R.H. Mihaescu - E.Mossel - S. Rao: MST-based framework for sequence based Tree re-construction, to appear (2005), 1–7.

30. U. Roshan: Algorithmic techniques for improving the speed and ac-curacy of phylogenetic methods, Ph.D Thesis, University Texas atAustin (2004) 1–256.

31. Mossel E, Vigoda E Response to comment on ”Phylogenetic MCMCalgorithms are misleading on mixtures of trees” SCIENCE 312 (5772):doi:10.1126/science.1124180 APR 21 2006

32. SCALING OF ACCURACY IN EXTREMELY LARGE PHYLOGE-NETIC TREES ORP Bininda-Emonds, SG Brady, J Kim, MJ Sander-son - Pacific Symposium on Biocomputing, 2001

33. C. Daskalakis - C. Hill - A. Jaffe - R.H. Mihaescu - E. Mossel - S. Rao:Maximal accurate forests from distance matrices, LECTURE NOTESIN COMPUTER SCIENCE 3909: 281-295 2006

34. R.H. Mihaescu - D. Adkins - C. Daskalakis - C. Hill - A. Jaffe - E.Mossel - S. Roche: A polynomial time algorithm for phylogenetic treereconstruction from logarithmic-size data, to appear (2005), 1–19.

35. S. Snir - A. Rao: Quartet semi-definite programming revisited, sub-mitted (2005), 1–12.

36. E. Mossel, Distorted metric on trees and phylogenetic forests, IEEE/ACMTrans. Comp. Biol. and Bioinf. 4 (1): 108-116 JAN-MAR 2007

37. V King, L Zhang, Y Zhou, On the Complexity of Distance-based Evo-lutionary Tree Reconstruction, SODA, SIAM PROCEEDINGS SE-RIES; 2003; p.444-453 (Conference: 14th Annual ACM-SIAM Sym-posium on Discrete Algorithms; January 12-14, 2003; BALTIMORE,MARYLAND)

38. Chor B, Tuller T Maximum likelihood of evolutionary trees: hardnessand approximation BIOINFORMATICS 21: I97-I106 Suppl. 1 JUN2005

39. A. Rokas, S. B. Carroll, More genes or more taxa? The relative con-tribution of gene number and taxon number to phylogenetic accuracy,Mol. Biol. Evol. 22(5) (2005),1337–1344.

40. E. Mossel - S. Roch: Learning nonsingular phylogenies and hiddenMarkov models, Proceedings of ACM STOC’05 (2005), 366–375.

82

Page 83: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

(full version arXiv:cs.LG/0502076 v1 18 Feb 2005) To appear in Annalsof Applied Probability, 2006.

41. Bryant D, Moulton V NeighborNet: An agglomerative method for theconstruction of planar phylogenetic networks LECT NOTES COM-PUT SC 2452: 375-391 2002

42. Desper R, Gascuel O Fast and accurate phylogeny reconstruction al-gorithms based on the minimum-evolution principle LECT NOTESCOMPUT SC 2452: 357-374 2002

43. C. Semple and M. A. Steel, Cyclic permutations and evolutionarytrees, Adv. Appl. Math. 32 (4) 669-680 MAY 2004

44. R. Desper, O. Gascuel, Fast and accurate phylogeny reconstruction al-gorithms based on the minimum-evolution principle J. Comput. Biol.9 (5) (2002), 687–705.

45. M. Csuros: Fast recovery of evolutionary trees with thousands ofnodes, J COMPUT BIOL 9 (2): 277-297 2002

46. L. Nakhleh, U. Roshan, K. St. John, J. Sun, T. Warnow, Designingfast converging phylogenetic methods

47. E. Mossel, Phase transitions in phylogeny, T AM MATH SOC 356 (6):2379-2404 2004

48. M. Csuros: Fast recovery of evolutionary trees with thousands ofnodes, RECOMB’01 Montreal, Canada, 2001, 104–113.

49. M. Csuros: Reconstructing Phylogenies in Markov Models of SequenceEvolution, Ph.D. Thesis Yale University, (2000), 1–232.

50. M.E. Cryan: Learning and approximation algorithms for problemsmotivated by evolutionary trees, Ph.D. Thesis, University of Warwick(1999), 1–176.

51. J. Kim - T. Warnow: Tutorial on phylogenetic tree estimation, inISMB’99, 7th Conf. Intell. Systems for Molecular Biology, Au-gust 6-10, Heidelberg, Germany, Tutorial Section, (1999), 1–29.

52. K. Atteson, The performance of neighbor-joining methods of phyloge-netic reconstruction, Algorithmica 25 251–278.

53. D. H. Huson, S. M. Nettles, and T. J. Warnow, Disk-covering, a fast-converging method for phylogenetic tree reconstruction, J. Comp.Biol. 6 (3–4) (1999), 369–386.

54. O. Gascuel: Evidence for a relationship between algorithmic schemeand shape of inferred trees, Data Analysis. Scientific Modellingand Practical Applications (ed. W. Gaul, O. Opitz, M. Schader)Springer (2000), 157–168.

55. T. Warnow - B.M.E. Moret - K. St. John: Absolute convergence: truetrees from short sequences, ACM Symp. on Discrete AlgorithmsSODA2001 (2001), 1–9.

83

Page 84: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

56. Susan P. Holmes, Phylogenies: An overview, Statistics and Genetics,(ed. Halloran and Geisser), IMA series, vol 112, Springer Verlag, NY,81–119.

57. T. Warnow, Some combinatorial optimization problems in phyloge-netics, in: Graph Theory and Combinatorial Biology, L. Lovaszet. al., eds. Bolyai Society Mathematical Studies 7, Janos BolyaiMathematical Society, Budapest, 1999, 363–413.

58. D. Huson, S. Nettles, T. Warnow, Obtaining highly accurate topol-ogy estimates of evolutionary trees from very short sequences, RE-COMB’99 Lyon, France (1999), 198–207.

59. M. Csuros, K-Y. Ming, Reconstructing evolutionary trees in a generalMarkov model, in preparation.

60. M. Csuros, M-Y. Kao, Provably fast and accurate recovery of evolu-tionary trees through harmonic greedy triplets, SIAM J. Computing31 (1) (2001) 306–322.

61. M. Farach, S. Kannan, Efficient algorithms for inverting evolution, J.ACM 46 (4) 437–449.

67./ P. L. Erdos, K. Rice, M. A. Steel, L. A. Szekely, and T. J.Warnow The Short Quartet Method, was appear in Math. Mod-elling and Sci. Computing, Special Issue of the papers presentedat the Computational Biology sessions at the 11th ICMCM,March 31 - April 2, 1997, Georgetown University ConferenceCenter, Washington, D.C., USA. Also to be published by Prin-cipia Scientia, St. Luis. (The volume was never published!)

References

1. M. Tarawneh: A novel quartet-based method for inferring evolution-ary trees from molecular data, Ph.D. Thesis, University of Sidney(2008), 1–151.

2. D. Shing-Min Liu - Che-Hao Wu: An effective approach for construct-ing the phylogenetic tree on a grid-based architecture, in Proc. 4thIEEE Symp. Bioinformatics, etc. BIBE’04 (2004), 134–141.

3. Hu, Badger, Kearney (2003), A Collapsing Method for the EfficientRecovery of Optimal. Edges in Phylogenetic

4. M. Csuros: Reconstructing Phylogenies in Markov Models of SequenceEvolution, Ph.D. Thesis Yale University, (2000), 1–232.

5. D. Huson - S. Nettles - L. Parida - T. Warnow - S. Yooseph, TheDisk-Covering Method for Tree Reconstruction, Proceedings of Proc.“Algorithms and Experiments”, (ALEX‘98), Trento, Italy (1998),62–75.

6. P. Kearney, The ordinal quartet method, RECOMB’98, 125–134.

7. M. Csuros, M-Y. Kao, Fast recovery of evolutionary trees throughharmonic greedy triplets, submitted.

84

Page 85: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

8. M. Csuros, M-Y. Kao, Recovery of evolutionary trees through har-monic greedy triplets, Tenth ACM-SIAM Symposium on DiscreteAlg., 1999, 261–268.

9. M. Csuros, K-Y. Ming, Reconstructing evolutionary trees in a generalMarkov model, in preparation.

68./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, On bipartitecrossings, largest biplanar subgraphs, and the linear arrange-ment problem, Workshop on Algorithms and Data Structures(WADS’97), August 6-8, 1997 Halifax, Nova Scotia, Canada,Lecture Notes in Computer Science Vol. 1272, Springer-Verlag,1997, 55–68.

References

1. Chang Wu Yu, On the complexity of the maximum biplanar subgraphproblem, Information Sciences 129 (2000). 239–250.

2. W Winterbach, The crossing number of a graph in the plane, MSc (Ap-plied Mathematics: Graph Theory) Thesis, University of Stellenbosch,2004.

3. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

4. M. Newton, O. Sykora, M. Uzovic, I. Vrto, New exact results andbounds for bipartite crossing numbers of meshes, LECTURE NOTESIN COMPUTER SCIENCE 3383: 360-370 2004

5. Newton M, Sykora O, Withall M, et al. A parallel approach to row-based VLSI layout using stochastic hill-climbing LECT NOTES AR-TIF INT 2718: 750-758 2003

6. P. Mutzel, An alternative method to crossing minimization on hierar-chical graphs, SIAM J. Optimiz. 11 (4) (2001), 1065–1080.

7. F. Shahrokhi,I. Vrt’o, On 3-layer crossings and pseudo arrangements,in: Graph Drawing Lecture Notes in Computer Science Vol 1731,225–231, 1999, Springer-Verlag.

8. P. Mutzel, Optimization in leveled graphs, in: Encyclopedia of Op-timization, (Pardalos, P. M., Floudas, C. A. eds.), Kluwer AcademicPublishers, 1999.

9. M. Stallmann, Brglez, D. Ghosh, Evaluating iterative heuristics forbigraph crossing number minimization, in: Proc. IEEE 1999 Intl.Symposium on Circuits and Systems, IEEE Press, 1999, p. 4.

69./ F. Shahrokhi and L. A. Szekely Integral uniform flows in sym-metric networks, Graph-Theoretic Concepts in Computer Science(WG’98, Smolenice), J. Hromkovic and O. Sykora eds., LectureNotes in Computer Science 1517, Springer-Verlag, 1998, 272–284.

85

Page 86: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. P. Ruzicka, On efficiency of path systems induced by routing and com-munication schemes, Computing and Informatics 20 (2) (2001), 181–205.

2. S. Cicerone, G. Di Stefano, M. Flammini, Low-congested interval rout-ing schemes for hypercubelike networks Networks 36 (3) 2000, 191–201.

70./ M. A. Steel and L. A. Szekely, Inverting random functions, An-nals of Combinatorics 3 (1999), 103–113.

References

1. Mahendra Mariadassou, Robustesse des arbres phylogenetiques, Uni-versite Paris Sud - Paris XI (2009-11-27), Avner Bar-Hen (Dir.)

2. Bin Ma and Louxin Zhang, Efficient estimation of the accuracy of themaximum likelihood method for ancestral state reconstruction, Jour-nal of Combinatorial Optimization DOI: 10.1007/s10878-009-9261-6

3. Guoliang Li, Jian Ma, Louxin Zhang, Greedy Selection of Species forAncestral State Reconstruction on Phylogenies: Elimination Is Betterthan Insertion, PLoS ONE 5(2): e8985. doi:10.1371/journal.pone.0008985

4. Constantinos Daskalakis and Sebastien Roch, Alignment-Free Phylo-genetic Reconstruction, Research in Computational Molecular BiologyLecture Notes in Computer Science, 2010, Volume 6044/2010, 123-137,

5. Sebastien Roch, Phase Transition in Distance-Based Phylogeny Re-construction

6. Holder MT, Sukumaran J, Lewis PO, A Justification for Reportingthe Majority-Rule Consensus Tree in Bayesian Phylogenetics Source:SYSTEMATIC BIOLOGY Volume: 57 Issue: 5 Pages: 814-821 Pub-lished: 2008

7. Guoliang Li, Mike Steel, Louxin Zhang, More Taxa Are Not Necessar-ily Better for the Reconstruction of Ancestral Character States, SystBiol (2008) 57 (4): 647-653.

8. C. Daskalakis - E. Mossel - S. Roch: Phylogenies without BranchBounds: Contracting the Short, Pruning the Deep, arXiv:0801.4190v1(2008), 1–19.

9. F.S. Roberts: Challenges for Discrete Mathematics and TheoreticalComputer Science in the Defense against Bioterrorism, in Bioterror-ism: Mathematical Modeling Applications in Homeland Security(ed. by H. T. Banks and Carlos Castillo-Chavez), Proceeding of DI-MACS and NFS, 2002, SIAM (2003), Chapter 1.

10. E. Mossel, M. Steel, How much can evolved characters tell us aboutthe tree that generated them?

11. E. Mossel, M. Steel, A phase transition for a random cluster model onphylogenetic trees, Math. Biosci. 187 (2004) 189–203.

86

Page 87: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

12. M Steel, J HEIN, Reconstructing pedigrees: A combinatorial perspec-tive. J Theor Biol, 2005

13. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

14. Holmes S, Statistics for phylogenetic trees THEOR POPUL BIOL 63(1): 17-32 FEB 2003

15. M. Steel, D. Penny, Parsimony, likelihood and the role of models inmolecular phylogenetics, Mol. Biol. Evol. 17 (6) (2000) 839–850.

71./ R. Howard, G. Karolyi, L. A. Szekely, Towards a Katona typeproof for the 2-intersecting Erdos-Ko-Rado theorem, ElectronicJ. Combinatorics, 8 (1) (2001), R31.

References

1. F. Brunk, Intersection problems in combinatorics, Ph.D. Thesis, St.Andrews University, 2008.

2. Tran Dan Thu, An AZ-style identity and Bollobas deficiency, Journalof Combinatorial Theory, Series A Volume 114, Issue 8, November2007, Pages 1504-1514

3. K. Ford, Maximal collections of intersecting arithemetic progressions,Combinatorica 23 (2003), 263–282.

4. G. O. H. Katona, The cycle method and its limits, Numbers, Infor-mation and Complexity, Ingo Althofer, Ning Cai, Gunther Dueck,Levon Khachatrian, Mark S. Pinsker, Andras Sarkozy, Ingo Wegenerand Zhen Zhang (eds.), Kluwer Academic Publishers, 2000, 129–141.

72./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, A new lowerbound for bipartite crossing numbers with applications, Theor.Comp. Sci. 245 (2) (2000), 281–294.

References

1. Judith R. Fredrickson, On the Crossing Number of Complete Graphs:Growing MinimalKn From MinimalKn?1, University of Nevada, Reno,2006.

2. Eliezer A Albacea, A Linear Algorithm for Bipartite Drawing withMinimum Edge Crossings of Complete Binary Trees, Philippine Com-puting Journal, Vol 1, No 1 (2006).

3. M Newton, O Sykora, M Withall, I Vrto, A PVM Computation ofBipartite Graph Drawings

4. E. Makinnen, H. Siirtola, The barycenter heuristic and the reorderablematrix, Informatica 29 (2005), 357–363.

5. M. Newton, O. Sykora, I. Vrto, Two new heuristics for two-sided bi-partite graph drawing, Lecture Notes In Computer Science; Vol. 2528(Revised Papers from the 10th International Symposium on GraphDrawing) Pages: 312 - 319 , 2002 ISBN:3-540-00158-1

87

Page 88: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

6. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

7. M. Newton, O. Sykora, M. Uzovic, I. Vrto, New exact results andbounds for bipartite crossing numbers of meshes, LECTURE NOTESIN COMPUTER SCIENCE 3383: 360-370 2004

8. Newton M, Sykora O, Withall M, et al. A parallel approach to row-based VLSI layout using stochastic hill-climbing LECT NOTES AR-TIF INT 2718: 750-758 2003

73./ P. L. Erdos, and L. A. Szekely, Erdos-Ko-Rado theorems ofhigher order, in: Numbers, Information and Complexity, IngoAlthofer, Ning Cai, Gunther Dueck, Levon Khachatrian, Mark S.Pinsker, Andras Sarkozy, Ingo Wegener and Zhen Zhang (eds.),Kluwer Academic Publishers, 2000, 117–124.

References

1. C.Y. Ku, D. Renshaw, Erdos-Ko-Rado theorems for permutations andset partitions, J. Comb. Theory (A) (2008), 1–13.

doi:10.1016/j.jcta.2007.12.004

2. K Meagher, M Math COVERING ARRAYS ON GRAPHS: CON-NECTIONS TO DESIGN THEORY, EXTREMAL COMBINATORICSAND ALGEBRAIC COMBINATORICS, Ph.D. Thesis, University ofOttawa, 2004.

3. K. Meagher, L. Moura, Erdos-Ko-Rado Theorems for uniform set par-tition systems Elect. J. Comb. 12 (1) (2005), Art. No. R40.

4. R. Ahlswede: Advances on extremal problems in number theory andcombinatorics, in European Congress of Mathematics, Barcelona,2000 Vol. 1, Progress in Mathematics 201 (2001), 147–175.

74./ F. Shahrokhi and L. A. Szekely, Constructing integral uniformflows in symmetric networks and application to the edge-forwardingindex problem, Discrete Applied Math. 108 (2001), 175–191.

References

1. Hou XM, Xu JM, Xu M, The Forwarding Indices of Wrapped ButterflyNetworks, NETWORKS 53 (2009) Issue: 4 329-333.

2. Elsasser R, Lorenz U, Sauerwald T, On randomized broadcasting inStar graphs : DISCRETE APPLIED MATHEMATICS Volume: 157Issue: 1 Pages: 126-139 Published: JAN 6 2009

3. Hou XM, Xu JM, Xu M, The Forwarding Indices of Wrapped But-terfly Networks NETWORKS Volume: 53 Issue: 4 Pages: 329-333Published: JUL 2009

4. Jun Yan; Chao Yang Forwarding Index of Cube-Connected Cycles,DISCRETE APPLIED MATHEMATICS Volume: 157 Issue: 1 Pages:1-7 Published: JAN 6 2009

88

Page 89: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

5. Xu M, Xu JM The forwarding indices of augmented cubes INFOR-MATION PROCESSING LETTERS 101 (5): 185-189 MAR 16 2007

6. Xinmin Hou, Min Xu, Jun-Ming Xu, Forwarding indices of folded n-cubes, DISCRETE APPLIED MATHEMATICS 145 (3): 490-492 JAN30 2005

7. Xinmin Hou, Min Xu, Jun-Ming Xu, Forwarding indices of Cartesianproduct graphs TAIWANESE JOURNAL OF MATHEMATICS 10(5): 1305-1315 SEP 2006

75./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, On bipartitedrawings and the linear arrangement problem, SIAM J. Com-puting 30 (6) (2001), 1773–1789.

References

1. Meysam Tavassoli, Mohammd Ghodsi, Farnoosh Khodakarami, S. MehdiHashemi, An Algorithm for 3D-biplanar Graph Drawing

2. Christian Bachmaier, A Generalized Framework for Drawing DirectedGraphs, Habilitation Thesis, Universitat Passau, 2009.

3. Johannes Uhlmann and Mathias Weller, Two-Layer Planarization Pa-rameterized by Feedback Edge Set, Theory and Applications of Mod-els of Computation Lecture Notes in Computer Science, 2010, Volume6108/2010, 431-442, DOI: 10.1007/978-3-642-13562-0 39.

4. Zoheir Ezziane, Experimental Comparison Between Evolutionary Al-gorithm and Barycenter Heuristic for the Bipartite Drawing Problem,Journal of Computer Science 3 (9): 717-722, 2007.

5. Seok-Hee Hong, Hiroshi Nagamochi, New Approximation to the One-sided Radial Crossing Minimization, Journal of Graph Algorithms andApplications http://jgaa.info/ vol. 13, no. 2, pp. 179–196 (2009)

6. Harrigan, M.; Healy, P., Journal of Graph Algorithms and Applica-tions http://jgaa.info/ vol. 12, no. 3, pp. 293317 (2008)

7. Eliezer A Albacea, A Linear Algorithm for Bipartite Drawing withMinimum Edge Crossings of Complete Binary Trees, Philippine Com-puting Journal, Vol 1, No 1 (2006).

8. Harrigan, M.; Healy, P., Efficiently drawing a significant spanning treeof a directed graph, in: Visualization, 2007. APVIS ’07. 2007 6thInternational Asia-Pacific Symposium on Issue Date: 5-7 Feb. 2007,53 - 59 .

9. Reeti Sharma and Kamal Srivastava, A new hybrid Evolutionary Al-gorithm for the MinLA problem, International Journal of OperationalResearch Volume 5, Number 2 / 2009, 229 - 249

10. Hong SH, Nagamochi H, Approximating Crossing Minimization in Ra-dial Layouts, LATIN 2008: Theoretical Informatics Lecture Notes inComputer Science, 2008, Volume 4957/2008, 461-472, DOI: 10.1007/978-3-540-78773-0 40.

89

Page 90: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

11. Hong SH, Nagamochi H, : Approximation Algorithms for MinimizingEdge Crossings in Radial Drawings, ALGORITHMICA 58(2) (2010)Pages: 478–497

12. : Amaral ARS, A mixed 0-1 linear programming formulation for theexact solution of the minimum linear arrangement problem, OPTI-MIZATION LETTERS Volume: 3 Issue: 4 Pages: 513-520 Published:SEP 2009

13. Liu XC, Yang XG, Tang YY, Molecular solution to the optimal lineararrangement problem based on DNA computation Source: JOURNALOF MATHEMATICAL CHEMISTRY Volume: 44 Issue: 1 Pages:172-183 Published: JUL 2008

14. Gurski F, Graph parameters measuring neighbourhoods in graphs -Bounds and applications Source: DISCRETE APPLIED MATHE-MATICS Volume: 156 Issue: 10 Pages: 1865-1874 Published: MAY28 2008

15. W Ahmad, A Khokhar - cHawk: An Efficient Biclustering Algorithmbased on Bipartite Graph Crossing Minimization

16. T. Poranen, E. Makinen, Tie-breaking heuristics for the barycenterand median algorithms

17. I Safro, D Ron, A Brandt Multilevel algorithms for linear orderingproblems- 2005 - wisdomarchive.wisdom.weizmann.ac.il

18. H Fernau, Parameterized Algorithmics: A Graph-Theoretic Approach,Habilitation Thesis, Universitat Tubingen, 2005,

19. E. Makinnen, H. Siirtola, The barycenter heuristic and the reorderablematrix, Informatica 29 (2005), 357–363.

20. R Hochberg, Minimum Linear Arrangement of Trees, Master’ Thesis,2002, NCSU.

21. Poranen T A genetic hillclimbing algorithm for the optimal linear ar-rangement problem FUNDAMENTA INFORMATICAE 68 (4): 333-356 DEC 2005

22. M. Forster, Crossings in clustered graphs, Ph. D. Thesis, UniversitatPassau, 2004.

23. Falk Schreiber, Visualisierung bichemisher Reaktions, Ph. D. Thesis,Universitat Passau, 2001.

24. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

25. V. Dujmovic, A. Por, David R. Wood, Track layouts of graphs, Dis-crete Mathematics and Computer Science 6(2004) 497–522.

26. M. Newton, O. Sykora, I. Vrto, Two new heuristics for two-sided bi-partite graph drawing, Lecture Notes In Computer Science; Vol. 2528(Revised Papers from the 10th International Symposium on GraphDrawing) Pages: 312 - 319 , 2002 ISBN:3-540-00158-1

90

Page 91: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

27. Munoz, X; Unger, W; Vrt’o, One sided crossing minimization is NP-hard for sparse graphs, LECTURE NOTES IN COMPUTER SCI-ENCE; 2002; v.2265, p.115-123 (Conference: 9th International Sympo-sium on Graph Drawing (GD 2001); September 23-26, 2001; VIENNA,AUSTRIA)

28. V. Dujmovic, M. Fellows, M. Hallett, M. Kitching, G. Liotta, C.McCartin, N. Nishimura, P. Ragde, F. Rosamond, M. Suderman, S.Whitesides, D. R. Wood Proc. Graph Drawing (GD’01) A Fixed-Parameter Approach to Two-Layer Planarization, Lecture Notes inComputer Science 2265 (2002), 1-15.

29. Dujmovic, V., Fellows, M., Hallett, M., Kitching, M., Liotta, G., Mc-cartin, C., Nishimura, N., (...), Wood, D.R., A fixed-parameter ap-proach to 2-layer planarization , Algorithmica (New York) 45 (2006)(2),pp. 159-182

30. Thilikos DM, Serna M, Bodlaender HL Cutwidth II: Algorithms forpartial w-trees of bounded degree JOURNAL OF ALGORITHMS 56(1): 25-49 JUL 2005

31. Dimitrios M. Thilikos, Maria J. Serna, Hans L. Bodlaender, A polyno-mial time algorithm for the cutwidth of bounded degree graphs withsmall treewidth Lecture Notes in Computer Science 2001

32. Matthias Stallmann, Franc Brglez, Debabrata Ghosh, Heuristics, Ex-perimental Subjects, and Treatment Evaluation in Bigraph CrossingMinimization ACM Journal of Experimental Algorithms, 2001

33. Debabrata Ghosh, Franc Brglez, Matthias Stallmann, Generation ofTightly Controlled Circuit Classes for Problems in Physical Design(2000)

34. Matthias Stallmann, Franc Brglez, Debabrata Ghosh, Evaluating It-erative Improvement Heuristics for Bigraph Crossing Minimization(1999)

35. Debabrata Ghosh, Franc Brglez, Matthias Stallmann First Steps To-wards Experimental Design in Evaluating Layout Algorithms: WireLength versus Wire Crossing in Linear Placement Optimization (1998)

36. Matthias Stallmann, Franc Brglez, Debabrata Ghosh, Heuristics andExperimental Design for Bigraph Crossing Number Minimization (1999)ALENEX

37. Diaz J, Petit J, Serna M A survey of graph layout problems ACMCOMPUT SURV 34 (3): 313-356 SEP 2002

38. R. A. Hochberg, M. F. Stallmann, Optimal one-page tree embeddingsin linear time, INFORM PROCESS LETT 87 (2): 59-66 JUL 31 2003

76./ L. A. Szekely, Erdos on unit distances and the Szemeredi-Trottertheorems, Paul Erdos and his Mathematics II., eds. G. Halasz, L.Lovasz, M. Simonovits, and V. T. Sos, Bolyai Society Mathemat-ical Studies 11, Janos Bolyai Mathematical Society, Budapest,2002, 649–666.

91

Page 92: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. A. B. Kupavskii and A. M. Raigorodskii, On the chromatic number ofR9, Journal of Mathematical Sciences Volume 163, Number 6, 720-731,DOI: 10.1007/s10958-009-9708-4

2. A. E. Guterman, V. K. Lyubimov, A. M. Raigorodskii and S. A. Us-achev, On independence numbers of distance graphs with vertices in{−1, 0, 1}n: estimates, conjectures, and applications to the Nelson-ErdosHadwiger problem and the Borsuk problem, Journal of Mathe-matical Sciences Volume 165, Number 6, 689-709, DOI: 10.1007/s10958-010-9835-y

3. Sebastian M. Cioaba, Eigenvalues, Expanders and Gaps between Primes,Ph.D. Thesis, Queen’s University, Kingston CA, 2005.

4. Raigorodskii AM, Rubanov OI, Distance graphs with large chromaticnumber and without large cliques, MATHEMATICAL NOTES 87(3-4)(2010) 392–402

5. Kupavskii AB, Lifting of a bound for the chromatic number of a”e(n) to higher dimensions, DOKLADY MATHEMATICS 80(3)(2009)833–836.

6. A.B. Kupavskii, A.M. Raigorodskii, On the chromatic numbers ofsmall-dimensional Euclidean spaces, Electronic Notes in Discrete Math-ematics Volume 34, 1 August 2009, Pages 435-439

7. Lyubimov VK, Raigorodskii AM, Lower bounds for the independencenumbers of some distance graphs with vertices in -1,0,1 (n) : DOK-LADY MATHEMATICS 80(2009) issue 1 547-549.

8. Gorskaya ES, Mitricheva IM, Protasov VY, et al., Estimating the chro-matic numbers of Euclidean space by convex minimization methods,SBORNIK MATHEMATICS 200 (2009) Issue: 5-6 783-801.

9. Raigorodskii AM, On distance graphs with large chromatic numberbut without large simplices, RUSSIAN MATHEMATICAL SURVEYSVolume: 62 Issue: 6 Pages: 1224-1225 2007.

10. Raigorodskii AM, Shitova IM, Chromatic numbers of real and rationalspaces with real or rational forbidden distances, SBORNIK MATHE-MATICS Volume: 199 Issue: 3-4 Pages: 579-612 2008.

11. C. Bachoc, G. Nebe, F. M. de Oliveira Filho, F. Vallentin, Lowerbounds for measurable chromatic numbers GEOMETRIC AND FUNC-TIONAL ANALYSIS 19 (2009) 3 Pages: 645-661.

12. F. M. de Oliveira Filho, F. Vallentin, Fourier analysis, linear program-ming and densities of distance avoiding sets in Rn

13. Raigorodskii AM On Ramsey numbers for special complete distancegraphs MATHEMATICAL NOTES 82 (3-4): 426-429 SEP-OCT 2007

14. Raigorodskii, A.M. Colorings of spaces, and random graphs (2007)Journal of Mathematical Sciences, 146 (2), pp. 5723-5730.

92

Page 93: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

15. Moshchevitin NG, Raigorodskii AM Colorings of the space R-n withseveral forbidden distances MATHEMATICAL NOTES 81 (5-6): 656-664 MAY-JUN 2007

16. Boris Bukh, Measurable sets with excluded distances (2007) ElectronicNotes in Discrete Mathematics, 29 (SPEC. ISS.), pp. 65-71

17. Boris Bukh, Measurable sets with excluded distances, GEOMETRICAND FUNCTIONAL ANALYSIS Volume: 18 Issue: 3 Pages: 668-697,2008

18. Raigorodskii, A.M., On the chromatic number of a space with twoforbidden distances, Doklady Mathematics 73 (3), pp. 417-420

19. Raigorodskii, A.M., On the Borsuk and Erdos-Hadwiger numbers,Mathematical Notes 79 (5), pp. 854-863

20. Raigorodskii, A.M., On the structure of distance graphs with largechromatic numbers, Mathematical Notes 80 (3-4), pp. 451-453

21. SM Cioaba, Eigenvalues, Expanders and Gaps between Primes, Ph.D.Thesis, Queen’s University, 2005, 101 pages.

22. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry,2005, 499 pages.

23. Stefan Felsner, Geometric Graphs and Arrangements, Some Chap-ters from Combinatorial Geometry, Advanced Lectures in Mathemat-ics, Vieweg & Sohn Verlag, Wiesbaden, 2004.

24. Raigorodskii AM, On the Brosuk and Erdos-Hadwiger numbers MATH-EMATICAL NOTES 79 (5-6): 854-863 MAY-JUN 2006

25. Raigorodskii AM The Erdos-Hadwiger problem and the chromaticnumbers of finite geometric graphs SBORNIK MATHEMATICS 196(1-2): 115-146 JAN-FEB 2005

26. A. M. Raigorodskii, The Erdos-Hadwiger problem and the chromaticnumbers of finite geometric graphs, Doklady Math. 392 no. 3, 313–317. (DOKLADY MATHEMATICS 68 (2): 216-220 SEP-OCT 2003)

27. G. Elekes, SUMS versus PRODUCTS in number theory, algebra, andErdos geometry, in: Paul Erdos and his Mathematics II, Bolyai Studies11, Springer-Verlag, 2002, 241–290.

28. G. Kubicki, J. Lehel, and M. Morayne, Patch colorings and rigid col-orings of the rational n-space, J. Comb. Theory B 84 (1) 45–53.

29. A. Raigorodskii, Borsuk’s problem and the chromatic number of cer-tain metric spaces, Russ. Math. Surv. 56 (1) (2001) 103–109.

77./ O. Sykora, L. A. Szekely and I. Vrto, Fractional length and cross-ing numbers, in: Graph Drawing 2002, Lecture Notes in Com-puter Science Vol. 2528, Springer Verlag, Berlin, 2002, 186–192.

93

Page 94: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Melanie Agnew, Investigation into properties of natural embeddings

2. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

78./ M. Fischermann, A. Hoffmann, D. Rautenbach, L. Szekely andL. Volkmann, Wiener index versus maximum degree in trees,Discrete Math. 122 (1–3) (2002), 127–137.

References

1. Muhuo Liua, and Bolian Liu, On the variable Wiener indices of treeswith given maximum degree, Mathematical and Computer ModellingVolume 52, Issues 9-10, November 2010, Pages 1651-1659

2. M. Saheli, A.L. Ashrafi, The Eccentric Connectivity Index of Zig-ZagPolyhex Nanotubes and Nanotori, Journal of Computational and The-oretical Nanoscience, Volume 7, Number 10, October 2010 , pp. 1900-1903(4)

3. Stevanovic D., Maximizing Wiener index of graphs with fixed max-imum degree, Communications in Mathematical and in ComputerChemistry / MATCH 2008, vol. 60, br. 1, str. 71-83

4. Wang S., Guo X., Trees with extremal Wiener indices, Communica-tions in Mathematical and in Computer Chemistry / MATCH 2008,vol. 60, br. 2, str. 609-622

5. A.R. Ashrafi, M. Sahelia and M. Ghorbania, The eccentric connectiv-ity index of nanotubes and nanotori , Journal of Computational andApplied Mathematics doi:10.1016/j.cam.2010.03.001

6. Mahboubeh Saheli, Ali Reza Ashrafi, THE ECCENTRIC CONNEC-TIVITY INDEX OF ARMCHAIR POLYHEX NANOTUBES, Mace-donian Journal of Chemistry and Chemical Engineering, Vol. 29, No.1, pp. 7175 (2010)

7. Aleksandar Ilic and Dragan Stevanovic, The Estrada index of chemicaltrees, Journal of Mathematical Chemistry Volume 47, Number 1, 305-314, DOI: 10.1007/s10910-009-9570-0

8. Xuezheng Lv, Yan Yan, Aimei Yu and Jingjing Zhang, Ordering treeswith given pendent vertices with respect to Merrifield-Simmons indicesand Hosoya indices, Journal of Mathematical Chemistry Volume 47,Number 1, 11-20, DOI: 10.1007/s10910-009-9526-4

9. Dong H., Guo X., Ordering trees by their wiener indices, Communica-tions in Mathematical and in Computer Chemistry / MATCH 2006,vol. 56, br. 3, str. 527-540

10. Lv, X., Yu, A., The Merrifield-Simmons indices and Hosoya indices oftrees with a given maximum degree, Communications in Mathematicaland in Computer Chemistry / MATCH 2006, vol. 56, br. 3, str. 605-616

94

Page 95: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

11. Shubo Chen, Weijun Liu, Molecular Structure Descriptors for VolkmanTrees,

12. Balakrishnan R, Sridharan N, Iyer KV, Wiener index of graphs withmore than one cut-vertex, APPLIED MATHEMATICS LETTERSVolume: 21 Issue: 9 Pages: 922-927 Published: SEP 2008

13. Xiao-Dong Zhang, Min-Xian Han, The maximum Wiener index oftrees with given degree sequence, Communications in Mathematicaland in Computer Chemistry / MATCH 2008, vol. 60, br. 2, str.623-644

14. Hua Wang, Sums of distances between vertices-leaves in k-ary trees,Bull. Inst. Comb. Appl.

15. Simic SK, Tosic DV, The index of trees with specified maximum degreeSource: MATCH-COMMUNICATIONS IN MATHEMATICAL ANDIN COMPUTER CHEMISTRY Volume: 54 Issue: 2 Pages: 351-362Published: 2005

16. Alkanes with greatest Estrada index Author(s): Gutman I, Furtula B,Markovic V, et al. Source: ZEITSCHRIFT FUR NATURFORSCHUNGSECTION A-A JOURNAL OF PHYSICAL SCIENCES Volume: 62Issue: 9 Pages: 495-498 Published: SEP 2007

17. Gutman I, Radenkovic S, Furtula B, et al., Relating Estrada index withspectral radius Source: JOURNAL OF THE SERBIAN CHEMICALSOCIETY Volume: 72 Issue: 12 Pages: 1321-1327 Published: 2007

18. Spanning trees with many leaves and average distance Author(s): DelaV-ina E, Waller B Source: ELECTRONIC JOURNAL OF COMBINA-TORICS Volume: 15 Issue: 1 Article Number: R33 Published: FEB11 2008

19. Stevanovic D, Maximizing Wiener index of graphs with maximum de-gree Source: MATCH-COMMUNICATIONS IN MATHEMATICALAND IN COMPUTER CHEMISTRY Volume: 60 Issue: 1 Pages: 71-83 Published: 2008

20. Zhang XD, Xiang QY, Xu LQ, et al., The Wiener index of treeswith given degree sequences Source: MATCH-COMMUNICATIONSIN MATHEMATICAL AND IN COMPUTER CHEMISTRY Volume:60 Issue: 2 Pages: 623-644 Published: 2008

21. Kirk R, Wang H, Largest number of subtrees of trees with a givenmaximum degree SIAM JOURNAL ON DISCRETE MATHEMATICSVolume: 22 Issue: 3 Pages: 985-995 Published: 2008

22. Gelen, Ebil-lun, Untersuchungen des adjuvanten Effekts des viralenTegumentproteins VP22 auf die Induktion Melanom-spezifischer cy-totoxischer T-Zellen in C57BL/6 Musen nach DNA-Immunisierung,Dissertation : Universitat Heidelberg, Fakultat fur Chemie und Ge-owissenschaften, 2004

23. T Jansen, M Theile - Stability in the self-organized evolution of net-works, Proceedings of the 9th annual conference on Genetic, 2007 -

95

Page 96: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

24. C Heuberger, SG Wagner, Asymptotics of the extremal values of cer-tain graph parameters in trees with bounded degree

25. C Heuberger, SG Wagner, Maximizing the number of independent sub-sets over trees with bounded degree, JOURNAL OF GRAPH THE-ORY Volume: 58 Issue: 1 Pages: 49-68 Published: MAY 2008

26. Hua Wang, The extremal values of the Wiener index of a tree with agiven degree sequence DISCRETE APPLIED MATHEMATICS Vol-ume: 156 Issue: 14 Pages: 2647-2654 Published: 2008

27. Fischermann, M., Rautenbach, D., Volkmann, L., Extremal trees withrespect to dominance order, Ars Combinatoria 76, pp. 249-255

28. Simic, S.K., Tosic, D.V., The index of trees with specified maximumdegree, Match 54 (2), pp. 351-362

29. M. Fischermann, I. Gutman, A. Hoffmann, D. Rautenbach, D. Vidovic,and L. Volkmann, Extremal chemical trees, Z. Naturforschung 57 a(2002)49–52.

30. S. Bereg, H. Wang, Wiener indices of balanced binary trees Interna-tional Workshop on Bioinformatics Research and Applications, LNCS3515, pp. 851-859, 2005.

31. S. Bereg, H. Wang, Wiener indices of balanced binary trees, DiscreteApplied Mathematics 2006 Volume 155, Issue 4, Pages 457-467

32. I. Gutman, P. Hansen, H. Melot, Variable neighborhood search ex-tremal graphs 10. Comparison of irregularity indices for chemical trees,Journal of Chemical Information and Modeling 45 (2), pp. 222-230

33. P. Hansen, M. Aouchiche, G. Caporossi, H. Melot, D. Stevanovic,What forms do interesting conjectures have in graph theory? LesCahiers du GERAD ISSN: 0711-2440

34. F. Jelen, Superdominance order and distance of trees, Ph. D. Thesis,Rheinisch-Westfalischen Technischen Hochschule Aachen, 2002

35. C. Delorme, O. Favaron, D. Rautenbach, On the Randic’ index, Dis-crete Mathematics 257 (2002), 29–38.

36. Markovic Z, Ivanov-Petrovic V, Gutman I Extremely branched alkanesJ MOL STRUC-THEOCHEM 629: 303-306 JUL 4 2003

37. F. Jelen, E. Triesch, Superdominance order and distance of trees withbounded maximum degree, Discrete Appl. Math 125 (2003), 225–233.

79./ I. B. Rogozin, K. S. Makarova, Y. I. Wolf, J. Murvai, E. Cz-abarka, L. A. Szekely, R. L. Tatusov, and E. V. Koonin, Con-nected gene neighborhoods in prokaryotic genomes, Nucleic AcidsRes. 30 (10) (2002), 2212–2223.

96

Page 97: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Arcady R. Mushegian, Foundations of comparative genomics, ix+259,2007, Elsevier Academic Press.

2. A Amira, L Gasieniecc, R Shaloma, Improved approximate commoninterval, Information Processing Letters, 103 (2007) 142149

3. QIAN PENG, MAX A. ALEKSEYEV, GLENN TESLER, AND PAVELA. PEVZNER, DECODING THE GENOMIC ARCHITECTURE OFMAMMALIAN AND PLANT GENOMES: SYNTENY BLOCKS ANDLARGE-SCALE DUPLICATIONS, COMMUNICATIONS IN INFOR-MATION AND SYSTEMS, Vol. 10, No. 1, pp. 1-22, 2010

4. P. Wanchanthuek, Comparative genomics to investigate genome func-tion and adaptations in the newly sequenced Brachyspira hyodysente-riae and Brachyspira pilosicoli, PhD thesis, Murdoch University, Aus-tralia, 2009.

5. Alexander Bolshoy,Zeev Volkovich,Valery Kirzhner,Zeev Barzily, GenomeClustering: From Linguistic Models to Classification of Genetic Texts,Springer, 2010, xiii+223.

6. Lynette Yee-Shee Lau, Sequence Analysis of the Bacterial ProteinElongation Factor P, Master Thesis in Biology, University of Waterloo,2008.

7. S Firas, S Ron, Assessing the Quality of Whole Genome Alignmentsin Bacteria, Advances in Bioinformatics, 2009 - hindawi.com

8. MA Pyatnitskiy, AV Lisitsa, AI Archakov, Prediction of function-ally related proteins by comparative genomics in silico, Biochemistry(Moscow) Supplemental Series B: Biomedical Chemistry Volume 3,Number 4, 323-334, DOI: 10.1134/S1990750809040015

9. Vey G, Moreno-Hagelsieb G, Beyond the bounds of orthology: func-tional inference from metagenomic context, : MOLECULAR BIOSYS-TEMS 6(7)(2010) 1247–1254

10. Koonin EV, Wolf YI, Constraints and plasticity in genome and molecular-phenome evolution, NATURE REVIEWS GENETICS 11(7) (2010)487–498

11. Osbourn AE, Field B, Operons, CELLULAR AND MOLECULARLIFE SCIENCES Volume: 66 Issue: 23 Pages: 3755-3775 Published:DEC 2009

12. Fondi M, Emiliani G, Fani R Origin and evolution of operons andmetabolic pathways, RESEARCH IN MICROBIOLOGY Volume: 160(2009) Issue: 7 502-512.

13. Thybert D, Avner S, Lucchetti-Miganeh C, et al. Computer-AssistedAutomatic Classifications, Storage, Queries and Functional Assign-ments of Orthologs and In-Paralogs Proteins, CURRENT BIOINFOR-MATICS Volume: 4 Issue: 2 Pages: 129-140 Published: MAY 2009

97

Page 98: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

14. Bolshoy A, Volkovich Z, Whole-genome prokaryotic clustering basedon gene lengths, DISCRETE APPLIED MATHEMATICS Volume:157 Issue: 10 Special Issue: Sp. Iss. SI Pages: 2370-2377 Published:MAY 28 2009

15. Hu PZ, Janga SC, Babu M, et al. Global Functional Atlas of Es-cherichia coli Encompassing Previously Uncharacterized Proteins, PLOSBIOLOGY Volume: 7 Issue: 4 Pages: 929-947 Published: APR 2009

16. Lou XL, Han B, Evolutionary conservation of neighbouring gene pairsin plants, GENE Volume: 437 Issue: 1-2 Pages: 71-79 Published:MAY 15 2009

17. Ling X, He X, Xin D, Detecting gene clusters under evolutionary con-straint in a large number of genomes, BIOINFORMATICS Volume:25 Issue: 5 Pages: 571-577 Published: MAR 1 2009

18. Uchiyama I, Multiple genome alignment for identifying the core struc-ture among moderately related microbial genomes, BMC GENOMICSVolume: 9 Article Number: 515 Published: OCT 31 2008

19. Koonin EV, Evolution of genome architecture, INTERNATIONALJOURNAL OF BIOCHEMISTRY & CELL BIOLOGY Volume: 41Issue: 2 Pages: 298-306 Published: FEB 2009

20. : Rocha EPC, The Organization of the Bacterial Genome, ANNUALREVIEW OF GENETICS Volume: 42 Pages: 211-233 Published:2008

21. Danchin A, Bacteria as computers making computers, FEMS MICRO-BIOLOGY REVIEWS Volume: 33 Issue: 1 Pages: 3-26 Published:JAN 2009

22. Koonin EV, Wolf YI, Genomics of bacteria and archaea: the emerg-ing dynamic view of the prokaryotic world, NUCLEIC ACIDS RE-SEARCH Volume: 36 Issue: 21 Pages: 6688-6719 Published: DEC2008

23. Martinez-Guerrero CE, Ciria R, Abreu-Goodger C, et al., GeConT2: gene context analysis for orthologous proteins, conserved domainsand metabolic pathways, NUCLEIC ACIDS RESEARCH Volume: 36Pages: W176-W180 Supplement: Suppl. S Published: JUL 2008

24. Li J, Halgamuge SK, Tang SL, Genome classification by gene distri-bution: An overlapping subspace clustering approach, BMC EVOLU-TIONARY BIOLOGY Volume: 8 Article Number: 116 Published:APR 23 2008

25. Lacroix V, Cottret L, Thebault P, et al., An Introduction to MetabolicNetworks and Their Structural Analysis, IEEE-ACM TRANSACTIONSON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS Vol-ume: 5 Issue: 4 Pages: 594-617 Published: OCT-DEC 2008

26. Persistence drives gene clustering in bacterial genomes Author(s): FangG, Rocha EPC, Danchin A Source: BMC GENOMICS Volume: 9 Ar-ticle Number: 4 Published: JAN 7 2008

98

Page 99: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

27. Harrington ED, Jensen LJ, Bork P, Predicting biological networks fromgenomic data, FEBS LETTERS Volume: 582 Issue: 8 Pages: 1251-1258 Published: APR 9 2008

28. Analysis of gene order data supports vertical inheritance of the leuko-toxin operon and genome rearrangements in the 5 ’ flanking regionin genus Mannheimia Author(s): Larsen J, Kuhnert P, Frey J, et al.Source: BMC EVOLUTIONARY BIOLOGY Volume: 7 Article Num-ber: 184 Published: OCT 3 2007

29. Clusters of orthologous genes for 41 archaeal genomes and implicationsfor evolutionary genomics of archaea Author(s): Makarova KS, SorokinAV, Novichkov PS, et al. Source: BIOLOGY DIRECT Volume: 2Article Number: 33 Published: NOV 27 2007

30. Chi-Yuan Chan, Hung-I Yu, Wing-Kai Hon and Biing-Feng Wang, AFaster Query Algorithm for the Text Fingerprinting Problem LectureNotes in Computer Science Algorithms ESA 2007, 123-135,

31. Larsen, P Kuhnert, J Frey, H Christensen, M - Analysis of gene orderdata supports vertical inheritance of the leukotoxin operon and genomeBMC Evolutionary Biology, 2007

32. L KAJAN, K VLAHOVICEK, O CARUGO, V AGOSTON, Z Com-parison of sequences, protein 3D structures and genomes Essays inBioinformatics, D. S. Moss et al. eds., 2005, IOS Press,. 32-45.

33. Manuel J. Gomez, Ildefonso Cases and Alfonso Valencia, Gene orderin Prokaryotes: conservation and implications in: Molecules in Timeand Space Bacterial Shape, Division and Phylogeny 209-237

34. Shuo-Yong SHI, Xiao-Hui CAI, Da-fu DING Identification and Cate-gorization of Horizontally Transferred Genes in Prokaryotic GenomesActa Biochimica et Biophysica Sinica Volume 37 Issue 8 Page 561-566,August 2005

35. JM Bujnicki, L Droogmans, H Grosjean, SK - Bioinformatics-guidedidentification and experimental characterization of novel RNA - Prac-tical Bioinformatics. Springer-Verlag, Heidelberg, 2004 - Springer

36. Figeac Martin, Varre Jean-Stephane, Delahaye Jean-Paul Detectionde structures conservees dans les genomes de Procaryotes, LIFL 2004-numero 1.

37. S. Schultz, Genomvegleich von Prokaryoten mit formalsprachlichenMethoden, Universitat Bremen, 2004, Diplomarbeit.

38. Thomas Schmidt, Efficient algorithms for gene cluster detection inprokaryotic genomes, Ph.D. Thesis, Univeritat Bielefeld, 2005

39. Didier, G., Schmidt, T., Stoye, J., Tsur, D. Character sets of strings(2007) Journal of Discrete Algorithms, 5 (2 SPEC. ISS.), pp. 330-340

40. Manna, D., Porwollik, S., McClelland, M., Tan, R., Higgins, N.P.Microarray analysis of Mu transposition in Salmonella enterica, serovarTyphimurium: Transposon exclusion by high-density DNA bindingproteins (2007) Molecular Microbiology, 66 (2), pp. 315-328.

99

Page 100: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

41. Amir A, Gasieniec L, Shalom R Improved approximate common in-terval INFORMATION PROCESSING LETTERS 103 (4): 142-149AUG 16 2007

42. Shoemaker BA, Panchenko AR Deciphering protein-protein interac-tions. Part II. Computational methods to predict protein and do-main interaction partners PLOS COMPUTATIONAL BIOLOGY 3(4): 595-601 APR 2007

43. Barkan A, Klipcan L, Ostersetzer O, et al. The CRM domain: AnRNA binding module derived from an ancient ribosome-associated pro-tein RNA-A PUBLICATION OF THE RNA SOCIETY 13 (1): 55-64JAN 2007

44. Markov AV, Zakharov IA Large and small rearrangements in the evo-lution of prokaryotic genomes RUSSIAN JOURNAL OF GENETICS42 (11): 1303-1312 NOV 2006

45. Merkl, R., AMIGOS: A method for the inspection of genomic organi-sation or structure and its application to characterise conserved genearrangements, In Silico Biology 6 (4), pp. 281-306

46. Swidan F, Rocha EPC, Shmoish M, et al. An integrative methodfor accurate comparative genome mapping PLOS COMPUTATIONALBIOLOGY 2 (8): 870-889 AUG 2006

47. Morgan N. Price, Adam P. Arkin, Eric J. Alm, The Life-Cycle ofOperons, PLOS Genetics, Volume 2 — Issue 6 — JUNE 2006

48. L KAJA’N, K VLAHOVICEK, O CARUGO, V A’GOSTON, etc.Comparison of sequences, protein 3D structures and genomes,

49. H Wu, F Mao, Z Su, V Olman, Y Xu, Prediction of Functional Mod-ules Based on Gene Distributions in Microbial Genomes, Genome In-formatics 16(2): 247-259 (2005)

50. M Bailly-Bechet, A Danchin, M Iqbal, M Marsili, etc. Codon UsageDomains over Bacterial Chromosomes, PLOS Computational BiologyVolume 2 — Issue 4 — APRIL 2006

51. K St-Onge, A Bergeron, C Chauve Fast identification of gene clustersin prokaryotic genomes

52. Mao FL, Su ZC, Olman V, et al. Mapping of orthologous genes in thecontext of biological pathways: An application of integer programmingPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCESOF THE UNITED STATES OF AMERICA 103 (1): 129-134 JAN 32006

53. Haft DH, Selengut J, Mongodin EF, et al. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypesexist in prokaryotic genomes PLOS COMPUTATIONAL BIOLOGY1 (6): 474-483 NOV 2005

54. Massimo Pigliucci, Phenotypic Integration: Studying the Ecology andEvolution of Complex Phenotypes, Science, 2004, 464 pages.

100

Page 101: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

55. Combinatorial Pattern Matching: Proceedings of the 15th AnnualSymposium, CPM 2004 edited by Suleyman C. Sahinalp, S. Muthukr-ishnan, Ugur Dogrusoz - 2004 - 486 pages

56. Zheng Y, Anton BP, Roberts RJ, et al. Phylogenetic detection of con-served gene clusters in microbial genomes BMC BIOINFORMATICS6: Art. No. 243 OCT 3 2005

57. Arnold, R; Rattei, T; Tischler, P; Truong, MD; Stumpflen, V; Mewes,W., SIMAP - The similarity matrix of proteins, BIOINFORMATICS,21: 42-46 Suppl. 2 SEP 2005.

58. Shi SY, Cai XH, Ding DF Identification and categorization of horizon-tally transferred genes in prokaryotic genomes ACTA BIOCHIMICAET BIOPHYSICA SINICA 37 (8): 561-566 AUG 2005

59. Podar M, Eads JR, Richardson TH Evolution of a microbial nitrilasegene family: a comparative and environmental genomics study BMCEVOLUTIONARY BIOLOGY 5: Art. No. 42 AUG 6 2005

60. L KAJAN, K VLAHOVICEK, O CARUGO, V AGOSTON, Z - Com-parison of sequences, protein 3D structures and genomes Essays inBioinformatics, 2005 (D. S. Moss et al. eds.)

61. Franzot G, Carugo O Computational approaches to protein-protein in-teraction JOURNAL OF STRUCTURAL AND FUNCTIONAL GE-NOMICS 4 (4): 245-255 DEC 2003

62. Tom H. Wetjen, Discovery of frequent gene patterns in microbial genomes,TZI-Bericht 27, November 2002, Center for Computing technologies(TZI), University of Bremen.

63. Upstream - News in Genomics, Comp. Funct. Genom. 3 (2002),398–404.

64. Edwards MT, Rison SCG, Stoker NG, Lorenz W A universally applica-ble method of operon map prediction on minimally annotated genomesusing conserved genomic context NUCLEIC ACIDS RESEARCH 33(10): 3253-3262 JUN 2005

65. Price MN, Huang KH, Arkin AP, et al. Operon formation is drivenby co-regulation and not by horizontal gene transfer GENOME RE-SEARCH 15 (6): 809-819 JUN 2005

66. Janga SC, Collado-Vides J, Moreno-Hagelsieb G Nebulon: a systemfor the inference of functional relationships of gene products from therearrangement of predicted operons NUCLEIC ACIDS RESEARCH33 (8): 2521-2530 2005

67. Choi K, Ma Y, Choi JH, et al. PLATCOM: A Platform for Computa-tional Comparative Genomics BIOINFORMATICS 21 (10): 2514-2516MAY 15 2005

68. Mau B, Darling AE, Perna NT Identifying evolutionarily conservedsegments among multiple divergent and rearranged genomes LEC-TURE NOTES IN COMPUTER SCIENCE 3388: 72-84 2005

101

Page 102: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

69. Sankoff D, Lefebvre JF, Tillier E, et al. The distribution of inversionlengths in bacteria LECTURE NOTES IN COMPUTER SCIENCE3388: 97-108 2005

70. Saunders NFW, Goodchild A, Raftery M, et al. Predicted roles for hy-pothetical proteins in the low-temperature expressed proteome of theAntarctic archaeon Methanococcoides burtonii JOURNAL OF PRO-TEOME RESEARCH 4 (2): 464-472 MAR-APR 2005

71. Oliver B, Misteli T A non-random walk through the genome GENOMEBIOLOGY 6 (4): Art. No. 214 2005

72. Rosenfeld JA, Sarkar IN, Planet PJ, et al. ORFcurator: molecularcuration of genes and gene clusters in prokaryotic organisms BIOIN-FORMATICS 20 (18): 3462-3465 DEC 12 2004

73. Reams AB, Neidle EL Selection for gene clustering by tandem dupli-cation ANNUAL REVIEW OF MICROBIOLOGY 58: 119-142 2004

74. Pal C, Hurst LD Evidence against the selfish operon theory TRENDSIN GENETICS 20 (6): 232-234 JUN 2004

75. Rogozin IB, Makarova KS, Wolf YI, et al. Computational approachesfor the analysis of gene neighbourhood in prokaryotic genomes BRIEF-INGS IN BIOINFORMATICS 5 (2): 131-149 JUN 2004

76. Schmidt T, Stoye Quadratic time algorithms for finding common inter-vals in two and more sequences LECTURE NOTES IN COMPUTERSCIENCE 3109: 347-358 2004

77. Baquero F Opinion - From pieces to patterns: evolutionary engineeringin bacterial pathogens NAT REV MICROBIOL 2 (6): 510-518 JUN2004

78. Rodriguez-Valera F Environmental genomics, the big picture? FEMSMICROBIOL LETT 231 (2): 153-158 FEB 16 2004

79. Omelchenko MV, Makarova KS, Wolf YI, et al. Evolution of mo-saic operons by horizontal gene transfer and gene displacement in situGENOME BIOL 4 (9): Art. No. R55 2003

80. Makarova, KS; Koonin, EV Comparative genomics of archaea: howmuch have we learned in six years, and what’s next? GENOME BI-OLOGY; 2003; v.4, no.8, p.115

81. Yuzenkova J, Nechaev S, Berlin J, et al. Genome of Xanthomonasoryzae bacteriophage Xp10: An odd T-odd phage J MOL BIOL 330(4): 735-748 JUL 18 2003

82. Jensen LJ, Skovgaard M, Sicheritz-Ponten T, et al. Analysis of twolarge functionally uncharacterized regions in the Methanopyrus kand-leri AV19 genome BMC GENOMICS 4: art. no. 12 APR 2 2003

83. Osterman A, Overbeek R Missing genes in metabolic pathways: acomparative genomics approach CURR OPIN CHEM BIOL 7 (2): 238-251 APR 2003

102

Page 103: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

84. Huynen MA, Snel B, von Mering C, et al. Function prediction andprotein networks CURR OPIN CELL BIOL 15 (2): 191-198 APR 2003

85. Pevzner P, Tesler G Genome Rearrangements in mammalian evolution:Lessons from human and mouse genomes GENOME RES 13 (1): 37-45JAN 2003

86. (Anon) Upstream - nws in genomics COMPAR FUNCT GENOM 3(5): 398-404 OCT 2002

87. Rogozin IB, Makarova KS, Natale DA, et al. Congruent evolution ofdifferent classes of non-coding DNA in prokaryotic genomes NUCLEICACIDS RES 30 (19): 4264-4271 OCT 1 2002

88. Omelchenko MV, Makarova KS, Wolf YI, et al. Evolution of mo-saic operons by horizontal gene transfer and gene displacement in situGENOME BIOL 4 (9): Art. No. R55 2003

89. Pray L Microbiologists make discoveries in the sea, in the neighbor-hood SCIENTIST 16 (19): 43-43 SEP 30 2002

90. Teichmann SA, Babu MM Conservation of gene co-regulation in prokary-otes and eukaryotes TRENDS BIOTECHNOL 20 (10): 407-410 OCT2002

91. Snel B, Bork P, Huynen MA Conservation of gene co-regulation inprokaryotes and eukaryotes TRENDS BIOTECHNOL 20 (10): 410-410 OCT 2002

80./ O. Sykora, L. A. Szekely and I. Vrto, Two counterexamples ingraph drawing, Proc. 27th Intl. Workshop on Graph-TheoreticConcepts in Computer Science, Lecture Notes in Computer Sci-ence Vol. 2573, Springer Verlag, Berlin, 2002, 389-396.

References

1. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

81./ M. A. Steel and L. A. Szekely, Inverting random functions II:explicit bounds for discrete maximum likelihood estimation, withapplications, SIAM J. Discrete Math. 15 (4) (2002), 562–575.

References

1. Constantinos Daskalakis and Sebastien Roch, Alignment-Free Phylo-genetic Reconstruction, Research in Computational Molecular BiologyLecture Notes in Computer Science, 2010, Volume 6044/2010, 123-137,

2. S. Roch, Sequence Length Requirement of Distance-Based PhylogenyReconstruction: Breaking the Polynomial Barrier, Foundations of Com-puter Science, 2008. FOCS ’08. IEEE 49th Annual IEEE Symposiumon Issue Date: 25-28 Oct. 2008, 729 - 738 Philadelphia, PA.

103

Page 104: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

3. David L. Erickson, John Spouge, Alissa Resch, Lee A. Weigt, and W.John Kress, DNA BARCODING IN LAND PLANTS: DEVELOPINGSTANDARDS TO QUANTIFY AND MAXIMIZE SUCCESS, Taxon.2008 November 1; 57(4): 13041316.

4. Roch S, Toward Extracting All Phylogenetic Information from Ma-trices of Evolutionary Distances, SCIENCE Volume: 327 Issue: 5971(2010) Pages: 1376-1379

5. C. Daskalakis - E. Mossel - S. Roch: Phylogenies without BranchBounds: Contracting the Short, Pruning the Deep, arXiv:0801.4190v1(2008), 1–19.

6. Fischer M, Steel M, Sequence length bounds for resolving a deep phylo-genetic divergence, JOURNAL OF THEORETICAL BIOLOGY Vol-ume: 256 Issue: 2 Pages: 247-252 Published: JAN 21 2009

7. Holder MT, Sukumaran J, Lewis PO, A Justification for Reportingthe Majority-Rule Consensus Tree in Bayesian Phylogenetics Source:SYSTEMATIC BIOLOGY Volume: 57 Issue: 5 Pages: 814-821 Pub-lished: 2008

8. M. Steel, A. Rodrigo, MAXIMUM LIKELIHOOD SUPERTREES SYS-TEMATIC BIOLOGY Volume: 57 Issue: 2 Pages: 243-250 Published:2008

9. Li-San Wang, Large-Scale Phylogenetic Analysis, Ph. D. Thesis, 170pages, University of Texas, 2003.

10. E. Mossel, Distorted metric on trees and phylogenetic forests, IEEE/ACMTrans. Comp. Biol. and Bioinf. 4 (1): 108-116 JAN-MAR 2007

11. Chor B, Tuller T Maximum likelihood of evolutionary trees: hardnessand approximation BIOINFORMATICS 21: I97-I106 Suppl. 1 JUN2005

12. M. Spencer, E. Susko, A. J. Roger, Likelihood, parsimony, and hetero-geneous evolution, Mol. Biol. Evol. 22(5) (2005), 1161–1164.

13. F.S. Roberts: Challenges for Discrete Mathematics and TheoreticalComputer Science in the Defense against Bioterrorism, in Bioterror-ism: Mathematical Modeling Applications in Homeland Security(ed. by H. T. Banks and Carlos Castillo-Chavez), Proceeding of DI-MACS and NFS, 2002, SIAM (2003), Chapter 1.

14. E. Mossel, M. Steel, How much can evolved characters tell us aboutthe tree that generated them?

15. Mossel E, Steel M A phase transition for a random cluster model onphylogenetic trees MATH BIOSCI 187 (2): 189-203 FEB 2004

16. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

17. Holmes S Statistics for phylogenetic trees THEOR POPUL BIOL 63(1): 17-32 FEB 2003

82./ L. A. Szekely, A successful concept for measuring non-planarityof graphs: the crossing number, Discrete Math. 276 (2004), 1–3,331–352.

104

Page 105: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Petra Mutzel, The Crossing Number of Graphs: Theory and Compu-tation, Lecture Notes in Computer Science, 2009, Volume 5760/2009,305-317, DOI: 10.1007/978-3-642-03456-5 21.

2. JAROSLAV NEˇSETˇRIL, PATRICE OSSONA DE MENDEZ, ANDDAVID R. WOOD, CHARACTERISATIONS AND EXAMPLES OFGRAPH CLASSES WITH BOUNDED EXPANSION, preprint (arXiv:0902.3265 v2)

3. Chimani, Markus, Computing crossing numbers, Ph.D. Thesis, TUDortmund, 2009.

4. Vida Dujmovic, Ken-ichi Kawarabayashi, Bojan Mohar, David R. Wood,Improved upper bounds on the crossing number, SCG ’08 Proceedingsof the twenty-fourth annual symposium on Computational geometry,2008.

5. B Mohar, Do We Really Understand the Crossing Numbers? Mathe-matical Foundations of Computer Science 2010 Lecture Notes in Com-puter Science, 2010, Volume 6281/2010, 38-41, DOI: 10.1007/978-3-642-15155-2 5

6. R. B. RICHTER G. SALAZAR, Crossing numbers, 2008

7. B Mohar, S Cabello, M DeVos, R Samal, Crossing numbers of graphson the plane and on other surfaces, 2008, Japan

8. HIROYUKI TANAKA AND MASAKAZU TERAGAITO, TRIPLECROSSING NUMBERS OF GRAPHS, Arxiv preprint arXiv:1002.4231,2010

9. JAROSLAV NEˇSETˇRIL, PATRICE OSSONA DE MENDEZ, ANDDAVID R. WOOD, CHARACTERISATIONS AND EXAMPLES OFGRAPH CLASSES WITH BOUNDED EXPANSION, preprint (arXiv:0902.3265 v2)

10. Michael O. Albertson, Daniel W. Cranston, Jacob Fox, Crossings, col-orings, and cliques, The electronic journal of combinatorics 16 (2009),#R45

11. MO Albertson, Chromatic number, independence ratio, and crossingnumber, Ars Mathematica Contemporanea, 2008

12. Sergio Cabello, Bojan Mohar, CROSSING AND WEIGHTED CROSS-ING NUMBER OF NEAR-PLANAR GRAPHS, Graph Drawing, 2009.

13. Pelsmajer MJ, Schaefer M, Stefankovic D, REMOVING INDEPEN-DENTLY EVEN CROSSINGS, SIAM JOURNAL ON DISCRETEMATHEMATICS 24(2)(2010) 379–393

14. Barat J, Toth G, Towards the Albertson conjecture, ELECTRONICJOURNAL OF COMBINATORICS 17(1)(2010) Article Number: R73

15. Ho PT, The crossing number of some complete multipartite graphs,UTILITAS MATHEMATICA 79 (2009) Pages: 125-143.

105

Page 106: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

16. Ho PT, The crossing number of K1,m,n, DISCRETE MATHEMAT-ICS Volume: 308 Issue: 24 Pages: 5996-6002 Published: DEC 28 2008

17. Pelsmajer MJ, Schaefer M, Stefankovic D, Removing even crossings onsurfaces, EUROPEAN JOURNAL OF COMBINATORICS Volume:30 Issue: 7 Pages: 1704-1717 Published: OCT 2009

18. Alberston MO, Cranston DW, Fox J, : Crossings, colorings, andcliques, ELECTRONIC JOURNAL OF COMBINATORICS Volume:16 Issue: 1 Article Number: R45 Published: APR 3 2009

19. Ho PT, On the Crossing Number of Some Complete MultipartiteGraphs, UTILITAS MATHEMATICA Volume: 79 Pages: 125-143Published: JUL 2009

20. M. J. Pelsmajer, M. Schaefer, D. Stefankovic, Crossing numbers ofgraphs with rotation systems Lecture Notes In Computer Science Pro-ceedings of the 15th international conference on Graph drawing, Syd-ney, Australia Pages: 3-12 Year of Publication: 2007 ISBN ISSN:0302-9743 , 3-540-77536-6

21. The crossing number of flower snarks and related graphs Author(s):Zheng WP, Lin XH, Yang YS, et al. Source: ARS COMBINATORIAVolume: 86 Pages: 57-64 Published: JAN 2008

22. Zheng WP, Lin XH, Yang YS, et al. The crossing number of kn-odel graph W-3,W-n, UTILITAS MATHEMATICA Volume: 75 Pages:211-224 Published: MAR 2008

23. The minor crosssing number of graphs with an excluded minor Au-thor(s): Bokal D, Fijavz G, Wood DR Source: ELECTRONIC JOUR-NAL OF COMBINATORICS Volume: 15 Issue: 1 Article Number:R4 Published: JAN 1 2008

24. B. Mohar, The genus crossing number, ARS MATHEMATICA CON-TEMPORANEA, 2009

25. H Fernau, Parameterized Algorithmics: A Graph-Theoretic Approach,Habilitation Thesis, Universitat Tubingen, 2005,

26. Mohar, B. On the crossing number of almost planar graphs (2006)Informatica (Ljubljana), 30 (3), pp. 301-303.

27. Dujmovic V, Wood DR Graph treewidth and geometric thickness pa-rameters DISCRETE & COMPUTATIONAL GEOMETRY 37 (4):641-670 MAY 2007

28. Marco Cesati, Compendium of Parameterized Problems

29. DR Wood, JA Telle, Planar Decompositions and the Crossing Numberof Graphs with an Excluded Minor New York J. Math 13(2007), 117–146.

30. J Leanos, G Salazar, On the additivity of crossing numbers of graphs,JOURNAL OF KNOT THEORY AND ITS RAMIFICATIONS Vol-ume: 17 Issue: 9 Pages: 1043-1050 Published: SEP 2008

106

Page 107: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

31. S. Pan, On the Crossing Numbers of Complete Graphs, Master’s The-sis, University of Waterloo, 2006.

32. D. Bokal, Structural Approach to the Crossing Number of Graphs,Doctoral Thesis, University of Ljubljana, 2006.

33. DR Wood, A LINEAR UPPER BOUND ON THE RECTILINEARCROSSING NUMBER

34. De Klerk E, Maharry J, Pasechnik DV, et al. Improved bounds forthe crossing numbers of K-m,K-n and K-n(*) SIAM JOURNAL ONDISCRETE MATHEMATICS 20 (1): 189-202 2006

35. Salazar G On the crossing numbers of loop networks and generalizedPetersen graphs DISCRETE MATHEMATICS 302 (1-3): 243-253 Sp.Iss. SI OCT 28 2005

36. M. J. Pelsmajer, M. Schaefer, D. Stefankovic, Odd crossing number isnot crossing number, 2006 Lecture Notes in Computer Science 3843LNCS, pp. 386-396

37. Odd crossing number and crossing number are not the same Au-thor(s): Pelsmajer MJ, Schaefer M, Stefankovic D Source: DISCRETE& COMPUTATIONAL GEOMETRY Volume: 39 Issue: 1-3 Pages:442-454 Published: MAR 2008

38. Pelsmajer, M.J., Schaefer, M., Stefankovic, D. Removing Even Cross-ings on Surfaces (2007) Electronic Notes in Discrete Mathematics, 29(SPEC. ISS.), pp. 85-90.

39. M. J. Pelsmajer,M Schaefer Removing Even Crossings JOURNAL OFCOMBINATORIAL THEORY SERIES B 97 (4): 489-500 JUL 2007

40. S. Norine, Matching structure and Pfaffian orientations of graphs,Ph.D. Thesis, Georgia Tech, 2005.

41. Ivan Christov, The Crossing Number of a Graph, (2004).

42. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

43. W Winterbach, The crossing number of a graph in the plane, MSc (Ap-plied Mathematics: Graph Theory) Thesis, University of Stellenbosch,2004.

44. R. B. Richter, G. Salazar, A survey of good crossing number theoremsand questions,

45. Pach, J., Geometric graph theory. Surveys in combinatorics, 1999(Canterbury), 167–200, London Math. Soc. Lecture Note Ser., 267,Cambridge Univ. Press, Cambridge, 1999.

83./ O. Sykora, L. A. Szekely and I. Vrto, A note on Halton’s conjec-ture, Information Sciences164 (2004) (1-4) 61–64. .

107

Page 108: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Barat J, Matousek J, Wood DR, Bounded-degree graphs have arbitrar-ily large geometric thickness ELECTRONIC JOURNAL OF COMBI-NATORICS 13 (1): Art. No. R3 JAN 7 2006

2. Poranen T, Fast algorithms for the thickness of a graph

3. V DUJMOVIC, DR WOOD, GRAPH TREEWIDTH AND GEO-METRIC THICKNESS PARAMETERS DISCRETE & COMPUTA-TIONAL GEOMETRY 37 (4): 641-670 MAY 2007

4. Poranen T A simulated annealing algorithm for determining the thick-ness of a graph INFORMATION SCIENCES 172 (1-2): 155-172 JUN9 2005

5. T. Poranen, E. Makkinen, Remarks on the thickness and outerthick-ness of a graph, COMPUTERS & MATHEMATICS WITH APPLI-CATIONS 50 (1-2): 249-254 JUL 2005

84./ E. Czabarka, O. Sykora, I. Vrt’o, L. A. Szekely, Biplanar crossingnumbers: a survey of results and problems, More Sets, Graphsand Numbers, eds. E. Gyori, G. O. H. Katona, and L. Lovasz,Bolyai Society Mathematical Studies 15, Springer Verlag, 2006,57–77.

References

1. L Beaudou, D Bokal, On the sharpness of some results relating cutsand crossing numbers, the electronic journal of combinatorics 17 (2010),#R96

2. Laurent Beaudou, Autour de problemes de plongements de graphes,Ph.D. Thesis, Univ. Grenoble I, 2009.

3. Joshua K.Lambert, Finding a biplanar embedding of Cn×Cn×Cl×Pm

4. Joshua K.Lambert, The biplanar crossing number of Ck×Cl×C2m×Pn

5. A. Riskin, The biplanar crossing number of C4n, The Bulletin of the

ICA, 49 (2007) 79–85.

6. Pach J, Radoicic R, Tardos G, et al. Improving the Crossing Lemmaby finding more crossings in sparse graphs DISCRETE & COMPU-TATIONAL GEOMETRY 36 (4): 527-552 DEC 2006

7. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

8. Spencer, Joel The biplanar crossing number of the random graph.Towards a theory of geometric graphs, 269–271, Contemp. Math.,342, Amer. Math. Soc., Providence, RI, 2004.

9. J. Pach, R. Radoicic, G. Tardos, G. Toth, Improving the crossinglemma by finding more crossings in sparse graphs, Annual Symposiumon Computational Geometry archive Proceedings of the twentieth an-nual symposium on Computational geometry table of contents Brook-lyn, New York, USA SESSION: Session 3 table of contents Pages: 68- 75 Year of Publication: 2004 ISBN:1-58113-885-7

108

Page 109: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

85./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, Bounds onconvex crossing numbers, COCOON 2003, The Ninth Interna-tional Computing and Combinatorics Conference, Lecture Notesin Computer Science vol. 2697, Springer Verlag, 2003 487–495.

References

1. Kolman P, Matousek J Crossing number, pair-crossing number, andexpansion JOURNAL OF COMBINATORIAL THEORY SERIES B92 (1): 99-113 SEP 2004

2. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

86./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, The gapbetween the crossing number and the convex crossing number,in: Towards a Theory of Geometric Graphs, ed. J. Pach, Con-temporary Mathematics 342, Amer. Math. Soc. 2004, 249–258.

References

1. Radoslav Fulek, Hongmei He, Ondrej S?kora and Imrich Vr?o, Outer-planar Crossing Numbers of 3-Row Meshes, Halin Graphs and Com-plete p-Partite Graphs, SOFSEM 2005: Theory and Practice of Com-puter Science Lecture Notes in Computer Science, 2005, Volume 3381/2005,376-379, DOI: 10.1007/978-3-540-30577-4 43

2. Hongmei Hea, Ondrej Sykora, and Imrich Vrt’o, Crossing Minimi-sation Heuristics for 2-page Drawings, Electronic Notes in DiscreteMathematics Volume 22, 15 October 2005, Pages 527-534

3. DR Wood, JA Telle, Planar Decompositions and the Crossing Numberof Graphs with an Excluded Minor New York J. Math 13(2007), 117–146.

4. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry,2005, 499 pages.

5. Hongmei He and O. Sykora, New circular drawing algorithms,

6. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

87./ L. A. Szekely, Short proof for a theorem of Pach, Spencer, andToth, in: Towards a Theory of Geometric Graphs, ed. J. Pach,Contemporary Mathematics 342, Amer. Math. Soc. 2004, 281–283.

References

1. J. Fox, Csaba D. Toth, On the decay of crossing numbers, J. Comb.Theory Ser. B 98(2008) 33–42.

2. J. Cerny, J. Kyncl, G. Toth, Improvement on the decay of crossingnumbers

109

Page 110: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

3. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

4. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry,2005, 499 pages.

88./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, Bounds andmethods for k-planar crossing numbers, Graph Drawing 2004,Lecture Notes in Computer Science Vol. 2912, Springer Verlag,Berlin, 2004, 37–46.

89./ L. A. Szekely, Counting rooted spanning forests in complete mul-tipartite graphs, Ars Combinatoria 73 (2004), 97–100.

90./ E. Czabarka, O. Sykora, L. A. Szekely and I. Vrto, OuterplanarCrossing Numbers, Circular Arrangement Problem, and Isoperi-metric Functions, Elect. J. Combinatorics 11 (1) (2004) R81 (20pages).

References

1. DR Wood, JA Telle, Planar Decompositions and the Crossing Numberof Graphs with an Excluded Minor New York J. Math 13(2007), 117–146.

2. A Riskin, The circulark-partite crossing number ofKm,n, Arxiv preprintmath.CO/0605235, 2006

3. H Fernau, Parameterized Algorithmics: A Graph-Theoretic Approach,Habilitation Thesis, Universitat Tubingen, 2005,

91./ L. A. Szekely and Hua Wang, On subtrees of trees, Adv. Appl.Math. 34 (2005), 138–155.

References

1. Andreas Maunz, Christoph Helma and Stefan Kramer, Efficient miningfor structurally diverse subgraph patterns in large molecular databases,Machine Learning DOI: 10.1007/s10994-010-5187-6

2. Chehreghani MH, Chehreghani MH, Lucas C, et al., Efficient rulebased structural algorithms for classification of tree structured data,INTELLIGENT DATA ANALYSIS Volume: 13, 1 165-188 : 2009

3. C Heuberger, SG Wagner, Asymptotics of the extremal values of cer-tain graph parameters in trees with bounded degree

4. Heuberger C, Wagner SG, Maximizing the number of independent sub-sets over trees with bounded degree JOURNAL OF GRAPH THEORYVolume: 58 Issue: 1 Pages: 49-68 Published: MAY 2008

5. Hua Wang, Sums of distances between vertices-leaves in k-ary trees,Bull. Inst. Comb. Appl.

110

Page 111: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

6. M. Hamina, M. Peltola, Least-central subtrees, center and centroid ofa tree

7. Hua Wang, The extremal values of the Wiener index of a tree with agiven degree sequence

8. R. Kirk, Hua Wang, Largest number of subtrees of trees with a givenmaximum degree, SIAM JOURNAL ON DISCRETE MATHEMAT-ICS Volume: 22 Issue: 3 Pages: 985-995 Published: 2008

9. Teufl, E., Wagner, S. Enumeration problems for classes of self-similargraphs (2007) Journal of Combinatorial Theory. Series A, 114 (7), pp.1254-1277.

10. Yan, W., Yeh, Y. N., Enumeration of subtrees of trees, Enumeration ofsubtrees of trees THEORETICAL COMPUTER SCIENCE 369 (1-3):256-268 DEC 15 2006

11. The On-Line Encyclopedia of Integer Sequences, A092781.http://www.research.att.com/˜njas/sequences

12. Hua Wang, Subtrees of Trees, Wiener Index and Related Problems,Ph. D. Thesis, University of South Carolina, 2005.

13. C. Heuberger, H. Prodinger, On α-greedy expansions of numbers, Ad-vances in Applied Mathematics 38 (2007)(4): 505-525

14. S. Wagner, Correlation of graph-theoretical indices, SIAM JOURNALON DISCRETE MATHEMATICS 21 (1): 33-46 2007

92./ L. A. Szekely, Progress on crossing number problems, SOFSEM2005: Theory and Practice of Computer Science: 31st Confer-ence on Current Trends in Theory and Practice of ComputerScience Liptovsky Jan, Slovakia, January 22-28, 2005. Editors:P. Vojtas, M. Bielikova, B. Charron-Bost, et al. Lecture Notesin Computer Science Vol. 3381, 2005, Springer-Verlag, 53–61.

References

1. The minor crosssing number of graphs with an excluded minor Au-thor(s): Bokal D, Fijavz G, Wood DR Source: ELECTRONIC JOUR-NAL OF COMBINATORICS Volume: 15 Issue: 1 Article Number:R4 Published: JAN 1 2008

2. H Fernau, Parameterized Algorithmics: A Graph-Theoretic Approach,Habilitation Thesis, Universitat Tubingen, 2005,

3. Pinchasi, R. Linear algebra approach to geometric graphs (2007) Jour-nal of Combinatorial Theory. Series A, 114 (8), pp. 1363-1374.

93./ F. Shahrokhi, O. Sykora, L. A. Szekely and I. Vrto, k-planarcrossing numbers, Discrete Appl. Math. 155 (2007), 1106–1115.

94./ P. L. Erdos, A. Seress and L. A. Szekely, Non-trivial t-intersectionin the function lattice, Annals of Combinatorics 9 (2005) 177–187.

111

Page 112: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. Li YS, Wang J Erdos-Ko-Rado-type theorems for colored sets ELEC-TRONIC JOURNAL OF COMBINATORICS 14 (1): Art. No. R1JAN 3 2007

95./ L. A. Szekely, Hua Wang, and Yong Zhang, Some non-existenceresults on Leech trees, Bull. Inst. Comb. Appl. 44 (2005).

References

1. Hua Wang, Subtrees of Trees, Wiener Index and Related Problems,Ph. D. Thesis, University of South Carolina, 2005.

96./ Linyuan Lu and L. A. Szekely, Using Lovasz Local Lemma inthe space of random injections, Electronic J. Comb. 14 (2007)R63, pp. 13.

References

1. D. Scheder, P. Zumstein, Unsatisfiable CNF formulas need many con-flicts, Arxiv preprint arXiv:0806.1148, 2008

2. Heidi Gebauer, Robin A. Moser, Dominik Scheder and Emo Welzl, TheLovasz Local Lemma and Satisfiability, Efficient Algorithms LectureNotes in Computer Science, 2009, Volume 5760/2009, 30-54.

3. D. Scheder, P. Zumstein, How many conflicts does it need to be unsat-isfiable?, Lecture Notes In Computer Science, Proceedings of the 11thinternational conference on Theory and applications of satisfiabilitytesting, Guangzhou, China Pages: 246-256 2008.

4. D. Scheder, Unsatisfiable Linear CNF Formulas Are Large, and Diffi-cult to Construct Explicitely, 27th International Symposium on The-oretical Aspects of Computer Science - STACS 2010, Nancy : France(2010), 621-632

5. JULIA BOTTCHER, YOSHIHARU KOHAYAKAWA, AND ALDOPROCACCI, PROPERLY COLOURED COPIES AND RAINBOWCOPIES OF LARGE GRAPHS WITH SMALL MAXIMUM DEGREE,Arxiv preprint arXiv:1007.3767, 2010

97./ L. A. Szekely and Hua Wang, Binary trees with the largest num-ber of subtrees, Discrete Appl. Math. 155 (2007), 374-386.

References

1. C Heuberger, SG Wagner, Asymptotics of the extremal values of cer-tain graph parameters in trees with bounded degree

2. R. Kirk, Hua Wang, Largest number of subtrees of trees with a givenmaximum degree, SIAM JOURNAL ON DISCRETE MATHEMAT-ICS Volume: 22 Issue: 3 Pages: 985-995 Published: 2008

112

Page 113: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

3. Yan, W., Yeh, Y. N., Enumeration of subtrees of trees, THEORETI-CAL COMPUTER SCIENCE 369 (1-3): 256-268 DEC 15 2006

4. Heuberger C, Wagner SG, Maximizing the number of independent sub-sets over trees with bounded degree Source: JOURNAL OF GRAPHTHEORY Volume: 58 Issue: 1 Pages: 49-68 Published: MAY 2008

5. The On-Line Encyclopedia of Integer Sequences, A092781.http://www.research.att.com/˜njas/sequences

6. C. Heuberger, H. Prodinger, On α-greedy expansions of numbers, Ad-vances in Applied Mathematics 38 (2007)505-525

7. Hua Wang, Subtrees of Trees, Wiener Index and Related Problems,Ph. D. Thesis, University of South Carolina, 2005.

98./ L. A. Szekely and Hua Wang, Binary trees with the largest num-ber of subtrees with at least one leaf, Congressus Numerantium177 (2005), 147–16.

References

1. Yan WG, Yeh YN Enumeration of subtrees of trees THEORETICALCOMPUTER SCIENCE 369 (1-3): 256-268 DEC 15 2006

2. R. Kirk, Hua Wang, Largest number of subtrees of trees with a givenmaximum degree, SIAM JOURNAL ON DISCRETE MATHEMAT-ICS Volume: 22 Issue: 3 Pages: 985-995 Published: 2008

3. Hua Wang, Subtrees of Trees, Wiener Index and Related Problems,Ph. D. Thesis, University of South Carolina, 2005.

99./ E. Czabarka, O. Sykora, L. A. Szekely and I. Vrto, Crossing num-bers and biplanar crossing numbers II: using the probabilisticmethod, Random Structures and Algorithms 33 (2008) 480–496.

References

1. Joshua K.Lambert, Finding a biplanar embedding of Cn×Cn×Cl×Pm

2. Joshua K.Lambert, The biplanar crossing number of Ck×Cl×C2m×Pn

3. P. Brass, W. Moser, J. Pach, Research Problems in Discrete Geometry,2005, 499 pages.

4. Pach, J., Geometric graph theory. Surveys in combinatorics, 1999(Canterbury), 167–200, London Math. Soc. Lecture Note Ser., 267,Cambridge Univ. Press, Cambridge, 1999

100./ M. A. Steel and L. A. Szekely, Teasing apart two trees, Combi-natorics, Probability, and Computing 16 (2007) (6) 203–222.

113

Page 114: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. M. Steel, CONSISTENCY OF BAYESIAN INFERENCE OF RE-SOLVED PHYLOGENETIC TREES, arXiv:1001.2864v1 [q-bio.PE]17 Jan 2010

2. Louxin Zhang, Jian Shen, Jialiang Yang and Guoliang Li, Analyzingthe Fitch Method for Reconstructing Ancestral States on Ultramet-ric Phylogenetic Trees, Bulletin of Mathematical Biology Volume 72,Number 7, 1760-1782, DOI: 10.1007/s11538-010-9505-8

3. Olivier Gascuela, and Mike Steel, Inferring ancestral sequences intaxon-rich phylogenies, Mathematical Biosciences Volume 227, Issue2, October 2010, Pages 125-135

101./ M. A. Steel and L. A. Szekely, On the variational distance of twotrees, ANNALS OF APPLIED PROBABILITY 16 (3): 1563-1575 AUG 2006

References

1. Mahendra Mariadassou, Robustesse des arbres phylogenetiques, Uni-versite Paris Sud - Paris XI (2009-11-27), Avner Bar-Hen (Dir.)

102./ D. Bokal, E. Czabarka, L. A. Szekely, and I. Vrto, Graph minorsand the crossing number of graphs, Electronic Notes in DiscreteMath.

References

1. Janos Pach, Jozsef Solymosi, Gabor Tardos, Crossing numbers of im-balanced graphs, Journal of Graph Theory Volume 64, Issue 1, pages1221, May 2010

2. Chimani, Markus, Computing crossing numbers, Ph.D. Thesis, TUDortmund, 2009.

3. GASPER FIJAVZ AND DAVID R. WOOD GRAPH MINORS ANDMINIMUM DEGREE, arXiv:0812.1064v1 [math.CO] 5 Dec 2008

4. D BOKAL, G FIJAVZ, DR WOOD -THE MINOR CROSSING NUM-BER OF GRAPHS WITH AN EXCLUDED MINOR Arxiv preprintmath.CO/0609707, 2006 - arxiv.org

5. H Fernau, Parameterized Algorithmics: A Graph-Theoretic Approach,Habilitation Thesis, Universitat Tubingen, 2005,

103./ L. A. Szekely, An optimality criterion for the crossing number,Ars Mathematica Contemporena 1(2008), 32–37.

114

Page 115: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

2. M. J. Pelsmajer, M. Schaefer, D. Stefankovic, : REMOVING IN-DEPENDENTLY EVEN CROSSINGS, SIAM JOURNAL ON DIS-CRETE MATHEMATICS 24(2)(2010) 379–393.

3. M. J. Pelsmajer, M. Schaefer, D. Stefankovic, Crossing numbers ofgraphs with rotation systems Lecture Notes In Computer Science Pro-ceedings of the 15th international conference on Graph drawing, Syd-ney, Australia Pages: 3-12 , 2007 ISBN ISSN:0302-9743 , 3-540-77536-6

104./ A. Sali and L. A. Szekely, On the existence of Armstrong in-stances with bounded domains, Foundations of Information andKnowledge Systems (FoIKS 2008), Lecture Notes in ComputerScience Vol. 4932, pp. 151–157, 2008, Springer-Verlag.

References

1. Sven Hartmann, Uwe Leck and Sebastian Link, On Codd Familiesof Keys over Incomplete Relations, The Computer Journal AdvanceAccess published September 29, 2010

2. Sven Hartmann, Henning Kohler, and Thu Trinh, On the Existenceof Armstrong Data Trees for XML Functional Dependencies, S. Linkand H. Prade (Eds.): FoIKS 2010, LNCS 5956, pp. 94113, 2010.

105./ E. Czabarka, P. Dankelmann, L. A. Szekely, Diameter of 4-colorable graphs, Europ. J. Comb. 30 (2009) 1082–1089.

106./ M. A. Steel, L. A. Szekely, E. Mossel, Phylogenetic informationcomplexity: is testing a tree easier than finding it? J. Theor.Biology 25 (2009) 95–102.

References

1. Matthias Dehmer, Marina Popovscaia, Towards Structural NetworkAnalysis, BULETINUL ACADEMIEI DE STIINTE A REPUBLICIIMOLDOVA. MATEMATICA Number 1(62), 2010, Pages 322

107./ L. A. Szekely, Yiting Yang, On the expectation and varianceof the reversal distance, Acta Univ. Sapientiae, Mathematica 1(2009) (1) 5–20.

108./ E. Czabarka, L. A. Szekely, S. Wagner, The inverse problem forcertain tree parameters, Discrete Applied Math. 157(15)(2009),3314–3319.

115

Page 116: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

109./ Hyunju Kim, Z. Toroczkai, I. Miklos, P. L. Erdos, L. A. Szekely,On realizing all simple graphs with a given degree sequence Phys.Lett. A Math. Theor. 42 (2009) 392001.

References

1. Del Genio CI, Kim H, Toroczkai Z, et al., Efficient and Exact Samplingof Simple Graphs with Given Arbitrary Degree Sequence, PLOS ONEVolume: 5 Issue: 4 (2010) Article Number: e10012

2. Erdos PL, Miklos I, Toroczkai Z, A simple Havel-Hakimi type algo-rithm to realize graphical degree sequences of directed graphs, ELEC-TRONIC JOURNAL OF COMBINATORICS 17 (1)(2010) ArticleNumber: R66

3. Klinkowski, AnyTraffic routing algorithm for label-based forwarding,IEEE GLOBCOM 2009 proceedings.

4. Charo I Del Genio, Hyunju Kim, Zoltan Toroczkai, Kevin E. Bassler,Efficient and exact sampling of simple graphs with given arbitrarydegree sequence

5. Ginestra Bianconi, Entropy of network ensembles, Physical ReviewE 79, 036114 (2009).

110./ M. A. Steel and L. A. Szekely, Inverting random functions III:discrete MLE revisited, Annals Comb. 13 (2009) 373–390.

References

1. M. Steel, CONSISTENCY OF BAYESIAN INFERENCE OF RE-SOLVED PHYLOGENETIC TREES, arXiv:1001.2864v1 [q-bio.PE]17 Jan 2010

2. Mahendra Mariadassou, Robustesse des arbres phylogenetiques, Uni-versite Paris Sud - Paris XI (2009-11-27), Avner Bar-Hen (Dir.)

111./ M. A. Steel, L. A. Szekely, An improved bound on the MaximumAgreement Subtree problem, Appl. Math. Letters 22 (2009)1778–1780.

References

1. J Goodrich, Phylogenetic Pipeline for the Detection of Horizontal GeneTransfer

112./ H. Aydinian, E. Czabarka, P. L. Erdos, L. A. Szekely, A tour ofM -part L-Sperner families, to appear in J. Comb Theory Ser A.

113./ H. Aydinian, E. Czabarka, K. Engel, P. L. Erdos, L. A. Szekely,A note on full transversals and mixed orthogonal arrays, Aus-tralasian J. Comb. 48(2010), 133–141.

116

Page 117: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

114./ L. A. Szekely, Hua Wang, and Taoyang Wu, The sum of dis-tances between the leaves of a tree and the ’semi-regular’ prop-erty, Discrete Math. (2010)

115./ D. Bokal, E. Czabarka, L. A. Szekely, and I. Vrto, General lowerbounds for the minor crossing numbers of graphs, Discrete andComputational Geometry 44(2010), 463–483.

OTHER PUBLICATIONS

116./ Combinatorial exercises, JATE University, Szeged, l983 (in Hun-garian).

References

1. P. Hajnal Elementary problems in combinatorics, Polygon, BolyaiInstitute, Szeged, 1997 (in Hungarian).

117./ L. A. Szekely, Analytic Methods in Combinatorics, Thesis forthe Candidate’s Degree, Hungarian Academy of Sciences, 1985.(in Hungarian)

References

1. Boris Bukh, Measurable sets with excluded distances

2. Quas A, Distances in positive density sets in R-d, JOURNAL OFCOMBINATORIAL THEORY SERIES A Volume: 116 Issue: 4 Pages:979-987 Published: MAY 2009

118./ An algebraic approach to the uniform concurrent multicommod-ity flow problem: theory and applications, Technical Report CRPDC-91-4, Department of Computer Science, University of North Texas,1991 (with F. Shahrokhi).

References

1. L Torok, Volumes of 3D Drawings of Homogenous Product Graphs(Extended Abstract),SOFSEM 2005: Theory and Practice of Com-puter Science: 31st Conference on Current Trends in Theory and Prac-tice of Computer Science Liptovsky’ Ja’n, Slovakia, January 22-28,2005. Proceedings, LNCS 3381/2005, p. 423. Editors: Peter Vojta’s(,Ma’ria Bielikova’, Bernadette Charron-Bost, et al.

2. P. Ruzicka, On efficiency of path systems induced by routing and com-munication schemes, Computing and Informatics 20 (2) (2001), 181–205.

3. P. Ruzicka, Efficient communication schemes, Theory and practice ofinformatics SOFSEM’98, Band 25, 244–263.

117

Page 118: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

4. L. Stacho, I. Vrto, Bisection width of transposition graphs, DiscreteAppl. Math. 84 (1998), 221–235.

5. O. Sykora, I. Vrto, On crossing numbers of hypercubes and cube-connected cycles, BIT Comp. Sci. and Num. Math. 33(1993)232–237.

6. O. Sykora, I. Vrto, On VLSI layouts of the star graph and relatednetworks, Integration, the VLSI Journal 17(1994), 83–93.

7. M. Scharbrodt, Die Kreuzungszahl von Graphen, Diplomarbeit, In-stitut fur Informatik der Universitat zu Koln, 1994.

8. I. Vrto, 2 remarks on expanding and forwarding, Discrete Appl. Math.58 (1995) (1) 85–89.

9. D. Barth, F. Pellegrini, A. Raspaud, J. Roman, On bandwith, cutwidth,and quotient graphs, RAIRO — Informatique Theoretique et Ap-plications — Theoretical Informatics and Applications 29 (1995)(6), 487–508.

10. M.-C. Heydemann, Cayley graphs and interconnection networks,in: Algebraic Methods and Applications, eds. G. Hahn and G.Sabidussi, NATO ASI Series C Vol. 497, Kluwer, 1997, 167–224.

119./ M.A. Steel - L.A. Szekely - P.L. Erdos: The number of nucleotidesites needed to accurately reconstruct large evolutionary trees,DIMACS, Rutgers University, New Brunswick, New Jersey, USA1996. DIMACS Technical Reports 96-19

References

1. AWM Dress, PL Erdoes, X-Trees and Weighted Quartet Systems, An-nals of Combinatorics, 7 (2003) 155 - 169.

2. M. Farach, S. Kannan, Efficient algorithms for inverting evolution, J.ACM 46 (4) (1999), 437–449.

3. M. Csuros: Reconstructing Phylogenies in Markov Models of SequenceEvolution, Ph.D. Thesis Yale University, (2000), 1–232.

120./ L. A. Szekely, Zarankiewicz crossing number conjecture, arti-cle in: Kluwer Encyclopaedia of Mathematics, Supplement IIIManaging Editor: M. Hazewinkel Kluwer Academic Publishers,2002, 451–452.

References

1. I. Vrto, Crossing Numbers of Graphs: A Bibliography,http://www.ifi.savba.sk/∼imrich

121./ Other communications:

118

Page 119: References to publications of - University of South Carolinapeople.math.sc.edu/laszlo/cita.pdf · 2. J. Beck, Inevitable randomness in discrete mathematics, University Lecture Notes

References

1. T.D. Porter, Binomial identities generated by counting spanning trees,ARS COMBINATORIA Volume: 82 Pages: 159-163

2. G. Elekes, Circle grids and bipartite graphs of distance, Combinator-ica 15(1995), 167–174.

3. G. Chartrand, P. Erdos, O. R. Oellerman, How to define an irregulargraph? College Math. Journal 19(1988), 36–42.

4. G. J. Szekely, Contests in Higher Mathematics, Problem Books inMathematics, Springer-Verlag, 1995, p. 34, p.36.

5. S. Fajtlowicz, Written on the Wall, p. 67.

6. C. T. Edwards, Double-elimination tournaments: Counting and cal-culating, Am. Stat. 50(1996)(1), 27–33.

7. G. Elekes, SUMS versus PRODUCTS in number theory, algebra, andErdos geometry, in: Paul Erdos and his Mathematics II, Bolyai Studies11, Springer-Verlag, 2002, 241–290.

8. V Ro”dl, B Nagle, J Skokan, M Schacht, , and Y. Kohayakawa Thehypergraph regularity method and its applications, PNAS, June 7,2005 — vol. 102 — no. 23 — 8109-8113.

9. V Roedl, J Skokan, Counting subgraphs in quasi-random 4-uniformhypergraphs, Random Structures and Algorithms, 2005 Volume 26,Issue 1-2 , Pages 160 - 203

10. Ben Gum, The secretary problem with a uniform distribution

11. Rodl, V. Skokan, J. Applications of the regularity lemma for uniformhypergraphs. (English. English summary) Random Structures Algo-rithms 28 (2006), no. 2, 180–194.

The number of references: 1603.

119