pavel tomancak - biocev 2013 pavel tomancak the 30th pattern recognition and computer vision...

CV 2013 Pavel Tomancak

Pavel Tomancak

Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

Pfotenhauerstrasse 108

D-01307 Dresden

Germany

Tel.: +49 351 210 2670

Email: [email protected] Homepage: http://www.mpi-cbg.de/research/research-groups/pavel-tomancak/research.html

Twitter: @PavelTomancak

BIOGRAPHICAL DATA

Born 27 March 1972, Frydek-Mistek, Czechoslovakia

Citizen of Czech Republic

single

EDUCATION

University of Heidelberg, Heidelberg, Germany, 1995-1999

Ph.D. in Developmental Biology, 1999,

Masaryk University, Brno, Czech Republic, 1990-1995

Mgr. in Natural Sciences, specializing in Molecular Biology and Genetics, 1995

FELLOWSHIPS AND AWARDS

ERC Starting grant 2010-2015

HFSP Young Investigator grant 2012-2015

HFSP Young Investigator grant 2008-2012

European Molecular Biology Laboratory predoctoral fellowship, 1995-1999

Masaryk University, Dean of faculty of Science Award, 1995

RESEARCH EXPERIENCE

Independent Research: Senior Permanent Research Group Leader, Max-Planck Institute of Molecular

Cell Biology and Genetics, Dresden, Germany, 2013-present

“Patterns of gene expression in development and evolution”

Research Group Leader, Max-Planck Institute of Molecular Cell Biology and

Genetics, Dresden, Germany, 2005-2013

“Patterns of gene expression in animal development”

Postdoctoral Research: Assistant Researcher at Dr. Gerald M. Rubin's laboratory

HHMI/Department of Molecular and Cell Biology,

University of California, Berkeley, 2002-2005

“Large scale Drosophila in situ projects”

Doctoral Research: EMBL, Heidelberg, Germany, 1995-1999 (Research advisor Dr. Anne Ephrussi)

“Establishment of polarity in Drosophila oocyte.”

mailto:[email protected]

http://www.mpi-cbg.de/research/research-groups/pavel-tomancak/research.html


Undergraduate Research: Masaryk University, Brno, Czech Republic, 1994-1995 (Research advisor Dr. Ing. Karel Chroust)

“Construction of transgenic Drosophila melanogaster carrying human genes for metabolizing

enzymes.”

RESEARCH RELATED ACTIVITIES

Conference Organization: EMBO course on Light Sheet Microscopy MPI-CBG Dresden, Germany, 18th -

28th August 2014

Bioimage Informatics 2012 MPI-CBG Dresden, Germany, 16th – 19th September

2012

Evolution and Development of Integrated Phenotype, International Congress of

Entomology, Daegu , South Korea, August 19th – 25th 2012

Image Analysis in Living Systems Workshop at the LeadNet meeting of the Max

Planck Society, May 8th 2012

Next Generation Resources plenary session at the 22nd European Drosophila

Research Conference in Lisbon, Portugal, September 21 - 24th 2011

Workshop on Image Analysis for Drosophila research at the 51st Annual

Drosophila Research Conference in Washington, April 7th - 11th 2010

Trilateral Workshop for young scientists from Czech Republic, Poland and

Germany on “Optical Techniques in Cell and Developmental Biology”, Dresden,

November 29th - December 1st 2009

The First Light Sheet based Fluorescence Microscopy Workshop

MPI-CBG, Dresden, September 24th - 25th 2009

Grant Reviewing: Welcome Trust, German-Israeli Foundation, NSF, DFG, Research Council KU

Leuven

Journal Reviewing: Nature Methods, Cell, Genome Biology, Nature Biotechnology, Developmental

Biology, Bioinformatics, BMC, PLoS Genetics, Journal of Microscopy, Bioessays,

PLoS One, JoVE

Editorial boards: BMC Bioinformatics, Gene

Recent invited talks at international meetings

Structured Illumination: Biomedical Applications and Future Developments, Oxford, October 2013

European Drosophila Research Conference, Barcelona, October 2013

European Bioimage Analysis Symposium, Barcelona, October 2013

Seeing is believing, EMBL Heidelberg, October 2013

5th EMBO meeting, Amsterdam, September 2013

15th Annual Meeting for the Society of Evolutionary Biology, Tsukuba, August 2013

Manipulation of Drosophila Genome, Janelia Farm, March 2013

BioTec Forum, Dresden, December 2012

Imaging in Cell Biology: Where Next, Cumberland Lodge, Windsor, October 2012

French Drosophila meeting, Clermont-Ferrand, September 2012

24th Entomological Congress, Daegu, South Korea, August 2012

The molecular and developmental biology of Drosophila, Kolymbari, Crete, June 2012

12th European Light Microscopy Initiative (ELMI) Meeting, Leuven, June 2012

ESF/EMBO Conference on Systems Biology of Drosophila development, Pultusk/Poland, May 2012


The 30th Pattern Recognition and Computer Vision Colloquium, Prague, April 2012

EMBO Practical Course on Microscopy, Johannesburgh, November 2011

DIPP Vision Talk, Dresden, September 2011

European Drosophila Reseacrh Conference, Lisbon, September 2011

Bioimage Informatics II Janelia Farm Research Campus, September 2011

INSERM workshop Emerging tools in quantitative fluorescence microscopy for systems biology,

Lisbon, September 2011

EMBO practical course on Drosophila, Lisbon, March 2011

Automated Imaging and High Throughput Phenotyping, CSHL, December 2010

The molecular and developmental biology of Drosophila, Kolymbari, Crete, June 2010

Open Microscopy Environment (OME) User’s meeting, Paris, June 2010

VizBi Visualization of Biological Data, EMBL, March 2010

Trilateral Workshop Dresden, December 2009

European Drosophila Research Conference, Nice, November 2009

The First Light Sheet based Fluorescence Microscopy Workshop, Dresden, September 2009

BioImage Informatics, Janelia Farm Research Campus, 2009

What Can Computer Vision Do for Neuroscience and Vice Versa? Janelia Farm Research Campus 2008

ISBI, Paris, France, 2008

Trilateral MPI Workshop on Regulation of gene expression in Prague, 2007

Cytokinematics in Hradec Kralove, Czech Republic, 2006

Recent invited talks at Universities and Academic Institutes

2013 Dec 17th University of Ostrava, Ostrava, invited by Marek Elias

2013 Nov 21st Advanced Techniques Day: Lightsheet microscopy, Prague, invited by Karel Drbal

2013 Nov 12th BIOCEV day, Prague, invited by Pavel Martasek

2013 Sep 17th Einstein College of Medicine, New York, invited by Rob Singer

2013 Sep 12th University of Wisconsin, Madison, invited by Kevin Eliceiri

2013 May 8th Leibnitz Institute for Neurobiology, Magdeburg, invited by Rainer Pielot

2013 Apr 10th Stowers Institute, Kansas City, invited by Julia Zeitlinger

2013 Mar 20th Janelia Farm Research Campus, invited by Albert Cardona

2013 Feb 5th College of Life Sciences, Dundee, invited by Mike Ferguson & Jason Swedlow

2012 Dec 17th Centrum for Organismal Studies Heidelberg, invited by Steffen Lemke

2012 Dec 13th ZMBH Heidelberg, invited by Bruce Edgar

2012 Nov 19th Department of Molecular Genetics, University of Toronto, invited by Howard Lipshitz

2012 Nov 8th, Department of Genetics, University of Cambridge, invited by Boris Adryan

2012 Nov 1st ETH Zurich Institute of Biochemistry, invited by Yves Barral

2012 July 3rd IMBB Heraklion, Crete, invited by Michaelis Averof

2012 June 12th VIB Leuven, invited by Bassem Hassan

2012 Feb 13th MPI for Developmental Biology, invited by Gaspar Jekely

2012 Feb 23rd UMC St Radboud, Nijmegen, invited by Annette Schenck

2012 Jan 20th Institute Curie, Paris, invited by Emmanuel Farge

2012 Jan 19th Institute Pasteur, Paris, invited by Jost Enninga

2012 Jan 9th Institute of Entomology, Ceske Budejovice, invited by Tomas Dolezal

2011 Dec 2nd CADB Madrid, invited by Acaimo Gonzalez Reyes

2011 Nov 4th CRG, Barcelona, invited by Yogi Jaeger

2011 Nov 3rd IRB, Barcelona, invited by Marco Milan

2011 Oct 13th Universite Paul Sabatier, Toulouse, invited by Alain Vincent

2011 June 20th MPI for Molecular Genetics Berlin, invited by S. Meijsing


2011 June 9th IRCM Montreal, invited by Eric Lecuyer

2011 May 23th IST, Vienna, invited by Carl-Phillip Heisenberg

2011 Apr 26th Institute of Molecular Genetics Prague, invited by Vaclav Horejsi

2011 Apr 18th Faculty of Life Science, University of Manchester, invited by Casey Bergman

2011 Feb 4th LOCI, University of Madison, invited by Kevin Eliceiri

2010 Dec 2nd The Donnelly Centre, University of Toronto, invited by Henry Krause

2010 October 19th Dept. of Cell Biology, Charles University in Prague, invited by Marian Novotny

2010 May 17th SFB610, Halle, invited by Gunter Reuter

2010 March 19th EMBL Heidelberg, invited by Francesca Peri

2009 August 12th Institute of Molecular Genetics, Prague, invited by Peter Sebo

2009 June 23rd EPFL, Lausanne, invited by Bruno Lemaitre

2009 June 22nd University of Geneva, invited by Marcos Gonzales-Gaitan

2009 June 16th IMP/IMBA, Wienna, invited by Alexander Stark

2008 December 15th EMBL, Heidelberg, invited by Anne Ephrussi

2008 October 14th MPI for Neurobiology in Martinsried, invited by Ilona Kadow

2008 April 18th IBDML, Marseille, invited by Nicolas Gompel

2008 April 11th Tokyo Metropolitan University, Japan, invited by Toshiro Aigaki

2007 July 10th A*STAR Bioinformatics Institute, invited by Martin Wasser

2006 April 27th MRC Laboratory of Molecular Biology, Cambridge invited by Sarah Teichmann


OPEN ACCESS ACTIVITIES

Resource

name Description Website

APOGEE Atlas of patterns of gene expression in Drosophila

embryogenesis. A widely used database of gene expression

patterns that I established.

http://www.fruitfly.org

Fly-FISH

Atlas of patterns of RNA localization in Drosophila

embryogenesis. A database companion to Cell paper

established in collaboration with Eric Lecuyer and Henry

Krause.

http://fly-

fish.ccbr.utoronto.ca

Disc-pattern

database

Atlas of patterns of genes expression in Drosophila

imaginal discs. Data collection finished, analysis in

progress.

upcoming

Ovary-FISH Atlas of patterns of RNA localization in the Drosophila

ovary. Data collection in progress. upcoming

Transgeneome

&

FLY2K

Online resource for genomic fosmid libraries for D.

melanogaster and D. pseudoobscura and an online voting

system for the community to prioritize gene tagging with

fluorescent proteins aiming at generating genome-wide

collection of tagged fosmid transgenes.

http://transgeneome.mpi-

cbg.de

Fiji (Fiji Is Just

ImageJ)

A wiki for powerfull ImageJ distribution called Fiji, which

focuses on image registration and segmentation. I publish

all my image analysis projects under Fiji, fully open source,

documented and USABLE. We organize a community of

talented Fiji developers and host the source code

management repository of the project.

http://fiji.sc

SPIM Wiki A wiki collecting information about annual Light Sheet

based Fluorescence Microscopy workshop iniated by

Pavel Tomancak and Emmanuel Reynaud

http://spim.mpi-cbg.de

OpenSPIM

A wiki presenting information on how to build and use an

simple, cost-effective version of SPIM microscope.

Combining the ideas of Open Hardware and Software to

empower biological research.

http://openspim.org

FUNDING

Current funding

MPG MPI-CBG Senior Permanent Research Group Leader Block Funding

09/2013 - present Salaries for myself, a technician, 2 post-docs and 2 PhD students;

Consumables of 75,000 Euro/y and 40,000 Euro/y facility budget

This represents the core funding for my group provided by the Max Planck Society through my permanent appointment at

the MPI-CBG.

ERC Quantitative Analysis of the Hourglass Model of Evolution of Development

09/2010 - 09/2015 1.500.000 Euro

http://www.fruitfly.org/

http://fly-fish.ccbr.utoronto.ca/

http://fly-fish.ccbr.utoronto.ca/

http://transgeneome.mpi-cbg.de/

http://transgeneome.mpi-cbg.de/

http://pacific.mpi-cbg.de/

http://spim.mpi-cbg.de/

http://openspim.org/


An ERC Starting Grant that extends the analysis of the hourglass model of development initiated under HFSP.

HFSP Quantitative modeling of expression pattern evolution in insect development

RENEWAL_APP

~09/2012 - 09/2015 ~ 100.000 Euro/y

A joint application with Dr. Uwe Ohler (Duke) and Dr. Casey Bergman (University of Manchester) to study the

divergence of gene expression patterns with respect to the hourglass model of morphological evolution. This is the first

time in the history of HFSP that a grant has been renewed.

FP7 GENCODYS: Genetic and Epigenetic Networks in Cognitive Disfunction

01/2010 - 01/2015 ~ 200.000 Euro per year (including 1 postdoc, 1 student)

This large EU network project, of which I am one of the 12 partners, aims to understand the molecular basis of cognitive

disorders by combining various functional genomics approaches in invertebrate and vertebrate model systems with clinical

studies. My role is to generate and study large collection of tagged fosmid transgenes for Drosophila orthologs of genes

implicated in human mental retardation.

MPG Innovation Fund

of the President A reverse genetic toolkit for systematic study of gene function and protein localization in

Drosophila.

03/2011 - 03/2014 1.700.000 Euro total award

A systematic effort to generate tagged genomic fosmid transgenes for all genes in the Drosophila genome. These reagents

will enable both, visualization of the tissue specificity and sub-cellular localization of proteins throughout Drosophila life-

cycle and purification of protein-protein or protein-DNA complexes, in a tissue-specific manner. A consortium of 4

participating MPG groups. Majority of the funding goes to Dresden where the resources will be generated.

BMBF Collective organization of cells and tissues: Systems biology of tissue size and shape.

2012 - 2015 1.200.000 Euro total award

A joint grant of 10 MPI-CBG group leaders designed to seed and support the newly established Center for Systems

Biology in Dresden.

Past

MPG MPI-CBG Junior Research Group Leader Block Funding

09/2005 - 08/2013 Salaries for myself, a technician, post-doc and pre-doctoral student;

Consumables of 60,000 Euro/y and 33,000 Euro/y facility budget

This represents the core funding for my group provided by the Max Planck Society through my permanent appointment at

the MPI-CBG.

HFSP Quantitative modeling of expression pattern evolution in insect development

09/2008 - 03/2012 ~ 100.000 Euro/y

A joint application with Dr. Uwe Ohler (Duke) and Dr. Casey Bergman (University of Manchester) to study the

divergence of gene expression patterns with respect to the hourglass model of morphological evolution.


DFG Genome-wide analysis of gene expression in imaginal discs of Drosophila melanogaster

01/2007 - 01/2010 ~ 12 000 Euro/y + one technician and two HiWis

A joint application with Christian Dahmann to map the patterns of gene expression in larval imaginal discs using RNA in

situ probes previously employed in similar survey in the fly embryo.

Supervision of PhD students and post-docs

PhD thesis completed under my guidance

Stephan Saalfeld Automatic inter-slice registration of tiled Transmission Electron Microscopy (TEM)

images, TU Dresden Faculty of Computer Science (2013), magna cum laude, subsequently Lab Head at

the Janelia Farm Research Campus

Stephan Preibisch Reconstruction of Multi-View Microscopic Acquisitions TU Dresden Faculty of

Computer Science, (2011) suma cum laude, subsequently HFSP funded post-doctoral fellow with Rob

Singer/Eugene Myers (Janelia Farm/MPI-CBG)

Radoslaw Kamil Ejsmont Toolkit for high-througput gene engineering in Drosophila TU Dresden

Faculty of Biology, (2011) magna cum laude, subsequently EMBO funded post-doctoral fellow with

Bassem Hassan (KU Leuven)

Jastrzebowska, Karolina Evolution of gene expression regulation during embryonic development of

Drosophila species TU Dresden Faculty of Biology, (2010) magna cum laude, subsequently post-

doctoral fellow with Ilan Davis (Oxford University)

Arunachalan, Manonmani Computational discovery of cis-regulatory elements in multiple Drosophila

species TU Dresden Faculty of Biology, (2009) magna cum laude, subsequently postdoctoral fellow with

Uwe Ohler (Duke University)

Other thesis completed under my guidance

Christopher Todd (undergraduate student) Sequence Heterochrony within populations University of

York under the ‘Year in Europe’ program.

Michael Weber Interspecimen registration of long-term, time-lapse selective plane illumination

microscopy recordings of Drosophila melanogaster embryogenesis TU Dresden (2010), subsequently

PhD with Jan Huisken (MPI-CBG)

Radostina Izhakarowa Dual color RNA in situ analysis of gene expression during Drosophila

embryogenesis TU Dresden, (2006)

Currently supervising

Helena Jambor, Ivana Viktorinova (maternity leave), Tobias Pietszch, Tassos Pavlopoulos (FP7

Marie-Curie fellowship), Monika Zuberova (FP7 Marie-Curie fellowship maternity leave), Mette

Handberg-Thorsager (post-docs)

Melek Asli Kayserili, Vineeth Surendranath (DIGGS-BB fellowship), Christopher Schmied,

Akanksha Jain (PhD students)

Pavel Mejstrik, Peter Pitrone (technicians)

Post-docs who completed their post-doctoral studies in my group

Alex Kalinka 2009-2013 funded by HFSP, subsequently Research Group Leader at Institute of

Population Genetics, University of Veterinary Medicine Vienna


Tassos Pavlopoulos 2012-2013 funded by FP7 Marie-Curie fellowship, subsequently Research Fellow

at the Janelia Farm Research Campus

Teaching experience

PhD training within The International Max Planck Research School for Molecular Cell Biology and

Bioengineering, 2 weeks per year since 2005, plus lectures.

SPIMmage processing tutorial at the 5th Light Sheet Fluorescence Microscopy Worskhop, Thornwood,

NY, September 12th 2013

Hellenic Pasteur Institute regional course “Digital image processing/analysis tools in Light

Microscopy: From the basics and beyond”, Athens Greece, June 10-17th 2013

EMBO Course “Imaging Infection and Immunity” Pretoria, South Africa, Mar 20-30th 2013

Wellcome Trust course “Drosophila Genetics and Genomics” Cambridge, UK, 12-20th August 2012

EMBO Course “Drosophila Techniques”, Lisbon, Portugal 11-28th of March 2011

EMBO Course “Imaging Infection: from single molecules to animals”, Pretoria, South Africa, Nov 2-

13th 2011

BIOTEC Dresden Master Course „Drosophila as a model system“ 2007-2011, 2013

Organization of hackathons that involves teaching activities

Fiji/ImageJ2 hackathon Dresden 10th – 19th December 2011

ImageJ2 hackathon Madison Wisconsin 27th January – 11th February 2011

Fiji hackathon EMBL 15th – 27th March 2010

Fiji hackathon Dresden 22nd March – 4 April 2009

Fiji hackathon Dresden 21st – 30th April 2008

Responsibilities and Committees at the MPI-CBG

Evaluating PhD applications from Czech Republic and Bulgaria, Romania, Moldova

Thursday Seminar Committee 2010-2011

Organization of parties and shows, exemplary attendance of beer hours, “acting” and generally making a

fool of oneself for the amusement of colleagues


PUBLICATIONS

Citation data from Google Scholar as of 29.04.2013, h-index = 22, i-10 index 28. Total number of citations 3599.

PUBLICATIONS DURING INDEPENDENT RESEARCH PERIOD: 2005 - present

1. Preibisch S., Amat F., Stamataki E., Sarov M., Myers E., Tomancak P. (2013) Efficient bayesian multi-

view deconvolution manuscript under revision at Nature Methods, http://arxiv.org/abs/1308.0730

2. Heyn P., Kircher M., Dahl A., Kelso J., Tomancak P., Kalinka A.T., Neugebauer K.M. (2013) The

earliest transcribed zygotic genes are short, newly evolved and different across species Cell Reports,

in press, co-corresponding author

3. Pitrone P., Schindelin J., Stuyvenberg L., Preibisch S., Weber M., Eliceiri K.W., Huisken J., Tomancak P.

(2013) OpenSPIM - an open access platform for light sheet microscopy Nature Methods, 10, 598–599

see also http://arxiv.org/abs/1302.1987 (2 citations)

Mentioned in Nature Methods editorial (2013) Sharing blueprints for better research Nature Methods

10, 591 and Nature Methods Methagora blog “Promoting shared hardware designs”, featured in HFSP

newsletter Sep 2013

4. Lewitus E., Kelava I., Kalinka A.T., Tomancak P., Huttner W.B. (2013) An Adaptive Threshold in

Mammalian Neocortical Evolution http://arxiv.org/abs/1304.5412

5. Kayserili M.A., Gerrard D., Tomancak P., Kalinka A. (2012) An excess of gene expression divergence

on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis PLoS

Genetics 8(12) http://arxiv.org/abs/1209.0968v1corresponding author (1 citation)

6. Pietszch T., Preibisch S., Tomancak P., Saalfeld S. (2012) Imglib2: Generic Image Processing in Java

Bioinformatics 28(22): 3009-3011 (6 citation)

7. Saalfeld S., Fetter R., Cardona A., Tomancak P. (2012) Elastic Volume

Reconstruction from Series of Ultra-thin Microscopy Sections Nature Methods

9(7), 717-720 (14 citations)

8. Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Preibisch S.,

Rueden C., Saalfeld S., Schmid B., Tinevez J., Hartenstein V., Eliceiri K., Tomancak

P., Cardona A. (2012) Fiji - an open source platform for biological image Nature

Methods 9(7), 676-682 corresponding author (383 citations)

9. Cardona A., Saalfeld S., Schindelin J., Arganda-Carreras I., Preibisch S., Longair M., Tomancak P.,

Hartenstein V., Douglas R.J. (2012) TrakEM2 software for neural circuit reconstruction. PLoS ONE

7(6):38011 (36 citation)

10. Kalinka A.T., Tomancak P. (2012) The evolution of early animal embryos: conservation or

divergence? Trends in Ecology and Evolution 27(7), 385-393 (9 citation)

11. Kelava I., Reillo, I., Murayama A.Y., Kalinka A. T., Stenzel D., Tomancak P., Matsuzaki F., Lebrand C.,

Sasaki E., Schwamborn J.C., Okano H., Huttner W.B., Borrell V. (2012) Abundant Occurrence of

Basal Radial Glia in the Subventricular Zone of Embryonic Neocortex of a Lissencephalic Primate,

the Common Marmoset Callithrix jacchus Cereb. Cortex, 22(2), 469-481 (32 citations)

12. Mohammad S.U., Lee H.K., Preibisch S., Tomancak, P. (2011) Restoring uneven illumination in

selective plane illumination microscopy images. Microscopy and Microanalysis Jun 20:1-7.

http://arxiv.org/abs/1308.0730



http://arxiv.org/abs/1209.0968v1


13. Kalinka A.T., Tomancak P. (2011) linkcomm: an R package for the generation, visualization, and

analysis of link communities in networks of arbitrary size and type. Bioinformatics 27(14) 2011-2012

(22 citations)

14. Kalinka A.T., Varga K.M., Gerrard D.T., Preibisch S., Jarrells J., Corcoran D., Ohler

U., Bergman C.M., Tomancak P. (2010) Gene expression divergence recapitulates

the developmental hourglass model Nature 468, 811–814 cover story (83 citations)

Highlighted in:

Prud'homme B, Gompel N. (2010) Evolutionary biology: Genomic hourglass. Nature

468:768-9

Casci T. (2010) Development: Hourglass theory gets molecular approval. Nat Rev Genet.

2010

Faculty of 1000: 2011. F1000.com/7774958 (FFa 8)

International Press: Frankfurter Allgemeine Zeitung, Discovery News, MSNBC; Evolution blogs: Pharyngula,

Panda’s thumb, Why Evolution Is True; Czech newspapers: iDnes, Literarni Noviny, 21 stoleti

15. Cardona A., Saalfeld S., Preibisch S., Schmid B., Cheng A., Pulokas J., Tomancak P., Hartenstein V.

(2010) An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-

assisted serial section electron microscopy. PLoS Biology 8(10): e1000502 (83 citation)

Highlighted in:

News in Brief : Mapping microcircuitry in the fly brain Nature Methods 2010 7(12): 949

16. Manonmani A., Karthik J., Tomancak P., Ohler U. (2010) An alignment-free method to identify

candidate orthologous enhancers in multiple Drosophila genomes. Bioinformatics 26 (17): 2109-

2115. corresponding author (5 citations)

17. Preibisch S., Saalfeld S., Schindelin J., Tomancak P. (2010) Software for bead-based registration of

selective plane illumination microscopy data. Nature Methods 7:418-419 (64 citations)

18. Saalfeld S., Cardona A., Hartenstein, V., Tomancak P. (2010) As-rigid-as-possible 2d-mosaicking and

3d-registration of large serial section TEM datasets. Bioinformatics 26 (12): i57-i63, ISMB

Proceedings paper (25 citations)

19. Langer C.C.H., Ejsmont R.K., Schönbauer C., Schnorrer F., Tomancak P. (2010) In vivo RNAi Rescue

in Drosophila melanogaster with Genomic Transgenes from Drosophila pseudoobscura. PLoS One

5(1) e8928 (17 citation)

20. Rach E.A., Yuan H.Y., Majoros W.H., Tomancak P., Ohler U. (2009) Motif composition, conservation

and condition-specificity of single and alternative transcription start sites in the Drosophila

genome. Genome Biol. 2009;10(7):R73 (27 citations)

21. Ejsmont R.K., Sarov M., Winkler S., Lipinski K., Tomancak P. (2009) A toolkit for

high-throughput, cross-species gene engineering in Drosophila. Nature Methods

Jun; 6(6):435-7 cover story (46 citations)

22. Saalfeld S., Cardona A., Hartenstein V., Tomancak P. (2009) CATMAID:

Collaborative Annotation Toolkit for Massive Amounts of Image Data.

Bioinformatics Aug 1;25(15):1984-6 (25 citations)

23. Preibisch S., Saalfeld S., Tomancak P. (2009) Globally optimal stitching of tiled 3D

microscopic image acquisitions. Bioinformatics Jun 1;25(11):1463-5 (119 citations)

24. Quijano C., Tomancak P., Lopez-Marti J., Suyama M., Bork P., Milan M., Torrents D., Manzanares M.

(2008) Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.

Genome Biol. 9(12):R176. (10 citation)


25. Lécuyer E., Yoshida H., Parthasarathy N., Alm C., Babak T., Cerovina T., Hughes T.R., Tomancak P.,

Krause H.M. (2007) Global analysis of mRNA localization reveals a prominent role in organizing

cellular architecture and function. Cell Oct 5;131(1):174-87 cover story (348

citations)

Highlighted in:


Selected by Nature as Research Highlight of 2007

26. Magalhães T.R., Palmer J, Tomancak P, Pollard K.S. (2007) Transcriptional

control in embryonic Drosophila midline guidance assessed through a whole

genome approach. BMC Neurosci. Jul 31;8:59. (6 citations)

CONFERENCE PROCEEDINGS PAPERS

27. Preibisch S., Tomancak P., Saalfeld S. (2010) Into Imglib – Generic Image Processing in Java In

Proceedings of the ImageJ User and Developer Conference (3 citation)

28. Preibisch S., Saalfeld S., Rohlfing T., Tomancak P. (2009) Bead-based mosaicing of single plane

illumination microscopy images using geometric local descriptor matching Proceedings of SPIE,

SPIE, Bellingham, no. 72592S, pp. 1-10 (12 citations)

29. Preibisch S., Ejsmont R.K., Rohlfing T., Tomancak P. (2008) Towards digital representation of

Drosophila embryogenesis 5th IEEE International Symposium on Biomedical Imaging: From Nano to

Macro, IEEE Service Center, Piscataway, pp. 324-327, peer reviewed (4 citations)

30. Preibisch S., Rohlfing T., Hasak M.P., Tomancak P. (2008) Mosaicing of Single Plane Illumination

Microscopy Images Using Groupwise Registration and Fast Content-Based Image Fusion Proceedings of SPIE Medical Imaging 2008: Image Processing, SPIE, Bellingham, Wash., pp. 69140E-1-

69140E-8 (10 citations)

31. Saalfeld S., Tomancak P. (2008) Automatic landmark correspondence detection for ImageJ In

Proceedings of the ImageJ User and Developer Conference, 128–133, Luxembourg (2 citations)

32. Preibisch S., Saalfeld S., Tomancak P. (2008) Fast stitching of large 3d biological datasets In

Proceedings of the ImageJ User and Developer Conference, 134–139, Luxembourg (2 citation)

REVIEWS AND COMMENTARIES

33. Eliceiri K. V., Berthold M. R., Goldberg I. G., Ibanez L., Manjunath B. S., Martone M. E., Murphy R. F.,

Peng H., Plant A. L., Roysam B., Stuurmann N., Swedlow J.R., Tomancak P., Carpenter A. E. (2012)

Biological Imaging Software Tools Nature Methods 9(7), 697-710 (46 citations)

34. Cardona A., Tomancak P. (2012) Current challenges in open-source bioimage informatics Nature

Methods 9(7), 661-665 (15 citation)

35. Reynaud E., Tomancak P. (2010) The First Light Sheet Based Fluorescence Microscopy Workshop.

Biotechnology Journal Aug;5(8):798-804 (7 citations)

36. Tomancak P., Ohler U. (2010) Mapping the complexity of transcription control in higher eukaryotes

Genome Biol., 11, no. 4 (2 citation)

37. Walter T., Shattuck D.W., Baldock R., Bastin M., Carpenter A.E., Duce S., Ellenberg J., Fraser A.,

Hamilton N., Pieper S., Ragan M.A., Schneider J., Tomancak P., Hériché J-K. (2010) Visualization of

image data from cells to organisms. Nature Methods 7, S26 - S41 (122 citations)


38. Cardona A., Saalfeld S., Tomancak P., Hartenstein V. (2009) Drosophila Brain Development: Closing

the Gap between a Macroarchitectural and Microarchitectural Approach. Cold Spring Harb Symp

Quant Biol. Dec 22 (5 citations)

39. Lécuyer E., Tomancak P. (2008) Mapping the gene expression universe. Curr Opin Genet Dev.

Dec;18(6):506-12. (13 citations)

BOOK CHAPTERS

40. Ejsmont R.K., Bogdanzaliewa M., Lipinski K.A., Tomancak P. (2011) Production of fosmid genomic

libraries optimized for liquid culture Methods in Molecular Biology : Molecular Methods for

Evolutionary Studies Volume 772, Part 6, 423-443 (1 citation)

41. Ejsmont R.K., Ahlfeld P., Pozniakovsky A., Stewart F., Tomancak P., Sarov M. (2011) Engineering of

large genomic DNA transgenes for protein tagging in Drosophila by Red/ET recombineering Methods in Molecular Biology : Molecular Methods for Evolutionary Studies Volume 772, Part 6, 445-

458 (1 citation)

PUBLICATIONS DURING POSTDOC PERIOD: 2000 - 2005

42. Tomancak P., Berman B.P., Beaton A., Weiszmann R., Kwan E., Hartenstein V., Celniker S.E., Rubin

G.M. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis.

Genome Biol. 8(7):R145. (190 citations)

43. Aboobaker A.A., Tomancak P., Patel N., Rubin G.M., Lai E.C. (2005) Drosophila microRNAs exhibit

diverse spatial expression patterns during embryonic development. Proc Natl Acad Sci U S A. 2005

Dec 13;102(50):18017-22. (155 citations)

44. Lai E.C., Tomancak P., Williams R.W., Rubin G.M. (2003) Computational

identification of Drosophila microRNA genes. Genome Biol. 4(7):R42 (648

citations) co-first author

Highlighted in:

Julius Brennecke and Stephen M Cohen (2003) Towards a complete description of the

microRNA complement of animal genomes Genome Biology 4:228

45. Tomancak P., Beaton A., Weiszmann R., Kwan E., Shu S., Lewis S. E., Richards S.,

Ashburner M., Hartenstein V., Celniker S. E., Rubin G. M., (2002) Systematic

determination of patterns of gene expression during Drosophila embryogenesis.

Genome Biol. 3(12):R88 (440 citations)

Highlighted in:

Haiqiong Montalta-He and Heinrich Reichert (2003) Impressive expressions: developing a

systematic database of gene-expression patterns in Drosophila embryogenesis Genome

Biology 2003, 4:205

46. Berman B.P., Nibu Y., Pfeiffer B.D., Tomancak P., Celniker S.E., Levine M., Rubin G.M., Eisen M.B.

(2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules

involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A. Jan 22;99(2):757-

62. (541 citations)

Highlighted in:


PUBLICATIONS DURING PHD TRAINING: 1995 - 1999


47. Tomancak P., Piano F., Riechmann V., Gunsalus K.C., Kemphues K.J., Ephrussi A. (2000) A Drosophila

melanogaster homologue of Caenorhabditis elegans par-1 acts at an early step in embryonic-axis

formation. Nat Cell Biol. 2(7), 458-60. (142 citations)

Highlighted in: Jason Morris, Ruth Lehmann and Caryn Navarro (2000) PARallels in Axis Formation Science Vol. 288 no. 5472

pp. 1759-1760

48. Tomancak P., Guichet A., Zavorsky P., Ephrussi, A. (1998) Oocyte polarity depends on regulation of

gurken by Vasa. Development 125, 1723-1732. (149 citations)

49. Muckenthaler M., Gunkel N., Frishman D., Cyrklaff A., Tomancak P., Hentze M.W. (1998) Iron-

regulatory protein-1 (IRP-1) is highly conserved in two invertebrate species--characterization of IRP-1

homologues in Drosophila melanogaster and Caenorhabditis elegans. Eur J Biochem. Jun 1;254(2):230-7.

(42 citations)


ACADEMIC REFERENCES

Dr. Anne Ephrussi

Head of Developmental Biology Unit, EICAT Coordinator and Senior Scientist

EMBL Heidelberg

Meyerhofstraße 1, 69117 Heidelberg, Germany

Tel: +49 6221 387- 8429/8283

E-mail: [email protected]

Dr. Gerald M. Rubin

Vice President and Executive Director of Janelia Farm Research Campus

Janelia Farm Research Campus

19700 Helix Drive

Ashburn, VA 20147

Email: [email protected]

Dr. Eugene Myers

Janelia Farm Research Campus

19700 Helix Drive

Ashburn, VA 20147

Tel: 571.209.4153


Dr. Marino Zerial

Director

Max Planck Institute of Molecular Cell Biology and Genetics, MPI-CBG


01307 Dresden, Germany

Tel: +49-351-210-1100


Dr. Jonathon Howard

Director




Tel: +49-351-210-2500


Dr. Elisabeth Knust

Director




Tel: +49-351-210-2500








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