Abate-Pella D, Freund DM, Slovin JP, Hegeman AD, and Cohen JD (2017) An improved method for fast and selective separation of carotenoids by LC-MS, Journal of Chromatography B, Available online 28 September 2017, https://doi.org/10.1016/j.jchromb.2017.09.039 Abate-Pella D, Freund DM, Slovin JP, Hegeman AD, and Cohen JD An improved method for fast and selective separation of carotenoids by LC-MS. J Chromatography B 1067:34-37 (2017) Abd El-Rahim WM, Moawad H, Abdel Azeiz AZ, Sadowsky MJ. Optimization of conditions for decolorization of azo-based textile dyes by multiple fungal species. J Biotechnol. 2017 Oct 20;260:11-17. doi: 10.1016/j.jbiotec.2017.08.022. Epub 2017 Aug 30. Abudayyeh, OO., Gootenberg, JS., Essletzbichler, P., Han, S., Joung, J., Belanto, JJ., Verdine, V., Cox, DBT., Kellner, MJ., Regev, A., Lander, ES., Voytas, DF., Ting, AY., Zhang, F. (2017) RNA targeting with CRISPR-Cas13. Nature. [Epub ahead of print] Ahmed W, Staley C, Hamilton KA, Beale DJ, Sadowsky MJ, Toze S, Haas CN. Amplicon-based taxonomic characterization of bacteria in urban and peri-urban roof-harvested rainwater stored in tanks. Sci Total Environ. 2017 Jan 15;576:326-334. doi: 10.1016/j.scitotenv.2016.10.090. Albert FW†, Bloom JS†, Siegel J, Day L, and Kruglyak L Genetics of trans-regulatory variation in gene expression bioRxiv (2017) doi: https://doi.org/10.1101/208447 Preprint (not peer reviewed); currently under journal review Allen MF, Morrell PL, Rice CW, Vaux HJ, Dahm CN, Hernandez RR (2017) Food and nutrition security in the United States of America. Challenges and opportunities for this century. editors. Food and nutrition security and agriculture. Mexico City Anderson JE, RM Stupar (2017) Structural Variation and the Soybean Genome. The Soybean Genome pp. 57-72. Andrew, A., B.W. Perry, D.C. Card, D.R. Schield, R.P. Ruggiero, S.E. McGaugh, A. Choudhary, S. M. Secor, and T. A. Castoe. 2017. Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. BMC Genomics. 18(1): 338. DOI: 10.1186/s12864-017-3743-1 Angela K. Spartz, Vai S. Lor, Hong Ren, Neil E. Olszewski, Nathan D. Miller, Guosheng Wu, Edgar P. Spalding, and William M. Gray* (2017) Constitutive Expression of Arabidopsis SMALL AUXIN UP RNA19 (SAUR19) in Tomato Confers Auxin-Independent Hypocotyl elongation Published by www.plantphysiol.org Copyright © 2017 American Society of Plant Biologists.

AR Leydon, C Weinreb, E Venable, A Reinders, JM Ward, MA Johnson The molecular dialog between flowering plant reproductive partners defined by SNP-informed RNA-Sequencing (2017) The Plant Cell 29 (5), 984-1006 Aukema, K.G., D. Escalante, M. Maltby, A. Aksan, and L.P. Wackett (2017) In silico identification of bioremediation potential: carbamazepine and other recalcitrant personal care products. Environ. Sci. Technol. 51:880-888. Bailey, J.V., Flood, B.E.*, Ricci, E.*, Delherbe, N.*, (2017) Imaging of cellular oxidoreductase activity suggests mixotrophic metabolisms in Thiomargarita spp. mBio. v. 8, No. 5, mBio01263-17. Ballhorn D, Elias J.D., Balkan M.A., Fordyce R.F., P.G. Kennedy 2017. Colonization by nitrogen- fixing Frankia bacteria causes short-term increases in herbivore susceptibility in red alder (Alnus rubra) seedlings. Oecologia 184: 497-506. Baltes, NJ., Gil-Humanes, J. Voytas, DF. (2017) Genome Engineering and Agriculture: Opportunities and Challenges. Prog Mol Biol Transl Sci. 149:1-26. Bandillo NB, Anderson JE, Kantar MB, Stupar RM, Specht JE, Graef GL, Lorenz AJ. (2017) Dissecting the Genetic Basis of Local Adaptation in Soybean. Sci Rep (in press). Beale DJ, Crosswell J, Karpe AV, Ahmed W, Williams M, Morrison PD, Metcalfe S, Staley C, Sadowsky MJ, Palombo EA, Steven ADL. A multi-omics based ecological analysis of coastal marine sediments from Gladstone, in Australia's Central Queensland, and Heron Island, a nearby fringing platform reef. Sci Total Environ. 2017 Dec 31;609:842-853. doi: 10.1016/j.scitotenv.2017.07.184. Beale DJ, Karpe AV, Ahmed W, Cook S, Morrison PD, Staley C, Sadowsky MJ, Palombo EA. A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System. Int J Environ Res Public Health. 2017 Mar 14;14(3). pii: E303. doi: 10.3390/ijerph14030303. PubMed PMID: 28335448 Beier, S., A. Himmelbach, C. Colmsee, X-Q. Zhang, R. Barrero, Q. Zhang, L. Li, M. Bayer, D. Bolser, S. Taudien, M. Groth, M. Felder, A. Hastie, H. Šimková, H. Stańková, J. Vrána, S. Chan, M. Muñoz-Amatriaín, R. Ounit, S. Wanamaker, T. Schmutzer, L. Aliyeva-Schnorr, S. Grasso, J. Tanskanen, D. Sampath, D. Heavens, S. Cao, B. Chapman, F. Dai, Y. Han, S. Li, J. McCooke, C. Tan, S. Wang, S. Yin, G. Zhou, J.A. Poland, M. Bellgard, A. Houben, J. Doležel, S. Ayling, S. Lonardi, P. Langridge, G.J. Muehlbauer, P. Kersey, M.D. Clark, M. Caccamo, A.H. Schulman, M. Platzer, T.J. Close, M. Hansson, G. Zhang, I. Braumann, C. Li, R. Waugh, U. Scholz, N. Stein and M. Mascher. 2017. Construction of the map-based reference sequence of the barley (Hordeum vulgare L.) genome. Scientific Data 4:170044.

Benson, J., J. Jonathan Sakkos, A. Radian, L.P. Wackett, and A. Aksan (2017) Enhanced biodegradation of atrazine by bacteria encapsulated in organically modified silica gels. J. Colloid Interface Sci. 510:57-68. doi: 10.1016/j.jcis.2017.09.044 Bera A, Aukema K, Elias M, Wackett L. Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel. Scientific Reports . PMID: 28345631 Bera, A.K., K.G. Aukema, M. Elias, and L.P. Wackett (2017) Structure of the cyanuric acid hydrolase TrzD reveals product exit channel. Scientific Reports Mar 27; 7:45277. doi: 10.1038/srep45277 Berg, L., Miller, S. S., Dornbusch, M. R., and Samac, D. A. 2017. Pythium and Fusarium species causing seed rot and damping of alfalfa in Minnesota. Plant Dis. 101:1860-1867. Bergonzi C, Schwab M, Chabriere E, Elias M. Purification, kinetic characterization, crystallization and crystallographic analysis of the quorum quenching lactonase from Alicyclobacter acidoterrestris. Acta Cryst F. 73:476-480. PMID: 28777091 Bhatia SP, Smanski MJ, Voigt CA, Densmore DM (2017) Genetic design via combinatorial constraint specification. ACS Synth. Biol. doi:10.1021/acssynbio.7b00154 Blackmon, H. and Y. Brandvain. 2017. Long-Term fragility of Y chromosomes is dominated by short-term resolution of sexual antagonism. Genetics 207: 1621-1629 Boenisch, M.J., Broz, K.L., Purvine, S.O., Chrisler, W.B., Nicora, C.D., Connolly, L.R., Freitag, M., Baker, S.E., Kistler, H.C. 2017. Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis. Scientific Reports doi: 10.1038/srep44 296 Breuer R, A. Bandyopathy, S. O’Brien, A. Barnes, R.C. Hunter, W.S. Hu, G. Dunny. 2017. Stochasticity in the enterococcal sex pheromone response revealed by quantitative analysis of transcription in single cells. PLoS Genetics. e1006878. Briscoe Runquist, R.D., M.A. Geber, M. Pickett-Leonard†, & D.A. Moeller. 2017. Mating system evolution under strong pollen limitation: Evidence of disruptive selection through male and female fitness in Clarkia xantiana. American Naturalist, 189:549-563. Brohammer, A., T. Kono, N. Springer, S. E. McGaugh, C. Hirsch. The limited role of differential fractionation in genome content variation in maize (Zea mays L.) inbred lines. In Press. Plant Journal. Brohammer, A., T. Kono, N. Springer, S. McGaugh, C. Hirsch. 2017. Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. bioRxiv doi:10.1101/179119 (in press at The Plant Journal)

Brohammer, A.B., Kono, T.J.Y., Springer, N.M., McGaugh, S.E., and Hirsch, C.N. (2017). The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. Plant J. Brown CM, Staley C, Wang P, Dalzell B, Chun CL, Sadowsky MJ. A High-Throughput DNA-Sequencing Approach for Determining Sources of Fecal Bacteria in a Lake Superior Estuary. Environ Sci Technol. 2017 Aug 1;51(15):8263-8271. doi: 10.1021/acs.est.7b01353. Epub 2017 Jul 10. Buell, C.R., Voytas, D.F. (2017) Technology turbocharges functional genomics. The Plant Cell. 29(5). Bughardt LT, Guhlin J, Chun C, Liu J, Sadowsky MJ, Stupar RM, Young ND, Tiffin P (2017) Host-dependent transcriptome responses to symbiont in the Legume-Ensifer mutualism. Mol Ecol doi: 10.1111/mec.14285 Burch TR, Sadowsky MJ, LaPara TM. Effect of Different Treatment Technologies on the Fate of Antibiotic Resistance Genes and Class 1 Integrons when Residual Municipal Wastewater Solids are Applied to Soil. Environ Sci Technol. 2017 Nov 28. doi: 10.1021/acs.est.7b04760. Burghardt LT, Guhlin J, Chun C, Liu J, Sadowsky MJ, Stupar RM, Young ND, Tiffin P (2017) Host-dependent transcriptome responses to symbiont in the Legume- Ensifer mutualism. Molecular Ecology 26: 6122–6135. doi: 10.1111/mec.14285. Burghardt LT, Guhlin J, Chun CL, Liu J, Sadowsky MJ, Stupar RM, Young ND, Tiffin P. Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism. Mol Ecol. 2017 Nov;26(21):6122-6135. doi: 10.1111/mec.14285. Burghardt LT, ND Young, P Tiffin. 2017. A Guide to Genome-Wide Association Mapping in Plants, Current Protocols in Plant Biology. Invited paper. Burghardt, Liana, J. Guhlin, C. Chun, J. Liu, M. Sadowsky, R. Stupar, N. Young, Nevin, P. Tiffin. 2017. Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism. Molecular Ecology 26: 6122-6135. Burghardt, LT, Young ND, Tiffin P (2017) A guide to genome-wide association mapping in plants. Current Protocols in Plant Biology 2:22-38. doi: 10.1002/cppb.20041. Bursac, T., J.A. Gralnick and J. Gescher. 2017. Acetoin production via unbalanced fermentation in Shewanella oneidensis. Biotechnol Bioeng. 114(6):1283-1289. doi: 10.1002/bit.26243

Cermak, T., Curtin, S.J., Gill-Humanes, J., Cegan, R., Kono, T.J.Y., Konecna, E., Belanto, J.J., Starker, C.G., Mathre, J.W., Greenstein, R.L., Votas, D.F. (2017) A multi-purpose toolkit to enable advance genome engineering in plants. The Plant Cell. 29(5). Chacon J, Moebius W, Harcombe WR (2017) The spatial and metabolic basis of colony size variation. ISME. In press. Chan CH, Levar CE, Jiménez-Otero F, Bond DR. 2017. Genome scale mutational analysis of Geobacter sulfurreducens reveals distinct molecular mechanisms for respiration and sensing of poised electrodes versus Fe(III) oxides. J Bacteriol 199:e00340-17. https://doi.org/10.1128/JB.00340-17. Chen, J., Upadhyaya, N.M., Ortiz, D., Sperschneider, J., Li, F., Bouton, C., Breen, S., Dong, C., Xu, B., Zhang, X., Mago, R., Newell, K., Xia, X., Bernoux, M., Taylor, J.M., Steffenson, B., Jin, Y., Zhang, P., Kanyuka, K., Figueroa, M., Ellis, J.F., Park, R.F., Dodds, P.N. Somatic recombination in wheat stem rust leads to virulence for Ug99-effective Sr50 resistance. Science (In press, accepted 25 th Oct 2017). Chen, L., P. Zhang, Y. Fan, J. Huang, J. Yan, G.J. Muehlbauer, P.S. Schnable, M. Dai, and L. Li. 2017. Transposons modulate transcriptomic and phenotypic variation via the formation of circular RNAs in maize. New Phytology DOI: 10.1111/nph.14901. Christenson, J.K., J.R. Richman, M.R. Jensen, J.Y. Neufeld, C. M. Wilmot, L.P. Wackett (2017) β-Lactone synthetase found in olefin biosynthesis pathway. Biochemistry 56: 348- 351, doi: 10.1021/acs.biochem.6b01199 Christenson, J.K., M.R. Jensen, B. Goblirsch, F. Mohamed, W. Zhang, C.M. Wilmot, L.P. Wackett (2017) Active multi-enzyme assemblies for long-chain olefinic hydrocarbon biosynthesis. J. Bacteriol. 199(9): e00890-16. doi: 10.1128/JB.00890-16. Christenson, J.K., S.L. Robinson, T.A. Engel, J.E. Richman, A.N. Kim, L.P. Wackett (2017) β-Lactone decarboxylase: Function, mechanism, and linkage to class III haloalkane dehalogenases. Biochemistry 56(10):5278-5287. doi: 10.1021/acs.biochem.7b00667. Chun CL, Peller JR, Shively D, Byappanahalli MN, Whitman RL, Staley C, Zhang Q, Ishii S, Sadowsky MJ. Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes. Sci Total Environ. 2017 Jan 1;574:872-880. doi: 10.1016/j.scitotenv.

Chun, C.L., J.R. Peller, D. Shively, M.N. Byappanahalli, R.L. Whitman, C. Staley, Q. Zhang, S. Ishii, and M.J. Sadowsky.* 2017. Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes. Sci. Total Environ. 574: 872-880. Cline L.C., Schilling J.S., Menke J., Groenhof E., P.G. Kennedy. Ecological and functional effects of fungal endophytes on wood decomposition. Functional Ecology, in press. Cline L.C., Song Z., Al-Ghalith G., Knights D., P.G. Kennedy 2017. Moving beyond de novo clustering in fungal community ecology. New Phytologist 216: 629-634. Cline, L. Schilling, J.S.*, Menke, J., Fleischauer, E., Kennedy, P.G. (online first) Ecological and functional effects of fungal endophytes on wood decomposition. Functional Ecology 00:1-11. DOI: 10.1111/1365- 2435.12949 Coleman, D.R., Poudel, S., Hamilton T.L., Havig, J.R., Selensky, M., Shock, E.L., Boyd, E.S. Geobiological feedbacks and the evolution of thermoacidophiles. In press. The ISME Journal. (doi: 10.1038/ismej.2017.162) Crosby, C.H.*, Bailey, J.V., (2017) Experimental precipitation of apatite pseudofossils resembling fossil embryos, Geobiology. 2017;00:1–8. doi.org/10.1111/gbi.12264 Crosby, C.H.*, Bailey, J.V., (2017), An economical apparatus for the observation and harvesting of mineral precipitation experiments with light microscopy. Biogeosciences 14, 2151–2154. Curtin SJ, Tiffin P, Guhlin J, Trujillo D, Burghardt LT, Atkins P, Baltes NJ, Denny R, Voytas DF, Stupar RM, Young ND (2017) Validating GWAS candidates by characterizing genes that control quantitative variation in nodulation. Plant Physiology 173:921-931. doi: 10.1104/pp.16.01923. Curtin SJ, Tiffin P, Guhlin J, Trujillo D, Burghart L, Atkins P, Baltes NJ, Denny R, Voytas DF, Stupar RM, Young ND. (2017) Validating Genome-Wide Association candidates controlling quantitative variation in nodulation. Plant Physiol 173:921-931. Curtin SJ, Tiffin P, Guhlin J, Trujillo DI, Burghardt LT, Atkins P, Baltes NJ, Denny R, Voytas DF, Stupar RM, Young ND. (2017) Validating Genome-Wide Association candidates through quantitative variation in nodulation. Plant Physiol. 173(2):921-931. Curtin SJ, Xiong Y, Michno JM, Campbell BW, Stec AO, Cermak T, Starker C, Voytas DF, Eamens AL, Stupar RM. (2017) CRISPR/Cas9 and TALENs generate heritable mutations for genes

involved in small RNA processing of Glycine max and Medicago truncatula. Plant Biotechnol J doi: 10.1111/pbi.12857 Curtin SJ, Xiong Y, Michno JM, Campbell BW, Stec AO, Čermák T, Starker C, Voytas DF, Eamens AL, Stupar RM. (2017) CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula. Plant Biotechnology Journal. [Epub ahead of print] Curtin, SF 1 , P. Tiffin 1 , J. Guhlin, DI Truhillo, LT Burghardt, P Atkins, NJ Baltes, R Denny DF Vortas RM Stupar, ND Young. 2017. Validating Genome-Wide Association candidates through quantitative variation in nodulation. Plant Physiology. doi: http://dx.doi.org/10.1104/pp.16.01923 1 contributed equally to this work. Davison JR, Lohith KM, Wang X, Bobyk K, Mandadapu SR, Lee SL, Cencic R, Nelson J, Simpkins S, Frank KM, Pelletier J, Myers CL, Piotrowski J, Smith HE, Bewley CA (2017) A New Natural Product Analog of Blasticidin S Reveals Cellular Uptake Facilitated by the NorA Multidrug Transporter. Antimicrobial agents and chemotherapy 61. http://www.ncbi.nlm.nih.gov/pubmed/28373194 Ding, T., Diao, X., and D.J. Baumler. 2017. Microbial risk analysis of produce grown on a sustainable chicken production farming system. Food Science and Nutrition Technology. August 9; 3(2). Dobbels AA, Michno J, Campbell BW, Virdi KS, Stec AO, Muehlbauer GJ, Naeve SL, Stupar RM (2017) An induced chromosomal translocation in soybean disrupts a KASI ortholog and is associated with a high sucrose and low oil seed phenotype. G3 (Bethesda) 7:1215-1223. Dobbels, A.A., J.-M. Michno, B.W. Campbell, K.S. Virdi, G.J. Muehlbauer, S.L. Naeve, and R.M. Stupar. 2017. An induced chromosomal translocation in soybean disrupts a KAS 1 ortholog and is associated with a high sucrose and low oil seed phenotype. Genes/Genomes/Genetics 7:1215-1223. Douglas SM, Chubiz LM, Harcombe WR, Marx CJ (2017) Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation. PLoS One 12(5), e0174345 Dukowic-Schulze S § , Liu C, and Chen C (2017). Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction. Plant Cell Rep. Doi: https://doi.org/10.1007/s00299-017- 2222-0.

Elakhdar, A., Kumamaru, T., Smith, K. P., Brueggeman, R. S., & Capo-chichi, L. J. A. (2017). Genotype by Environment Interactions ( GEIs ) for Barley Grain Yield Under Salt Stress Condition. J. Crop Sci. Biotech, 2017(10), 193–204 Ellinger J, Schmidt-Dannert C. Construction of a BioBrick™ compatible vector system for Rhodococcus. Plasmid. 2017 Mar;90:1-4. PubMed PMID: 28130036. Escalante, D., K. Aukema, A. Aksan, and L.P. Wackett (2017) Simulation of the bottleneck controlling access into a Rieske active site: scalable method for the prediction of substrates of naphthalene 1,2-dioxygenase. J. Comp. Inf. Modeling 57:550-561. doi: 10.1021/acs.jcim.6b00469. Essarioui, A., LeBlanc, N., Kistler, H.C., Kinkel, L.L., 2017. Plant community richness mediates inhibitory interactions and resource competition between Streptomyces and Fusarium populations in the rhizosphere. Microbial Ecology, 1-11. Fang G, Wang W, Paunic V, Heydari H, Costanzo M, et al. Discovering genetic interactions bridging pathways in genome-wide association studies. bioRxiv 182741 (2017); https://doi.org/10.1101/182741. Fernandez C.F., Nguyen N.H., Stefanski A., Han Y., Hobbie S.E., Montgomery R.A., Peter B. Reich P. B., P.G. Kennedy 2017. Ectomycorrhizal fungal response to warming is linked to poor host performance at the boreal-temperate ecotone. Global Change Biology 23:1598-1609. Fernandez C.W., and P.G. Kennedy. Melanization of mycorrhizal fungal necromass structures microbial decomposer communities. Journal of Ecology, in press. Figueroa M., Hammond-Kosack, K., Solomon, P. 2017. A review of wheat diseases: a field perspective. Molecular Plant Pathology (In Press, accepted 22 nd Sep 2017) doi: 10.1111/mpp. Flynn J.M., C. Phan, R.C. Hunter. 2017. Genome-wide survey of Pseudomonas aeruginosa PA14 reveals a role for the glyoxylate pathway and extracellular proteases in the utilization of mucin. Infect Immun. Freeman, MF § , Helf, MJ, Bhushan, A, Morinaka, BI, Piel, J § (2017) “Seven enzymes create extraordinary molecular complexity in an uncultivated bacterium” Nat. Chem. 9: 387-395. [Research Highlight: Nat. Chem. Biol. 2017 13: 129.] [Leading Edge: Cell 2017 169: 373.] Freund DM, Hegeman AD (2017) Recent Advances in Stable Isotope-Enabled Mass Spectrometry-Based Plant Metabolomics, Current Opinion in Biotechnology, 43, 41-48. Freund DM, Martin AC, Cohen JD, and Hegeman AD (2017) Direct detection of surface localized specialized metabolites from Glycyrrhiza lepidota (American licorice) by leaf spray mass

spectrometry, Planta, Available online September 27, https://doi.org/10.1007/s00425-017-2782-9 Freund DM, Martin AC, Cohen JD, Hegeman AD Direct detection of surface localized specialized metabolites from Glycyrrhiza lepidota (American licorice) by leaf spray mass spectrometry. Planta (online: DOI 10.1007/s00425-017- 2782-9) (2017) Gage, J., D. Jarquin, M. Romay, A. Lorenz, E. Buckler, S. Kaeppler, N. Alkhalifah, M. Bohn, D. Campbell, J. Edwards, D. Ertl, S. Flint-Garcia, J. Gardiner, B. Good, C. Hirsch, J. Holland, D. Hooker, J. Knoll, J. Kolkman, G. Kruger, N. Lauter, C. Lawrence- Dill, E. Lee, J. Lynch, S. Murray, R. Nelson, J. Petzoldt, T. Rocheford, J. Schnable, P. Schnable, B. Scully, M. Smith, N. Springer, S. Srinivasan, R. Walton, T. Weldekidan, R. Wisser, W. Xu, J. Yu, N. de Leon. 2017. The effect of artificial selection on phenotypic plasticity in maize. Nature Communications (in press). Gage, J.L. et al. (2017). The effect of artificial selection on phenotypic plasticity in maize. Nat. Commun. 8: 1348. Gao, L., M.N. Rouse, P.D. Mihalyov, P. Bulli, M.O. Pumphrey, and J.A. Anderson. 2017. Genetic characterization of stem rust resistance in a global spring wheat germplasm collection. Crop Sci. 57:2575-2589. doi: 10.2135/cropsci2017.03.0159. Gil-Humanes. J., Wang, Y., Liang, Z., Shan, Q., Ozuna, CV., Sánchez-León, S., Baltes, NJ., Starker, C., Barro, F., Gao, C., Voytas, DF. (2017) High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. Plant Journal. 89, 1251–1262. Gordon, S.P., Contreras-Moreira, B., Woods, D.P., Des Marais, D., Burgess, D., Shu., S., Stritt , C., Roulin, A., Schackwitz, W., Tyler, L., Martin, J., Lipzen, A., Dochy, N., Phillips, J., Barry, K., Geuten, K., Budak, H., ThoJuenger, T.E., Amasino, R., Caicedo, A.L., Goodstein, D., Davidson, P., Mur, L., Figueroa, M., Freeling, M., Catalan, P., Vogel, J.P. 2017. Extensive gene content variation in the Brachypodium distachyon pan genome correlates with population structure. Nature Communications (In press, accepted 3 rd Oct 2017). Gravina F, Dobrzanski T, Olchanheski LR, Galvão CW, Reche PM, Pileggi SA, Azevedo RA, Sadowsky MJ, Pileggi M. Metabolic Interference of sod gene mutations on catalase activity in Escherichia coli exposed to Gramoxone® (paraquat) herbicide. Ecotoxicol Environ Saf. 2017 May;139:89-96. doi: 10.1016/j.ecoenv.2017.01.027. Grev, A. M., Wells, M. S., Samac, D. A., Martinson, K. L., and Sheaffer, C. C. 2017. Yield and forage nutritive value of reduced lignin alfalfa. Agronomy J. 109:2749-2761. Gross, J. B., J. Weagley, B.A. Stahl, L. Ma, L. Espinasa, S.E. McGaugh. 2017. A local duplication of Melanocortin receptor 1 locus in Astyanax. Genome. Ecological and Evolutionary Genomics Special Issue. DOI: 10.1139/gen-2017-0049

Grossenbacher, D. L., Y. Brandvain, ..., B. Igic, J. W. Busch, S Kalisz, and E. E. Goldberg. 2017. Self-compatibility is over-represented on islands. New Phytologist 215: 469–478. Grotewold, E. and Springer, N.M. (2017). News from the plant world: Listening to transcription. Biochim. Biophys. Acta 1860: 1–2. Guendouze A, Plener L, Bzdrenga J, Jacquet P, Remy B, Elias M, Lavigne J-P, Daudé D, Chabrière E. Effect of quorum quenching lactonase in clinical isolates of Pseudomonas aeruginosa and comparison with quorum sensing inhibitors. Frontiers in Microbiology. PMID: 28261183 Guhlin J, Silverstein KAT, Zhou P, Tiffin P, Young ND (2017) ODG: Omics database generator – a tool for generating, querying, and analyzing multi-omics databases to facilitate biological understanding. BMC Bioinformatics 18: 367. Doi 10.1186/s12859-017- 1777-7. Guhlin J, Silverstein KAT, Zhou P, Tiffin P, Young ND. ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding. BMC Bioinformatics. 2017 Aug 10;18(1):367. doi: 10.1186/s12859-017-1777-7. PMID:28797229. Guhlin, J., KAT Silverstein, P Zhou, P Tiffin, ND Young. 2017. ODG: Omics database generator-a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding. BMC bioinformatics 18: 367. Gutierrez-Gonzalez, J.J., Garvin, D.F. 2017. De novo transciptome assembly in polyploid species. In:Gasparis, S. Oat: Methods and Protocols. Vol 1536. New York, NY: Springer. p. 209-221. Hager, S.E., Jensen, E., Johnson, T.J., and Mitchell, D. (2017) Adaptation of Escherichia coli to antibiotic cycling via single nucleotide polymorphisms. American Journal of Undergraduate Research 14:25-34. Hamilton, T.L., Welander, P., Albrecht, H.L., Fulton, J.M., Schaperdoth, I., Bird, L., Summons, R.,Freeman, K.H., Macalady, J.L. Microbial communities and organic biomarkers in a Proterozoic- analog sinkhole environment. Geobiology. 15: 784-797. (doi: 10.1111/gbi.12252) Hart T, Tong AHY, Chan K, Van Leeuwen J, Seetharaman A, Aregger M, Chandrashekhar M, Hustedt N, Seth S, Noonan A, Habsid A, Sizova O, Nedyalkova L, Climie R, Tworzyanski L, Lawson K, Sartori MA, Alibeh S, Tieu D, Masud S, Mero P, Weiss A, Brown KR, Usaj M, Billmann M, Rahman M, Constanzo M, Myers CL, Andrews BJ, Boone C, Durocher D, Moffat J (2017) Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens. G3 (Bethesda) 7:2719-2727. http://www.ncbi.nlm.nih.gov/pubmed/28655737

Hatsugai, N., Igarashi, D., Mase, K., Lu, Y., Tsuda, Y., Chakravarthy, S., Wei, H.-L., Foley, J. W., Collmer, A., Glazebrook, J., and Katagiri, F. (2017) “A plant effector-triggered immunity signaling sector is inhibited by pattern-triggered immunity” EMBO J 36, 2758- 2769. Hatsugai, N., Igarashi, D., Mase, K., Lu, Y., Tsuda, Y., Chakravarthy, S., Wei, H.-L., Foley J.W., Collmer, A., Glazebrook, J., and Katagiri, F. A plant effector‐triggered immunity signaling sector is inhibited by pattern‐triggered immunity. EMBO J. 36: 2758- 2769 DOI 10.15252/embj.201796529 (2017). He Y = , Wang M = , Dukowic-Schulze S §,= , Zhou A, Tiang CL, Shilo S, Sidhu GK, Eichten S, Bradbury P, Springer NM, Buckler ES, Levy AA, Sun Q, Pillardy J, Kianian PMA, Kianian SF, Chen C, and Pawlowski WP (2017). Genomic features shaping the landscape of meiotic double-strand- break hotspots in maize. PNAS. 114 (46): 12231-12236. Doi: 10.1073/pnas.1713225114. Heinsch SC, Otto-Hanson L, Hsu SY, Kinkel L, Smanski MJ (2017) Genome sequences for Streptomyces spp. isolated from disease suppressive soils and long-term ecological research sites. ASM Genome Announcements. 5:e00493-17. Hillmer, R. A., Tsuda, K., Rallapalli, G., Asai, S., Truman, W., Papke, M. D., Sakakibara, H., Jones, J. D. G., Myers, C. L., and Katagiri, F. (2017) “The Highly Buffered Arabidopsis Immune Signaling Network Conceals the Functions of its Components” PLOS Genet 13, e1006639. http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006639 Hirsch C, Springer N. 2017. Transposable element influences on gene expression in plants. Biochimica et Biophysica Acta – Gene Regulatory Mechanisms. 1860(1): 157-165. Hirsch, C.D. and Springer, N.M. (2017). Transposable element influences on gene expression in plants. Biochim. Biophys. Acta 1860: 157–165. Holme, IB., Wendt, T., Gil-Humanes, J., Deleuran, LC., Starker, CG., Voytas, DF., Brinch-Pedersen, H. (2017) Evaluation of the mature grain phytase candidate HvPAPhy_a gene in barley (Hordeum vulgare L.) using CRISPR/Cas9 and TALENs. Plant Mol Biol. [Epub ahead of print] Howard W. Rines, Marisa E. Miller, Martin Carson, Shiaoman Chao, Tyler Tiede, Jochum Wiersma, Shahryar F. Kianian . 2017 Identification, introgression, and molecular marker genetic analysis and selection of a highly effective novel oat crown rust resistance from diploid oat, Avena strigose. Theoret. Appl. Genetics DOI: 10.1007/s00122-017- 3031-0 Hu, W., Samac, D. A., Liu, X., and Chen, S. 2017. Microbial communities in the cysts of soybean cyst nematode affected by tillage and biocide in a suppressive soil. Appl. Soil Ecol. 119:396-406.

Hummel AW, Chauhan RD, Cermak T, Mutka AM, Vijayaraghavan A, Boyher A, Starker CG, Bart R, Voytas DF, Taylor NJ. (2017) Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava. Plant Biotechnol J. [Epub ahead of print] Hwang N, Eom T, Gupta SK, Jeong SY, Jeong DY, Kim YS, Lee JH, Sadowsky MJ, Unno T. Genes and Gut Bacteria Involved in Luminal Butyrate Reduction Caused by Diet and Loperamide. Genes (Basel). 2017 Nov 28;8(12). pii: E350. doi: 10.3390/genes8120350. Ishii, S.,* N. Ashida, H. Ohno, T. Segawa, S. Yabe, S. Otsuka, A. Yokota, and K. Senoo. 2017. Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov. Intl. J. Syst. Evol. Microbiol. 67: 1841-1848. Ishimaru, C. A., T.A. Lansdell, J. Clardy, B. Duffy and T.H.M. Smits. 2017. The histidine- reversible antibiotic Herbicolin O produced by Pantoea vagans C9-1 is Pantocin A. Journal of Plant Pathology 99 (Special issue):91-97 DOI: 10.4454/jpp.v99i0.3910 Ito, T., M. Kitajima, T. Kato, S. Ishii, T. Segawa, S. Okabe, and D. Sano.* 2017. Target virus log10 reduction values determined for two reclaimed wastewater irrigation scenarios in Japan based on tolerable annual disease burden. Water Res. 125: 438-448. Jacquet P, Hiblot J, Daude D, Bergonzi C, Gotthard G, Armstrong N, Chabriere E, Elias M. Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase. Scientific Reports. 7:16745. PMID: 29196634 Jahansouz C, Staley C, Bernlohr DA, Sadowsky MJ, Khoruts A, Ikramuddin S. Sleeve gastrectomy drives persistent shifts in the gut microbiome. Surg Obes Relat Dis. 2017 Jun;13(6):916-924. doi: 10.1016/j.soard.2017.01.003. Jang, J., H.-G. Hur, M.J. Sadowsky, M.N. Byappanahalli, T. Yan, and S. Ishii.* 2017. Environmental Escherichia coli: implication for water quality and human health. J. Appl. Microbiol. 123: 570-581. Jaumann, S. and E. C. Snell-Rood. 2017. Tradeoffs between fecundity and choosiness in ovipositing butterflies. Animal Behaviour 123: 433-440. Jaumann, S. and E. Snell-Rood. 2017. Butterflies do not alter conspecific avoidance in response to variation in density. Integrative and Comparative Biology. Jelinski, N.A., Broz, K., Jonkers, W., Ma, L.-J., Kistler, H.C. 2017. Effector gene suites in some soil isolates of Fusarium oxysporum are not sufficient predictors of vascular wilt in tomato. Phytopathology 107: 842-851.

Jensen, MR, B.R. Goblirsch, J.K. Christenson, M. Esler, F.A. Mohamed, L.P. Wackett, and C.M. Wilmot (2017) OleA Glu117 is key to condensation of two fatty-acyl coenzyme A substrates in long-chain olefin biosynthesis. Biochem. J. Oct 12. pii: BCJ20170642. doi: 10.1042/BCJ20170642. Jiang, Y., Wang, X., Yu, X., Zhao, X., Luo, N., Pei, Z., Liu, H., Garvin, D.F. 2017. Quantitative trait loci associated with drought tolerance in Brachypodium distachyon. Frontiers in Plant Science 8:1-11. Jiao, Y. et al. (2017). Improved maize reference genome with single-molecule technologies. Nature 546: 524–527. JL Bowman, T Kohchi, KT Yamato, J Jenkins, S Shu, K Ishizaki, Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome (2017) ... Cell 171 (2), 287-304. e15 Johnson JR, Johnston BD, Delavari P, Thuras P, Clabots C, Sadowsky MJ. Phylogenetic Backgrounds and Virulence-Associated Traits of Escherichia coli Isolates from Surface Waters and Diverse Animals in Minnesota and Wisconsin. Appl Environ Microbiol. 2017 Dec 1;83(24). pii: e01329-17. doi: 10.1128/AEM.01329-17. Jones DS, Lapakko KA, Wenz ZJ, Olson MC, Roepke EW, Sadowsky MJ, Novak PJ, Bailey JV. Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA. Appl Environ Microbiol. 2017 Aug 1;83(16). pii: e00909-17. doi: 10.1128/AEM.00909-17. Jones, D.S.*, Lapakko, K.A., Wenz, Z.J., Olson, M.C., Roepke, E.W., Sadowsky, M.J., Novak, P.J., Bailey, J.V., (2017) Novel microbial assemblages dominate weathered sulfide-bearing rock from copper-nickel deposits in the Duluth Complex, Minnesota, USA. Applied and Environmental Microbiology. v.83, no.16. Jones, D.S.*, Roepke, E.W., Hua, A.*, Flood , B.E.*, and Bailey, J.V., (2017) Complete genome sequence of Sulfuriferula sp. str. AH1, a sulfur-oxidizing autotroph isolated from weathered sulfide-bearing mine tailings from the Duluth Complex in Minnesota. ASM genome announcements. v. 5, no. 32. Kanamori, H., Parobek, C.M., Juliano, J.J., Johnson, J.R., Johnston, B.D., Johnson, T.J., Weber, D.J., Rutala, W.A., and Anderson, D.J. (2017) Genomic analysis of multidrug-resistant Escherichia coli from North Carolina community hospitals: ongoing circulation of CTX-M- producing ST131-H30Rx and ST131-H30R1 strains. Antimicrobial Agents and Chemotherapy AAC.00912-17. Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, Khoruts A, Geis E, Maldonado J, McDonough-Means S, Pollard EL, Roux S, Sadowsky MJ, Lipson KS, Sullivan MB, Caporaso JG, Krajmalnik-Brown R. Microbiota Transfer Therapy alters gut ecosystem and improves

gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017 Jan 23;5(1):10. doi: 10.1186/s40168-016- 0225-7 Katagiri, F. (2017) “Network Reconstitution for Quantitative Subnetwork Interaction Analysis” in Methods Mol Biol, vol 1578, pp. 223-231. Katerndahl CD, Heltemes-Harris LM, Willette MJ, Henzler CM, Frietze S, Yang R, Schjerven H, Silverstein KAT, Ramsey LB, Hubbard G, Wells AD, Kuiper RP, Scheijen B, van Leeuwen FN, Müschen M, Kornblau SM, Farrar MA. Antagonism of B cell enhancer networks by STAT5 drives leukemia and poor patient survival. Nat Immunol. 2017 Apr 3. doi: 10.1038/ni.3716. PMID:28369050. Kennedy P.G., L.C. Cline, Z. Song. Probing promise versus performance in longer read fungal metabarcoding. New Phytologist, In press. Kisiela, D.I., Radey, M., Paul, S., Polukhina, K., Tchesnokova, V., Shevchenko, S., Chan, D., Aziz, M., Johnson, T.J., Price, L.B., Johnson, J.R., and Sokurenko, E.V. (2017) Inactivation of transcriptional regulators during within-household evolution of Escherichia coli. Journal of Bacteriology 199:e0036-17. Kohli M, Ho Y, Hillman DW, Van Etten JL, Henzler C, Yang R, Sperger JM, Li Y, Tseng E, Hon T, Clark T, Tan W, Carlson RE, Wang L, Sicotte H, Thai H, Jimenez R, Huang H, Vedell PT, Eckloff BW, Quevedo JF, Pitot HC, Costello BA, Jen J, Wieben ED, Silverstein KAT, Lang JM, Wang L, Dehm SM. Androgen Receptor Variant AR-V9 Is Coexpressed with AR-V7 in Prostate Cancer Metastases and Predicts Abiraterone Resistance. Clin Cancer Res. 2017 May 4. doi: 10.1158/1078-0432.CCR-17-0017. PMID:28473535. Kono TJY, Lei L, Shih CH, Hoffman PJ, Morrell PL, Fay JC (2017) Comparative genomics approaches accurately predict deleterious variants in plants. bioRxiv Le Signor C, Aimé D, Bordat A, Belghazi M, Labas V, Gouzy J, Tiffin P, Young ND, Prosperi J-M, Leprince O, Thompson RD, Buitink J, Burstin J, Gallardo K (2017) Genome-wide association studies with proteomics data reveal genes important for synthesis, transport and packaging of globulins in legume seeds. New Phytologist 214:1597-1613. doi: 10.1111/nph.14500. LeBlanc, N., Kinkel, L.L., Kistler, H.C., 2017. Plant diversity and plant identity influence Fusarium communities in soil. Mycologia 109:128-139. doi: 10.1080/00275514.2017.1281697. Li, Q., Hermanson, P.J., and Springer, N.M. (2018). Detection of DNA Methylation by Whole-Genome Bisulfite Sequencing. Methods Mol. Biol. 1676: 185–196. Li, R., P. Russell, D. Groth-Helms, S. Zhang, B. Davenport, K. Schuetz, C. A. Ishimaru. 201X. Development of a recombinase-polymerase amplification assay for Clavibacter michiganensis subsp. sepedonicus Phytopathology 2017 APS Annual Meeting San Antonia, TX

Li, X., H. Michlmayr, W. Schweiger, A. Malachova, S. Shin, Y. Huang, Y. Dong, G. Wiesenberger, S. McCormick, M. Lemmens, P. Fruhmann, C. Hametner, F. Berthiller, G. Adam and G.J. Muehlbauer. 2017. A barley UDP- glucosyltransferase inactivates nivalenol and provides Fusarium head blight resistance in transgenic wheat. J. Exp. Bot. 68:2187-2197. Li, Z., L. Coffey, J. Garfin, N. Miller, M. White, E. Spalding, N. de Leon, S. Kaeppler, P. Schnable, N. Springer, C. Hirsch. 2017. Genotype-by-environment interactions affecting heterosis in maize. bioRxiv doi:10.1101/131342 (accepted pending revisions at PLoS One) Liska, F., Landa, V., Zidek, V., Mlejnek, P., Silhavy, J., Simakova, M., Strnad, H., Trnovska, J., Skop, V., Kazdova, L., Strarker, C.G., Voytas, D.F., Izsvak, Z., Mancini, M., Seda, O., Kren, V., Pravenec, M. (2017) Downregulation of Plzf gene ameliorates metabolic and cardiac traits in the spontaneously hypertensive rat. Hypertension. 69(6):1084-1091. Liu Q, Zhou Y, Morrell PL, Gaut BS (2017) Deleterious variants in Asian rice and the potential cost of domestication. Mol Biol Evol 34: 908-924. Lofgren, L., Riddle, J., Dong, Y. Kuhnem, P.R., Cummings, J.A., Del Ponte, E.M., Bergstrom, G.C., Kistler, H.C. 2017. A high proportion of NX-2 genotype strains are found among Fusarium graminearum isolates from northeastern New York State. European Journal of Plant Pathology doi.org/10.1007/s10658-017- 1314-6 Lofgren, L.A., LeBlanc, N.R., Certano, A.K., Nachtigall, J., LaBine, K.M., Riddle, J., Broz, K., Dong, Y., Bethan, B., Kafer, C.W., Kistler, H.C. 2017. Fusarium graminearum: Pathogen or endophyte of North American grasses? New Phytologist doi: 10.1111/nph.14894. Lopez-Nievesa, S., Y. Yang, A. Timoneda, M.-M. Wang, T. Feng, S.A. Smith, S.F. Brockington, and H.A. Maeda. Relaxation of tyrosine pathway regulation underlies the evolution of betalain pigmentation in Caryophyllales. New Phytologist. doi: 10.1111/nph.14822 Lowder LG, Zhou J, Zhang Y, Malzahn A, Zhong Z, Hsieh TF, Voytas DF, Zhang Y, Qi Y. (2017) Robust transcriptional activation in plants using multiplexed CRISPR-Act2.0 and mTALE-Act systems. Mol Plant. pii: S1674-2052. Lu, Y., Ishimaru, C., Glazebrook, J., and Samac, D.A. Comparative genomic analyses of Clavibacter michiganensis subsp. insidiosus and pathogenicity on Medicago truncatula. Phytopathology, https://doi.org/10.1094/PHYTO-05- 17-0171- R. in press. Lu, Y., Ishimaru, C.A. Glazebrook, J., and Samac, D. A. 2017. Comparative genomic analyses of Clavibacter michiganensis subsp. insidiosus and aggressiveness on Medicago truncatula Phytopathology. https://doi.org/10.1094/PHYTO-05- 17-0171- R.

Luca F., S. S. Kupfer, D. Knights, A. Khoruts, and R. Blekhman*. Functional genomics of host-microbiome interactions in humans. In press, Trends in Genetics Lucas S., R. Yang, J. Dunitz, H. Boyer, R.C. Hunter. 2017. 16S rRNA gene sequencing reveals site specific signatures in the upper and lower airways of cystic fibrosis patients. Journal of Cystic Fibrosis. doi:j10.1016/j.jcf.2017.08.007 Lynch J.^, K. Tang^, S. Priya^, J. Sands^, M. Sands^, E. Tang^, S. Mukherjee, D. Knights, and R. Blekhman*. HOMINID: A framework for identifying associations between host genetic variation and microbiome composition. Accepted, GigaScience. Mascher, M., H. Gundlach, A. Himmelbach, S. Beier, S. Twardziok, T. Wicker, V. Radchuk, C. Dockter, P. Hedley, J. Russell, M. Bayer, L. Ramsay, P. Flores, H. Liu, G. Haberer, X-Q. Zhang, Q. Zhang, R. Barrero, L. Li, S. Taudien, M. Groth, M. Felder, A. Hastie, H. Šimková, H. Stańková, J. Vrána, S. Chan, M. Muñoz- Amatriaín, R. Ounit, S. Wanamaker, D. Bolser, C. Colmsee, T. Schmutzer, L. Aliyeva-Schnorr, S. Grasso, J. Tanskanen, A. Chailyan, D. Sampath, D. Heavens, S. Cao, B. Chapman, F. Dai, Y. Han, S. Li, J. McCooke, C. Tan, P. Wang, S. Wang, S. Yin, G. Zhou, J.A. Poland, M. Bellgard, L. Borisjuk, A. Houben, J. Doležel, S. Ayling, S. Lonardi, P. Kersey, P. Langridge, G.J. Muehlbauer, M.D. Clark, M. Caccamo, A.H. Schulman, K.F.X. Mayer, M. Platzer, T.J. Close, U. Scholz, M. Hansson, G. Zhang, I. Braumann, M. Spannagl, C. Li, R. Waugh and N. Stein. 2017. A chromosome conformation capture ordered sequence of the barley genome. Nature 544:427-433. Maselko M, Heinsch SC, Chacon J, Harcombe W, Smanski MJ (2017) Engineering species-like barriers to sexual reproduction. Nat. Comm. 8:883 doi:10.1038/s41467-017- 01007-3 Maselko M, Heinsh SC, Chacon JM, Harcombe WR, Smanski MJ (2017) Engineering species-like barriers to sexual reproduction. Nature Communications. 8: 883 Mc Nally, R. R., B. T. Webster, R. D. Curland, C. A. Ishimaru, D. K. Malvick. 201X. Interactions between diverse Clavibacter michiganensis subsp. nebraskensis isolates and maize inbred and hybrids influence severity of Goss’s wilt. Phytopathology 2017 APS Annual Meeting San Antonia, TX Mc Nally, R. R., D. K. Malvick, C. A. Ishimaru. 201X. Comparative genomic analysis of Clavibacter michiganensis subsp. nebraskensis isolates representing naturally occurring virulence diversity. Phytopathology 2017 APS Annual Meeting San Antonia, TX McGaugh, S.E. and T. Schwartz. 2017. Here and there, but not everywhere: the repeated loss of uncoupling protein 1 in amniotes. Biology Letters. 13: 20160749. DOI:10.1098/rsbl.2016.0749 McNally, R. R., R. D. Curland, B. T. Webster, A. P. Robinson, and C. A. Ishimaru. 2017. First report of Pectobacterium carotovorum subsp. brasiliensis causing blackleg and stem rot in

commercial and seed potato fields in Minnesota and North Dakota. Plant Disease 101:1672. https://doi.org/10.1094/PDIS-04- 17-0605- PDN McNally, R. R., R. D. Curland, B. T. Webster, A. P. Robinson, and C. A. Ishimaru. 2017. First report of blackleg and tuber soft rot of potato caused by Pectobacterium parmentieri in Minnesota and North Dakota. Plant Disease 101:2144 https://doi.org/10.1094/PDIS-04- 17-0608- PDN McNally, R. R., R. D. Curland, B. T. Webster, A. P. Robinson, and C. A. Ishimaru. 2017. First report of stem rot on potato caused by Dickeya chrysanthemi in Minnesota. Plant Disease (in press) https://doi.org/10.1094/PDIS-07- 17-0966- PDN Mechanic LE, Lindstrom S, Daily KM, Sieberts SK, Amos CI, Chen HS, Cox NJ, Dathe M, Feuer EJ, Guertin MJ, Hoffman J, Liu Y, Moore JH, Myers CL, Ritchie MD, Schildkraut J, Schumacher F, Witte JS, Wang W, Williams SM, Gillanders EM (2017) Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology. PLoS genetics 13:e1006945. http://www.ncbi.nlm.nih.gov/pubmed/28957327 Mei, W., Liu, S., Schnable, J.C., Yeh, C.-T., Springer, N.M., Schnable, P.S., and Barbazuk, W.B. (2017). A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize. Front. Plant Sci. 8: 694. Meyers-Wallen VN, Boyko AR, Danko CG, Grenier JK, Mezey JG, Hayward JJ, Shannon LM, Gao C, Shafquat A, Rice EJ, Pujar S, Eggers S, Ohnesorg T, Sinclair AH (2017) XX Disorder of Sex Development is associated with an insertion on chromosome 9 and downregulation of RSPO1 in dogs (Canis lupus familiaris). PLoS One. 12(10): e0186331. Michelmore, R., Coaker, G., …, Katagiri, F., et al. (2017) “Foundational and Translational Research Opportunities to Improve Plant Health” Mol Microbe Interact 30, 515-516. Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu Junqi, Stupar R, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT (2017) Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics 18:541. doi: 10.1186/s12864-017- 3927-8. Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT (2017) Hybrid Assembly with Long and Short Reads Improves Discovery of Gene Family Expansions. BMC Genomics 18:541. Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT. Hybrid assembly with long and short reads improves discovery of gene family

expansions. BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8. PMID:28724409. Miller ME, Zhang Y, Omidvar V, Sperschneider J, Schwessinger B, Raley C, Palmer JM, Garnica D, Upadhyaya N, Rathjen J, Taylor J, Park RF, Dodds PN, Hirsch CD, Kianian SF, Figueroa M. 2017. De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronate f. sp. avenae, the causal agent of oat crown rust. bioRxiv, 179226. doi: https://doi.org/10.1101/179226. Miller, JR, P.hou, J. Mudge, J. Gurtowski, H. Lee, T. Ramaraj, BP Walenz, J Liu, R Stupar, R Denny, L Song, N Singh, LG. Maron, SR McCouch, WR McCombie, MC. Schatz, P Tiffin, ND. Young, KAT Silverstein. 2017. Hybrid Assembly with Long and Short Reads Improves Discovery of Gene Family Expansion. BMC Genomics. 18: 541 Miller, M.E., Zhang, Y., Omidvar, V., Sperschneider, J., Schwessinger, B., Raley, C., Palmer, J.M., Garnica, D., Upadhyayah, N., Rathjen,J., Taylor, J.M., Park, R.F., Dodds, P.N., Hirsch, C.D., Kianian, S.F., Figueroa, M. 2017. De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust. mBio (Accepted 30th Oct 2017) Milne RJ, A Reinders, JM Ward, CE Offler, JW Patrick, CPL Grof Contribution of sucrose transporters to phloem unloading within Sorghum bicolor stem internodes (2017) Plant Signaling & Behavior, 1-3 Mitchell, T., Myers, E.M. Tucker, J., and S.E. McGaugh. 2017. Righting performance does not predict survival: a field experiment with hatchling Trachemys scripta. Biological Journal of the Linnaean Society B. 120 (3): 553-562. DOI: 10.1111/bij.12896 Moeller, D.A., R.D. Briscoe Runquist, A.M. Moe, M.A. Geber, C. Goodwillie, P.-O. Cheptou, C.G. Eckert, E. Elle, M.O. Johnston, S. Kalisz, R.H. Ree, R.D. Sargent, M. Vallejo-Marin, & A.A. Winn. 2017. Global biogeography of mating system variation in seed plants. Ecology Letters, 20:375- 384 Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J (2017) Strategies for utilizing bionano and dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. BMC Genomics 18:587 doi: 10.1186/s12864-017- 3971-4. Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J. Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017- 3971-4.

Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J. (2017) Strategies for Optimizing BioNano and Dovetail Explored Through a Second Reference Quality Assembly for the Legume Model, Medicago truncatula. BMC Genomics 18:578. Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J. Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017-3971-4. PMID:28778149. Moll, KM, P Zhou, T Ramaraj, D Fajardo, NP.Devitt; MJ. Sadowsky, RM. Stupar, P Tiffin, JR. Miller,; ND. Young, KAT Silverstein, J Mudge, 2017. Strategies for Optimizing BioNano and Dovetail Explored Through a Second Reference Quality Assembly for the Legume Model, Medicago truncatula. BMC Genomics. 18: 578 Morinaka, BI, Verest, M, Freeman, MF, Gugger, M, Piel, J (2017) “An orthogonal D 2 O-based induction system provides insights into D-amino acid pattern formation by radical S- adenosylmethionine peptide epimerases”, Angew. Chem. Int. Ed. Engl. 56: 762-766. Moyers BT, Morrell PL, McKay JK (2017) Genetic costs of domestication and improvement. Journal of Heredity Nallu, S, J Hill, K Don, C Sahagun, W Zhang, C Meslin, E Snell-Rood et al. The Molecular Genetic Basis of Herbivory between Butterflies and their Host-Plants. In revision, and bioRxiv, 154799, 2017 Nazareno, E., Smith, M, Park, R.F., Shahryar, K.F., Figueroa, M. 2017. Puccinia coronata f. sp. avenae: a threat to global oat production. Molecular Plant Pathology (In Press, accepted 24th Aug 2017) doi: 10.1111/mpp.12608. Nelson J, Karempelis P, J Dunitz, R Hunter, H Boyer. 2017. Pulmonary aspiration of sinus secretions in patients with cystic fibrosis. Int Forum Allerg Rhinol. Accepted. Nelson J, Simpkins SW, Safizadeh H, Li SC, Piotrowski JS, Hirano H, Yashiroda Y, Osada H, Yoshida M, Boone C, Myers CL (2017) MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action. Bioinformatics. http://www.ncbi.nlm.nih.gov/pubmed/29206899 Nelson MS, Chun CL, Sadowsky MJ. Type IV Effector Proteins Involved in the Medicago-Sinorhizobium Symbiosis. Mol Plant Microbe Interact. 2017 Jan;30(1):28-34. doi: 10.1094/MPMI-10- 16-0211- R.

Neyhart, J.,T. Tiede, A. J. Lorenz, and K. P. Smith. 2017. Evaluating Methods of Updating Training Data in Long-Term Genomewide Selection. G3 May 2017 7:1499-1510; early online March 17, 2017. doi:10.1534/g3.117.040550 Nice, L. M., B.J. Steffenson, T.K. Blake, R.D. Horsley, K.P. Smith and G.J. Muehlbauer. 2017. Mapping agronomic traits in a wild barley advanced backcross nested association mapping (AB-NAM) population. Crop Sci. 57: 3: 1199-1210. doi:10.2135/cropsci2016.10.0850 Nice, L., and A.J. Lorenz. 2017. Training population design and resource allocation for genomic selection in plant breeding. In R. Varshney, M. Roorkiwal, and M. Sorrells (Eds.) Genomic Selection for Crop Improvement. Springer. Nice, L.M., B.J. Steffenson, T. Blake, R. Horsley, K.P. Smith and G.J. Muehlbauer. 2017. Mapping agronomic traits in a wild barley advanced backcross nested association mapping (AB-NAM) population. Crop Science 57:1-12. Nir, I., Shohat, H., Panizel, I., Olszewski, N.E., Aharoni, A., and Weiss, D. (2017). The Tomato DELLA Protein PROCERA Acts in Guard Cells to Promote Stomatal Closure. Plant Cell DOI: https://doi.org/10.1105/tpc.17.00542 Noyszewski, A.K., Y-. Liu, C.M.L. Alves, and A.G. Smith. 2017. Polymorphism and structure of style–specific arabinogalactan proteins of Nicotiana as determinants of pollen tube growth. Submitted to BMC Genomics, 17:186, https://doi.org/10.1186/s12862-017-1011-2. O’Sullivan, D.J (2017) “Genetic engineering approaches for bifidobacteria and lactic acid bacteria” Proceedings of the 9th Asian Conference on Lactic Acid Bacteria, Gwangju, Korea Oates L.G., H.W. Read, J.L.M. Gutknecht, D.S. Duncan, T.B. Balser, R.D. Jackson. 2017. A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples. Journal of visualized experiments: JoVE Oka, R., Zicola, J., Weber, B., Anderson, S.N., Hodgman, C., Gent, J.I., Wesselink, J.-J., Springer, N.M., Hoefsloot, H.C.J., Turck, F., and Stam, M. (2017). Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 18: 137. Older, C.E., Diesel, A., Patterson, A.P., Meason-Smith, C., Johnson, T.J., Mansell, J., Suchodolski, J.S., and Rodrigues Hoffmann, A. (2107) The feline skin microbiota: the bacteria inhabiting the skin of healthy and allergic cats. PLoS ONE 12:e0178555. Pardey, P.G. and J.M. Beddow. Revitalizing Agricultural Research and Development to Sustain US Competitiveness. Policy Brief, Philadelphia, PA: Farm Journal Foundation, February 28, 2017, pp. 11.

Pegos V, Hey L, LaMirande J, Pfeffer R, Lipsh R, Amitay M, Gonzalez D, Elias M. Purification, characterization, crystallization and S-SAD phasing of the Phosphate-Binding Protein from Polaromonas JS666. Acta Cryst F . F73, 342-346. PMID: 28580922 Pei, Z., D. Eichenberg, H. Bruelheide, W. Kröber, P. Kühn, Y. Li, G. von Oheimb, O. Purschke, T. Scholten, F. Buscot, J.L.M. Gutknecht. 2017. Leaf litter diversity affects the microbial community structure and functions in Chinese subtropical forest. Biogeochemistry. 134 (1- 2), 163-181 Peng Zhou, Ph.D., Kevin A. T. Silverstein, Thiruvarangan Ramaraj, Joseph Guhlin, Roxanne L. Denny, Junqi Liu, Andrew D. Farmer, Kelly P. Steele, Robert M. Stupar, Jason R. Miller, P Tiffin, Joann Mudge,Nevin D. Young. 2017. Exploring Structural Variation and Gene Family Architecture with De Novo Assemblies of 15 Medicago Genomes. BMC Genomics 18: 261 Periyannan, S., Milne, R. J., Figueroa, M., Lagudah, E. S., Dodds, P. N. 2017. An overview of genetic rust resistance: From broad to specific mechanisms. PLoS Pathogens 13(7): e1006380. Peterson, J. J., Samac, D. A., and Grau, C. R. 2017. First report of Fusarium wilt of alfalfa caused by Fusarium oxysporum f. sp. medicaginis in Wisconsin. Plant Dis. https://doi.org/10.1094/PDIS-07- 17-1107- PDN. Phillips, K, M. Kobiela, E. Snell-Rood. 2017. Developmental lead exposure has mixed effects on butterfly cognitive processes. Animal Cognition 20: 87-96. Pincelli-Souza RP, Tillmann M, Esler M, Alves CCD, Cohen JD Hybrid hazelnut: micropropagation, rooting and acclimatization. Acta Hort (in press) Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J, Shirahige K, Baryshnikova A, Brown GW, Hirano H, Costanzo M, Andrews B, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C (2017) Functional annotation of chemical libraries across diverse biological processes. Nature chemical biology 13:982-993. http://www.ncbi.nlm.nih.gov/pubmed/28759014 Polme S, Bahram M, Jacquemyn H, Kennedy P.G., Kohout P., Moora M., Oja J., Opik M., Pecoraro L., L. Tedersoo. Host preference and network properties in biotrophic plant-fungal associations. New Phytologist, in press. Presley, G., Schilling, J.S.* (2017) Distinct growth and secretome strategies in two taxonomically-distinct brown rot fungi. Applied & Environmental Microbiology 83:7 11 e02987-16 (spotlight article). Presley, G.N., Zhang, J., Schilling, J.S.* (online first) A genomics-informed study of oxalate and cellulose regulation by brown rot wood-degrading fungi. Fungal Genetics & Biology doi.org/10.1016/j.fgb.2016.08.004.

Purg. M, Elias M, Kamerlin SCL. Similar Active Sites and Mechanisms Do Not Lead to Cross- Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering. JACS. PMID: 29113434 Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem. 2017 May 23;15(20):4260-4271. PubMed PMID: 28374039. Robinson, S.L. and Wackett, L.P. (2017) Diversity and taxonomy of aliphatic hydrocarbon producers. In (Alfons J. M. Stams and Diana Z. Sousa, Eds.) Handbook of Hydrocarbon and Lipid Microbiology Series. Biogenesis of Hydrocarbons. Rossbach JD, Fink RC, Sadowsky MJ, Tong C, Diez-Gonzalez F. Factors influencing the Salmonella internalization into seedpods and whole plants of Arachis hypogaea (L.). Food Microbiol. 2017 Sep;66:184-189. doi: 10.1016/j.fm.2017.05.005. Roy R, Schmitt AJ, Thomas JB, Carter CJ (2017) Nectar biology: From molecules to ecosystems, Plant Science, 262: 148-164. Rubenstein, M.A., Crowther, T.W. Maynard, D.S., Schilling, J.S., Bradford, M.A.* (2017) Decoupling direct and indirect effects of warming on decomposition. Soil Biology & Biochemistry 112: 110-116. Sadowsky MJ, Staley C, Heiner C, Hall R, Kelly CR, Brandt L, Khoruts A. Analysis of gut microbiota - An ever changing landscape. Gut Microbes. 2017 May 4;8(3):268-275. doi: 10.1080/19490976.2016.1277313. Epub 2017 Jan 4. PubMed PMID: 28051919. Sakkos, J.K., B. Mutlu, L.P. Wackett and A. Aksan (2017) Biodegrading silica adsorbent for water remediation. ACS Appl. Materials Interfaces 9(32):26848-26858. doi: 10.1021/acsami.7b06791 Sallam, A., P. Tyagi, G. Brown-Guedira, G.J. Muehlbauer, A. Hulse, and B.J. Steffenson. 2017. Genome-wide association mapping of stem rust resistance in Hordeum vulgare subsp. spontaneum. Genes/Genomes/Genetics 7:3491-3507. Sánchez-León, S., Gil-Humanes J, Ozuna CV, Giménez MJ, Sousa C, Voytas DF, Barro F. (2017) Low-gluten, non-transgenic wheat engineered with CRISPR/Cas9. Plant Biotechnol J. [Epub ahead of print] Schaefer RJ, Michno JM, Myers CL (2017) Unraveling gene function in agricultural species using gene co- expression networks. Biochimica et biophysica acta 1860:53-63. http://www.ncbi.nlm.nih.gov/pubmed/27485388

Schmidt-Dannert C. The future of biologically inspired next-generation factories for chemicals. Microb Biotechnol. 2017 Sep;10(5):1164-1166. PubMed PMID: 28805317; PubMed Central PMCID: PMC5609277. Schmidt, J., T. Fester, E. Schulz, B. Michalzik, F. Buscot, and J.L.M. Gutknecht. 2017. Effects of plant-symbiotic relationships on the living soil microbial community and microbial necromass in a long-term agro-ecosystem. Science of the Total Environment. volumes 581- 582, pgs 756-765 Schuler C., Havig, J.R., Hamilton, T.L. Carbon fixation across geochemical gradients in the Greater Obsidian Pool Area. Frontiers in Earth Science. 5:97. (doi: 10.3389/feart.2017.00097) Shah SH, Noureen A, Deeba F, Sultana T, Dukowic-Schulze S, Chen C, and Naqvi SMS (2017). Transgenic analysis reveals 5’- abbreviated OsRCLP2 promoter (s) as responsive to abiotic stresses. Mol. Biotechnol. Doi: 10.1007/s12033-017- 0031-x. Siddhanta, S. Paidi, S., Bushley, K., Prasad, R., Barman, I. 2017. Exploring morphological and biochemical linkages in fungal growth with label-free light sheet microscopy and Raman spectroscopy. ChemPhysChem 18(1): 72-78. Sikkink, K. M. Kobiela, and E. Snell-Rood. 2017. Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. BMC Genomics 18: 412. Simpkins, S. W., Nelson, J., Deshpande, R., Li, S. C., Piotrowski, J. S., Wilson, E. H., Gebre, A. A., Okamoto, R., Ohya, Y., Osada, H., Yoshida, M., Boone, C., Myers, C. L. Large-scale interpretation of chemical-genetic interaction profiles using a genetic interaction network. bioRxiv, doi:10.1101/111252 (2017). Singh N, Albert FW, Trut L, Pääbo S, and Harvati K Facial shape differences between rats selected for tame and aggressive behaviors PLoS One (2017) 12(4), e0175043 Singh RK, Singh S, Anandhan S, Shannon LM, Quiroz-Figueroa FR, Ruiz-May E (2017) First insights into the biochemical and molecular response to cold stress in Cicer microphyllum, a crop wild relative of chickpea (Cicer arientinum). Russian Journal of Plant Physiology. 64(5): 758. Smanski MJ, Mead D, Gustafsson C, Thomas MG (2017) Meeting Report for Synthetic Biology for Natural Products 2017: The Interface of (Meta)Genomics, Machine Learning, and Natural Product Discovery. ACS Synth. Biol. 6:737-743. Smith, A.G. and A.K. Noyszewski. 2017. Mutagenesis Breeding for Seedless Varieties of Popular Landscape Plants. Acta Horticulturae, in press.

Smith, S.A., J.W. Brown, Y. Yang, R. Bruenn, C.P. Drummond, S.F. Brockington, J.F. Walker, N. Last, N.A. Douglas, and M.J. Moore. Disparity, diversity, and duplications in the Caryophyllales. New Phytologist. doi:10.1111/nph.14772 Song Z., Kennedy P.G., Liew F.J., Schilling J.S. 2017. Fungal endophytes as priority colonizers initiating wood decomposition. Functional Ecology 31: 407-418. Song, Z., Kennedy, P.G., Liew, F.J., Schilling, J.S.* (2017) Fungal endophytes as priority colonizers during wood decomposition. Functional Ecology 31:407-418. Songstad, D,D., Petolino, J.F., Voytas, D.F., Reichert, N.A. (2017) Genome Editing of Plants. Critical Reviews in Plant Sciences. 1-23. Spartz, A.K., Lor, V.S., Ren, H., Olszewski, N.E., Miller, N.D., Wu, G., Spalding, E.P., and Gray, W.M. (2017). Constitutive Expression of Arabidopsis SMALL AUXIN UP RNA19 (SAUR19) in Tomato Confers Auxin- Independent Hypocotyl Elongation. Plant Physiol 173, 1453-1462. Springer, N.M. and Schmitz, R.J. (2017). Exploiting induced and natural epigenetic variation for crop improvement. Nat. Rev. Genet. Staley C, Ferrieri AP, Tfaily MM, Cui Y, Chu RK, Wang P, Shaw JB, Ansong CK, Brewer H, Norbeck AD, Markillie M, do Amaral F, Tuleski T, Pellizzaro T, Agtuca B, Ferrieri R, Tringe SG, Paša-Tolić L, Stacey G, Sadowsky MJ. Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism. Microbiome. 2017 Jun 24;5(1):65. doi: 10.1186/s40168-017- 0287 1. Staley C, Hamilton MJ, Vaughn BP, Graiziger CT, Newman KM, Kabage AJ, Sadowsky MJ, Khoruts A. Successful Resolution of Recurrent Clostridium difficile Infection using Freeze-Dried, Encapsulated Fecal Microbiota; Pragmatic Cohort Study. Am J Gastroenterol. 2017 Jun;112(6):940-947. doi: 10.1038/ajg.2017.6. Staley C, Kaiser T, Beura LK, Hamilton MJ, Weingarden AR, Bobr A, Kang J, Masopust D, Sadowsky MJ, Khoruts A. Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning. Microbiome. 2017 Aug 1;5(1):87. doi: 10.1186/s40168-017- 0306-2. Staley C, Kaiser T, Gidley ML, Enochs IC, Jones PR, Goodwin KD, Sinigalliano CD, Sadowsky MJ, Chun CL. Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs. Appl Environ Microbiol. 2017 May 1;83(10). pii: e03378-16. doi: 10.1128/AEM.03378-16. Staley C, Khoruts A, Sadowsky MJ. Contemporary Applications of Fecal Microbiota Transplantation to Treat Intestinal Diseases in Humans. Arch Med Res. 2017 Nov 25. pii: S0188-4409(17)30235- 7. doi: 10.1016/j.arcmed.2017.11.006.

Staley C, Vaughn BP, Graiziger CT, Sadowsky MJ, Khoruts A. Gut-sparing treatment of urinary tract infection in patients at high risk of Clostridium difficile infection. J Antimicrob Chemother. 2017 Feb;72(2):522-528. doi: 10.1093/jac/dkw499. Staley C, Vaughn BP, Graiziger CT, Singroy S, Hamilton MJ, Yao D, Chen C, Khoruts A, Sadowsky MJ. Community dynamics drive punctuated engraftment of the fecal microbiome following transplantation using freeze-dried, encapsulated fecal microbiota. Gut Microbes. 2017 May 4;8(3):276-288. doi: 10.1080/19490976.2017.1299310. Staley C, Weingarden AR, Khoruts A, Sadowsky MJ. Interaction of gut microbiota with bile acid metabolism and its influence on disease states. Appl Microbiol Biotechnol. 2017 Jan;101(1):47-64. doi: 10.1007/s00253-016- 8006-6. Steck, M, and E. Snell-Rood. 2017. The host specialization and foraging accuracy of individual butterflies in complex and simple environments. In press, Behavioral Ecology Stoltz KL, Erickson R, Staley C, Weingarden AR, Romens E, Steer CJ, Khoruts A, Sadowsky MJ, Dosa PI. Synthesis and Biological Evaluation of Bile Acid Analogues Inhibitory to Clostridium difficile Spore Germination. J Med Chem. 2017 Apr 27;60(8):3451-3471. doi: 10.1021/acs.jmedchem.7b00295. Tahir, M., Holland, C., Samac, D. A., and Mollov, D. 2017. First report of 16SrII subgroup D phytoplasma in alfalfa in Sudan. Plant Dis. 101:2144. Tamura, K., Fukao, Y., Hatsugai, N., Katagiri, F., Hara-Nishimura, I. (2017) “Nup82 functions redundantly with Nup136 in a salicylic acid-dependent defense response of Arabidopsis thaliana” Nucleus 8, 301-311. http://www.tandfonline.com/doi/full/10.1080/19491034.2017.1279774?scroll=top&needAccess=true Tang, X., Lowder, L.G., Zhang, T., Malzahn, A.A., Zheng, X., Voytas, D.F., Zhong, Z., Chen, Y., Ren, Q., Li, Q., Kirkland, E.R., Zhang, Y., Qi, Y. (2017) A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nature Plants. 3. Tashiro, Y.,* H. Eida, S. Ishii, H. Futamata, and S. Okabe. 2017. Generation of small colony variants governed by a conjugative F plasmid in Escherichia coli biofilms. Microbes Environ. 32: 40-46. Thomas JB, Hampton ME, Dorn KM, Marks MD, Carter CJ (2017) The pennycress (Thlaspi arvense L.) nectary: structural and transcriptomic characterization. BMC Plant Biol, 17: 201.

Torres, S., Clayton, J.B., Danzeisen, J.L., Ward, T., Huang, H., Knights, D., and Johnson, T.J. (2017) Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time. PeerJ 5:e3075. Trogisch, S., A. Schuldt, J. Bauhus, J. Blum, S. Both, F. Buscot, N. Castro-Izaguirre, D. Chesters, W. Durka, D. Eichenberg, A. Erfmeier, M. Fischer, C. Geißler, M. Germany, P. Goebes, J. Gutknecht, C. Hahn, S. Haider, W. Härdtle, J. He, A. Hector, L. Hönig, Y. Huang, A. Klein, P. Kühn, M. Kunz, K. Leppert, Y. Li, X. Liu, P. Niklaus, Z. Pei, K. Pietsch, R. R. Prinz, T. Proß, M. Scherer-Lorenzen, K. Schmidt, T. Scholten, S. Seitz, Z. Song, M. Staab, G. von Oheimb, C. Weißbecker, E. Welk, C. Wirth, T. Wubet, B. Yang, C.D. Zhu, B. Schmid, K. Ma, and H. Bruelheide 2017. Towards a methodical framework for comprehensively assessing forest multifunctionality. Methods in Ecology and Evolution. In press Van der Velden, NS, Kaelin, N, Helf, MJ, Piel, J, Freeman, MF § , Kuenzler, M § (2017) “Autocatalytic backbone N-methylation in a family of ribosomal peptide natural products”, Nat. Chem. Biol. 13(8): 833-835. [News and Views: Nat. Chem. Biol. 2017 13: 821-822.] [Highlight: Angew. Chem. Int. Ed. Engl. 2017 56: 2-5.] Van Etten, JL., Nyquist, M., Li, Y., Yang, R., Ho, Y., Johnson, R., Ondigi, O., Voytas, DF., Henzler, C., Dehm, SM. (2017) Targeting a Single Alternative Polyadenylation Site Coordinately Blocks Expression of Androgen Receptor mRNA Splice Variants in Prostate Cancer. Cancer Res. 77(19):5228-5235. Van Tassel David L, Kenneth A. Albrecht, James D. Bever, Arvid A. Boe, Yaniv Brandvain, Timothy E. Crews, Markus Gansberger, Pedro Gerstberger, Luciana González-Paleo, Brent S. Hulke, Nolan C. Kane, Paul J. Johnson, Elena G. Pestsova, Valentín D. Picasso Risso, Jarrad R. Prasifka, Damian A. Ravetta, Brandon Schlautman, Craig C. Sheaffer, Kevin P. Smith, Pablo R. Speranza, M. Kathryn Turner, Alejandra E. Vilela, Philipp von Gehren, and Christian Wever. 2017 Accelerating Silphium Domestication: An Opportunity to Develop New Crop Ideotypes and Breeding Strategies Informed by Multiple Disciplines. Crop Science 57:1274–1284 Van Tassel David, D. K. Albrecht, J. Bever, A. Boe, Y. Brandvain, T. Crews, M. Gansberger, P. Gerstberger, L. González-Paleo, B. Hulke, N. Kane, P. Johnson, V. Picasso Risso, E. Pestsova, J. Prasifka, D. Ravetta, B. Schlautman, C. Sheaffer, K. Smith, P. Speranza, K. Turner, A. Vilela, P. von Gehren, and C. Weaver. 2017. Accelerating Silphium domestication: an opportunity to develop new crop ideotypes and breeding strategies informed by multiple disciplines. Crop Sci. 57: 3: 1274-1284. doi:10.2135/cropsci2016.10.0834. Vishwanathan, N., Bandyopadhyay, A., Fu, H.-Y., Johnson, K.C., Springer, N.M., and Hu, W.-S. (2017). A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines. Biotechnol. Bioeng. 114: 1903–1908. Wackett, L.P. (2017). Review of the book Biotechnology, Acta Cryst. D73.

Walker, J.F., Y. Yang, M.J. Moore, J. Mikenas, A. Timoneda, S.F. Brockington, and S.A. Smith. Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales. American Journal of Botany. 104(6): 858–867 Wang W, Xu ZZ, Costanzo M, Boone C, Lange CA, Myers CL (2017) Pathway-based discovery of genetic interactions in breast cancer. PLoS genetics 13:e1006973. http://www.ncbi.nlm.nih.gov/pubmed/28957314 Wang, R. J. Chen, J.A. Anderson, J. Zhang, W. Zhao, J. Wheeler, N. Klassen, D.R. See, and Y. Dong. 2017. Genome-wide association mapping of fusarium head blight resistance in spring wheat lines developed in the Pacific Northwest and CIMMYT. Phytopathol. 107:1486-1495. doi.org/10.1094/PHYTO-02- 17-0073- R. Waters AJ, Makarevitch J, Noshay J, Burghardt L, Hirsch CN, Hirsch CD, Springer NM. 2017. Natural variation for gene expression responses to abiotic stress in maize. Plant J, 89: 706-717. Waters, A., I. Makarevitch, J. Noshay, L. Burghardt, C.N. Hirsch, C.D. Hirsch, N. Springer. 2017. Natural variation for gene expression responses to abiotic stress in maize. Plant Journal. 89:706-717. Waters, A.J., Makarevitch, I., Noshay, J., Burghardt, L.T., Hirsch, C.N., Hirsch, C.D., and Springer, N.M. (2017). Natural variation for gene expression responses to abiotic stress in maize. Plant J. 89: 706–717. West, E.A., A. Jain and J.A. Gralnick. 2017. Engineering a native inducible expression system in Shewanella oneidensis to control extracellular electron transfer. ACS Synth Biol. doi: 10.1021/acssynbio.6b00349 Wilson M, Pawlus AD, Brinkman D, Gardner G, Hegeman AD, Spivak M, Cohen JD 3-acyl dihydroflavonols from poplar resins collected by honey bees are active against the bee pathogens Paenibacillus larvae and Ascosphaera apis. Phytochemistry 138:83-92 (2017) Wilson MB, Pawlus AD, Brinkman D, Gardner G, Hegeman AD, Spivak M, & Cohen JD (2017) 3-Acyl dihydroflavonols from poplar resins collected by honey bees are active against the bee pathogens Paenibacillus larvae and Ascosphaera apis. Phytochemistry, 138: 83-92. Wilson, M.C., Mutka, A.M., Hummel, A.W., Berry, J., Chauhan, R.D., Vijayaraghavan, A., Taylor, N.J., Voytas, D.F., Chitwood, D.H., Bart, R.S. (2017) Gene expression atlas for the food security crop cassava. New Phytologist. 213(4):1632-1641. Woods, D., Bednark, R., Bouche, F., Gordon, S., Vogel, J., Garvin, D.F., Amasino, R. 2017. Genetic architecture of flowering time variation in Brachypodium distachyon. Plant Physiology 173:269-279.

Xu D., P. Pavlidis, N. Alachiotis, C. Flanagan, R. Blekhman, S. Ruhl, and O. Gokcumen. Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation. In press, Molecular Biology and Evolution - Highlighted in Science Magazine and The Guardian Xu Y, Ma Y, Howard NP, Chen C, Tong CBS, Celio G, DeEll JR, Moran RE. 2017 Microstructure of soft scald in 'Honeycrisp' apples. J Amer Soc Hort Sci 142(6):1-6. doi: 10.21273/JASHS04250- 17. Yakub, M and P Tiffin. 2017. Living in the city: urban environments shape the evolution of a native annual plant. Global Change Biology. doi: 10.1111/gcb.13528 Yang, Y., M.J. Moore, S.F. Brockington, A. Timoneda, T. Feng, H. E. Marx, J. F. Walker, and S.A. Smith. An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences 5(3): 1600128 Yang, Y., M.J. Moore, S.F. Brockington, J. Mikenas, J. Olivieri, J.F. Walker, and S.A. Smith. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. New Phytologist. doi:10.1111/nph.14812 Yoder, JB. and P. Tiffin. 2017 Effects of gene action, time since selection, and marker density on the performance of landscape genomic scans of local adaptation. Journal of Heredity Special Issue on Local Adaptation. in press Yoder, JB. and P. Tiffin. 2017. Sanctions, partner recognition, and variation in mutualism. American Naturalist 190: 491-505. Yu, L., and D.J. O’Sullivan. (2017) Immobilization of whole cells of Lactococcus lactis containing highlevels of a hyperthermostable β-galactosidase enzyme in chitosan beads for efficient galactooligosaccharide production. J. Dairy Science, in press Zacharoff Lori A., Lori A., Morrone Dana, Bond Daniel R.. 2017. Geobacter sulfurreducens extracellular multiheme cytochrome PgcA facilitates respiration to Fe(III) oxides but not electrodes. Frontiers in Microbiology; doi: https://doi.org/10.1101/172775 Zentella, R., Sui, N., Barnhill, B., Hsieh, W.P., Hu, J., Shabanowitz, J., Boyce, M., Olszewski, N.E., Zhou, P., Hunt, D.F., et al. (2017). The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA. Nat Chem Biol 13, 479-485. Zhang, H., Cheng, F., Xiao, Y., Kang, X., Wang, X., Kuang, R., and Ni, M. (2017). Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development (*equal contribution). Plant Journal doi: 10.1111/tpj.13542.

Zhang, J., Schilling, J.S.* (2017) Role of carbon source in the shift from oxidative to hydrolytic wood decomposition by Postia placenta. Fungal Genetics & Biology 106:1-8. Zhang, L. Y. Narita, L. Gao, M. Ali, M. Oshiki, S. Ishii, and S. Okabe.* 2017. Microbial competition among anammox bacteria in nitrite-limited bioreactors. Water Res. 125: 249-258. Zhang, X. S. Larson, L. Gao, S.L. Teh, L. DeHaan, M. Fraser, A. Sallam, T. Kantarski, K. Frels, J. Poland, D. Wyse, J. Anderson. 2017. Uncovering the genetic architecture of seed weight and size in intermediate wheatgrass through linkage and association mapping. The Plant Genome. doi: 10.3835/plantgenome2017.03.0022 Zhong C, Nelson M, Cao G, Sadowsky MJ, Yan T. Complete Genome Sequence of the Triclosan- and Multidrug-Resistant Pseudomonas aeruginosa Strain B10W Isolated from Municipal Wastewater. Genome Announc. 2017 Jan 19;5(3). pii: e01489-16. doi: 10.1128/genomeA.01489-16. PubMed PMID: 28104659; Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND. (2017) Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. BMC Genomics 18:261. Zhou P, Silverstein KAT, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND. Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. BMC Genomics. 2017 Mar 27;18(1):261. doi: 10.1186/s12864-017-3654-1. PMID:28347275. Zhou P, Silverstein KAT, Thiruvarangan R, Guhlin J, Denny RL, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin PL, Mudge J, Young ND (2017) Exploring structural variation and gene family architecture with de novo assemblies of 15 Medicago genomes. BMC Genomics 18:261 doi 10.1186/s12864-017- 3654-1. Zhou, M., Lu, Y., Bethke, G., Harrison, B. T., Hatsugai, N., Katagiri, F. and Glazebrook, J. WRKY70 prevents axenic activation of plant immunity by direct repression of SARD1. New Phytologist. doi:10.1111/nph.14846 (2017). Zhou, M., Lu, Y., Harrison, B. T., Hatsugai, N., Katagiri, F., and Glazebrook, J. (2017) “WRKY70 prevents axenic activation of plant immunity by direct repression of SARD1” New Phytol, Epub ahead of print.