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MPGI Publications 2015
A. Karpatne and V. Kumar. Adaptive heterogeneous ensemble learning using the context of test instances. International
Conference on Data Mining (ICDM 2015), Atlantic City, NJ. November 14-17, 2015.
A. Karpatne, A. Khandelwal, X. Chen, V. Mithal, J.H. Faghmous, and V. Kumar. Global monitoring of inland water
dynamics: State-of-the-art, challenges, and opportunities. In K. Morik, J. Lässig, and K. Kersting, Eds. Computational
Sustainability, Springer. 2015.
A. Khandelwal, V. Mithal, and V. Kumar. Post Classification Label Refinement Using Implicit Ordering Constraint Among
Data Instances. International Conference on Data Mining (ICDM 2015), Atlantic City, NJ. November 14-17, 2015.
A. M. Gomez, J. Rothman, K. Petrzelkova, C. Yeoman, K. Vlckova, J. Umaña, C. Monica, D. Modry, A. Todd, M. Torralba, K.
Nelson, R. Stumpf, B. Wilson, R. Blekhman, B. White, and S. Leigh. (2015) Temporal variation selects for diet-microbe co-
metabolic traits in the gut of Gorilla spp. ISME Journal, Aug 28. doi: 10.1038/ismej.2015.146
Abate-Pella D, Freund DM, Ma Y, Simón-Manso Y, Hollender J, Broeckling CD, Huhman DV, Krokhin OV, Stoll DR,
Hegeman AD, Kind T, Fiehn O, Schymanski EL, Prenni JE, Sumner LW, Boswell PG (2015) Retention Projection Enables
Accurate Calculation of Liquid Chromatographic Retention Times Across Labs and Methods, J Chromatog A, 1412: 43-51.
Ahmed W, Staley C, Sadowsky MJ, Gyawali P, Sidhu JP, Palmer A, Beale DJ, Toze S. Toolbox Approaches Using Molecular
Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water. Appl Environ
Microbiol. 2015 Oct 15;81(20):7067-77. doi: 10.1128/AEM.02032-15. Epub 2015 Jul 31. PMID: 26231650
Al-Ghalith GA, Knights D. Bygiene: The New Paradigm of Bidirectional Hygiene. Yale Journal of Biology and Medicine (in
press).
Al-Ghalith GA, Montassier E, Ward HN, Knights D. NINJA-OPS: Fast accurate marker gene alignment using concatenated
ribosomes. PLoS Computational Biology (in press).
Al-Ghalith GA, Vangay P, Knights D. The Guts of Obesity: Progress and Challenges in Linking Gut Microbes to Obesity.
Discovery Medicine 2015 Feb 19(103):81-8.
Ali Z, Abul-Faraj A, Li L, Ghosh N, Piatek M, Mahjoub A, Aouida M, Piatek A, Baltes NJ, Voytas DF, Dinesh-Kumar S,
Mahfouz MM. (March 2015) Efficient Virus-Mediated Genome Editing in Plants using the CRISPR/Cas9 System. Mol
Plant. pii: S1674-2052(15)00162-8.
Alissa Rauwerdink, Mark Lunzer, Titu Devamani, Bryan Jones, Joanna Mooney, Zhi-Jun Zhang, Jian-He Xu, Romas J.
Kazlauskas, Antony M. Dean (2015) Evolution of a catalytic mechanism. Mol. Biol. Evol., revisions in progress Oct 2015
Alissa Rauwerdink, Romas J. Kazlauskas (2015) How the same catalytic machinery catalyzes twenty-one different
reactions: the Ser-His-Asp catalytic triad of α/β-hydrolase fold enzymes. ACS Catal. 5, 6153–76;
http://doi.org/10.1021/acscatal.5b01539
Alston, Julian M., & Pardey, Philip G. (2015). Agricultural R&D, Food Prices, Poverty, and Malnutrition Redux. In D. E.
Sahn (Ed.), The Fight Against Hunger and Malnutrition: The Role of Food, Agriculture, and Targeted Policies (pp. 208-
239). New York, NY: Oxford University Press.
Alston, Julian M., Andersen, Matthew A., & Pardey, Philip G. (2015). The Rise and Fall of U.S. Farm Productivity Growth,
1910–2007 Staff Paper P15-2. St. Paul, MN: University of Minnesota, Department of Applied Economics.
Alston, Julian M., Martin, William J., & Pardey, Philip G. (2015). Agricultural R&D Policy and Long-Run Food Security. In A.
M. Balisacan, U. Chakravorty & M.-L. V. Ravago (Eds.), Sustainable Economics Development: Resources, Environment,
and Institutions (pp. 247-260). New York, NY: Academic Press.
2
Altimetry. J. H. Faghmous, I. Frenger, Y. Yao, R. Warmka, A. Lindell, and V. Kumar. A Daily Global Mesoscale Ocean Eddy
Dataset from Satellite . Scientific Data, Nature Publishing Group, 2. 2015.
Ames, N., A. Dreiseitl, B.J. Steffenson and G.J. Muehlbauer. 2015. Mining wild barley for powdery mildew resistance.
Plant Pathology doi: 10.1 111/ppa.12384.
Anderson J, Kono TJY, Stupar RM, Kantar MB, Morrell PL (in review) Environmental association analyses identify
candidates for abiotic stress tolerance in Glycine soja, the wild progenitor of cultivated soybeans. G3: Genes | Genomes
| Genetics
Anderson, J.A., J.J. Wiersma, G.L. Linkert, S. Reynolds, J.A. Kolmer, Y. Jin, R. Dill-Macky, and G.A. Hareland. 2015.
Registration of 'Rollag' Spring Wheat. J. Plant Registrations 9:201-207.
Aversano, R., Contaldi, F., Ercolano, M.R., Grosso, V., Iorizzo, M., Tatino, F., Xumerle, L., Molin, A.D., Avanzato, C.,
Ferrarini, A., Delledonne, M., Sanseverino, W., Cigliano, R.A., Capella-Gutierrez, S., Gabaldón, T., Frusciante, L., Bradeen,
J.M., and Carputo, D. 2015. The Solanum commersonii genome sequence provides insights into adaptation to stress
conditions and genome evolution of wild potato relatives. Plant Cell doi:10.1105/tpc.114.135954.
Badalamenti JP, Bond DR. 2015. Complete Genome of Geobacter pickeringii G13T, a Metal-Reducing Isolate from
Sedimentary Kaolin Deposits. Genome Announc 3.
Badalamenti JP, Krajmalnik-Brown R, Torres CI, Bond DR. 2015. Genomes of Geoalkalibacter ferrihydriticus Z-0531T and
Geoalkalibacter subterraneus Red1T, Two Haloalkaliphilic Metal-Reducing Deltaproteobacteria. Genome Announc 3.
Bajaj, R., Hu, W., Huang, Y., Chen, S., Prasad, R., Varma, A., and Bushley, K. 2015. The beneficial root endophyte
Piriformospora indica reduces egg density of the soybean cyst nematode. Biological Control 90: 193-199.
Bajgain, P., M.N. Rouse, and J.A. Anderson. 2016. Comparison between Genotyping by Sequencing and SNP-chip
Genotyping for QTL Mapping in Wheat. Crop Sci. 56: 1–17.
Bajgain, P., M.N. Rouse, P. Bulli, S. Bhavani, T. Gordon, R. Wanyera, P.N. Njau, W. Legesse, J.A. Anderson and M.O.
Pumphrey. 2015. Association Mapping of North American Spring Wheat Breeding Germplasm Reveals Loci Conferring
Resistance to Ug99 and Other African Stem Rust Races. BMC Plant Biology 15: 249 doi: 10.1186/s12870-015-0628-9
Bajgain, P., M.N. Rouse, S. Bhavani, and J.A. Anderson. 2015. QTL Mapping of Adult Plant Resistance to Ug99 Stem Rust
in the Spring Wheat Population RB07/MN06113-8. Mol. Breeding 35:170-184.
Balint, M., L. Barthe, R. O’Hara, M.S. Olson, U. Otte, R. Robertson, P. Tiffin, and I. Schmitt. 2015. Relocation, high-latitude
warming and host genetic identity shape the foliar fungal microbiome of poplars. Molecular Ecology. 24: 235-248.
Baltes NJ, Voytas DF. (Feb. 2015) Enabling plant synthetic biology through genome engineering. Trends in
Biotechnology. 33(2):120-131
Bao Y, Kurle JE, Anderson G, Young ND (2015) Assessing the potential of association mapping and genomic prediction for
resistance to sudden death syndrome in early maturing soybean germplasm. Molecular Breeding 35:128. doi:
10.1007/s11032-015-0324-3.
Barney BM, Eberhart LJ, Ohlert JM, Knutson CM, Plunkett MH. Gene Deletions Resulting in Increased Nitrogen Release
by Azotobacter vinelandii: Application of a Novel Nitrogen Biosensor. Appl Environ Microbiol. 2015 Jul;81(13):4316-28.
doi: 10.1128/AEM.00554-15. Epub 2015 Apr 17.
Barney BM, Ohlert JM, Timler JG, Lijewski AM. Altering small and medium alcohol selectivity in the wax ester synthase.
Appl Microbiol Biotechnol. 2015 Nov;99(22):9675-84. doi: 10.1007/s00253-015-6783-y. Epub 2015 Jul 24.
3
Beddow, Jason M., & Pardey, Philip G. (2015). Moving Matters: The Effect of Location on Crop Production. Journal of
Economic History, 75(1), 219-249. doi: doi: 10.1017/S002205071500008X
Beddow, Jason M., Hurley, Terrance M., Pardey, Philip G., & Alston, Julian M. (2015). Rethinking Yield Gaps Staff Paper.
St. Paul, MN: University of Minnesota, Department of Applied Economics.
Beddow, Jason M., Pardey, Philip G., Chai, Yuan, Hurley, Terrance M., Kriticos, Darren J., Braun, Hans-Joachim, Yonow,
Tania. (2015). Research Investment Implications of Shifts in the Global Geography of Wheat Stripe Rust. Nature Plants,
1(10), 15132. doi: 10.1038/nplants.2015.132
Belcher, A.R., R.C. Graebnera, A. Cuesta-Marcos, S. Fisk, T. Filichkina, K.P. Smith, V. Blake, and P.M. Hayesa. 2015.
Registration of the TCAP FAC-WIN6 Barley Panel for Genome Wide Association Studies. J. Plant Reg. 9:411-418.
doi:10.3198/jpr2014.12.0083crmp
Bennett, B.D., E.D. Brutinel and J.A. Gralnick. 2015. A ferrous iron exporter mediates iron resistance in Shewanella
oneidensis MR-1. Appl Environ Microbiol. 81(22):7938-44.
Bhatty, Minny, et al. Enterococcus faecalis pCF10‐encoded surface proteins PrgA, PrgB (aggregation substance) and PrgC
contribute to plasmid transfer, biofilm formation and virulence. Molecular microbiology 95.4 (2015): 660-677.
Bierbar, P, JLM Gutknecht, and B Michalzik (2015). Nest-mounds of the yellow meadow ant (Lasius flavus) at the “Alter
Gleisberg”, Central Germany: Hot or cold spots in nutrient cycling? Soil Biology and Biochemistry. 80: 209-217.
Bogar L.M., I. A. Dickie, P. G. Kennedy. 2015. Testing the co-invasion hypothesis: Ectomycorrhizal fungal communities
associated with Alnus glutinosa and Salix fragilis in New Zealand. Diversity and Distributions, 21:268-278.
Bolon, Y-T., A.O. Stec, J-M.S. Michno, J. Roessler, P.B. Bhuskar, L. Ries, A.A. Dobbels, B.W. Campbell, N.D. Young, J.E.
Anderson, D. Grant, J.H. Orf, S.L. Naeve, G.J. Muehlbauer, C.P. Vance, and R.M. Stupar. 2014. Genome resilience and
prevalence of segmental duplications following fast neutron irradiation of soybean. Genetics 198:967-981.
Bonhomme M, Boitart S, San Clemente H, Dumas B, Young ND, Jacquet C (2015) Genomic signature of selective sweeps
reveals adaptation of Medicago truncatula to root-associated microorganisms. Molecular Biology and Evolution, doi:
10.1093/molbev/msv092.
Bonis, B.M. and J.A. Gralnick. 2015. Marinobacter subterrani, a genetically tractable neutrophillic Fe(II)-oxidizing strain
isolated from the Soudan Iron Mine. Front Microbiol. 6:719.
Borewicz KA, Kim HB, Singer RS, Gebhart CJ, Sreevatsan S, Johnson T, Isaacson RE. Changes in the Porcine Intestinal
Microbiome in Response to Infection with Salmonella enterica and Lawsonia intracellularis. PLoS One. 2015 Oct
13;10(10):e0139106. doi: 10.1371/journal.pone.0139106. eCollection 2015. PubMed PMID: 26461107; PubMed Central
PMCID: PMC4604083.
Borrero, Juan, et al. Modified lactic acid bacteria detect and inhibit multiresistant Enterococci. ACS synthetic biology 4.3
(2014): 299-306.
Brady S, Burow M, Busch W, Carlborg O, Denby K, Glazebrook J, Hamilton E, Maloof J, Springer N, Kliebenstein D. 2015.
Reassess the t-test: interact with all your data via ANOVA. Plant Cell 27(8):2088-94.
Brandvain, Y., and G. Coop. 2015. Sperm should evolve to make female meiosis fair. Evolution 69: 1004–1014.
Bratsch, S. A., B. E. Lockhart, and C. Ishimaru. 2015. Confirmation of first report of Orchid fleck virus in Phalaenopsis
hybrid orchids in the USA. Plant Health Progress doi:10.1094/PHP-BR-15-0018.
Bridier-Nahmias A, Tchalikian-Cosson A, Menouni R, Fayol H, Flores A, Voytas DF, Lesage P, Baller JA, Saïb A, Werner M.
(2015). An RNA polymerase III subunit determines sites of retrotransposon integration. Science. 348 (6234): 585-588.
4
Bryan Jones, Romas Kazlauskas (2015) The road to L. Nat. Chem. 6, 11–12; http://doi.org/10.1038/nchem.2137
Bull, J.J. & Harcombe, W.R. 2009. Dynamical constraints on the cooperative evolution of cross-feeding. PLoS: One.
4(1):e4115
Burns MB, Lynch J, Starr TK, Knights D, Blekhman R. Virulence Genes are a Signature of the Microbiome in the Colorectal
Tumor Microenvironment. Genome Medicine (in press).
C. Schmidt-Dannert (2015) Biosynthesis of terpenoid natural products in fungi. Adv. Biochem Eng. Biotechnol. [Epub
ahead of print] PMID: 25414054.(Online 12/2014)
C. Schmidt-Dannert (2015) NextGen microbial natural products discovery. Microb Biotechnol 8:26-28.
Campbell BW, Mani D, Curtin SJ, Slattery RA, Michno JM, Ort DR, Schaus PJ, Palmer RG, Orf JH, Stupar RM. (2015)
Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants. G3 (Bethesda)
5: 123-31.
Carissimo, G., Bischoff, E., and Vernick, K. (2015). [Compartimentalization of immune responses in the mosquito
Anopheles gambiae: consequences for insect vector immunity research]. Med Sci (Paris) 31, 353-355.
Carissimo, G., Pondeville, E., McFarlane, M., Dietrich, I., Mitri, C., Bischoff, E., Antoniewski, C., Bourgouin, C., Failloux,
A.B., Kohl, A., et al. (2015). Antiviral immunity of Anopheles gambiae is highly compartmentalized, with distinct roles for
RNA interference and gut microbiota. Proc Natl Acad Sci U S A 112, E176-185.
Catalan, P., Chalhoub, B., Chochois, V., Garvin, D.F., Hasterok, R., Manzaneda, A.J., Mur, L.A., Pecchioni, N., Rasmussen,
S., Vogel, J.P., and Voxeur, A. 2014. Update on the genomics and basic biology of Brachypodium: International
Brachypodium Initiative (IBI). Trends in Plant Science 19:414-418.
Cermak T, Baltes NJ, Cegan R, Zhang Y, Voytas DF. (Nov. 2015) High-frequency, precise modification of the tomato
genome. Genome Biology. 16:232.
Cermak T, Starker CG, Voytas DF. (2015) Efficient design and assembly of custom TALENs using the Golden Gate
platform. Methods Mol Biol. 1239:133-59.
Chan CH, Levar CE, Zacharoff L, Badalamenti JP, Bond DR. 2015. Scarless Genome Editing and Stable Inducible Expression
Vectors for Geobacter sulfurreducens. Appl Environ Microb 81:7178–7186.
Chandrasekaran R, Hamilton MJ, Wang P, Staley C, Matteson S, Birr A, Sadowsky MJ. Geographic isolation of Escherichia
coli genotypes in sediments and water of the Seven Mile Creek - A constructed riverine watershed. Sci Total Environ.
2015 Dec 15;538:78-85. doi: 10.1016/j.scitotenv.2015.08.013. Epub 2015 Aug 22. PMID: 26298250.
Chapman, J.A., M. Mascher, A. Buluç, K. Barry, E. Georganas, V. Strnadova, A. Session, S. Seghal, L. Oliker, J. Schmutz,
K.A. Yelick, U. Scholz, R. Waugh, J.A. Poland, G.J. Muehlbauer, N. Stein and D.S. Rokhsar. 2015. Chromosome-scale
assembly of the hexaploid wheat genome from whole genome shotgun sequencing. Genome Biology 16:26.
Chen C., Farmer A.D., Langley R.J., Mudge J., Crow J.A., May G.D., Huntley J., Smith A.G., Retzel E.F. 2010. Meiosis-
specific gene discovery in plants: RNA-seq applied to isolated Arabidopsis male meiocytes. BMC Plant Biol. 10(1):280.
Chen, C., Xiao, Y., Li, X., and Ni, M. (2012). Light-regulated stomatal aperture in Arabidopsis. Molecular Plant 5(3): 566-
572.
Choi MJ, Torremorell M, Bender JB, Smith K, Boxrud D, Ertl JR, Yang M, Suwannakarn K, Her D, Nguyen J, Uyeki TM,
Levine M, Lindstrom S, Katz JM, Jhung M, Vetter S, Wong KK, Sreevatsan S, Lynfield R. Live Animal Markets in Minnesota:
A Potential Source for Emergence of Novel Influenza A Viruses and Interspecies Transmission. Clin Infect Dis. 2015 Nov
1;61(9):1355-62. doi: 10.1093/cid/civ618. Epub 2015 Jul 29. PMID: 26223994.
5
Chubiz LM, Granger BR, Segre D, Harcombe WR. Species interactions differ in their genetic robustness. Frontiers in
Microbiol. 2015;6:271.
Chubiz, L. Douglas, S. Harcombe, W.R. 2014. Combining engineering and evolution to create metabolic mutualisms
between species. Methods in Molecular Biology 1151:39-47.
Clasen BM, Stoddard TJ, Luo S, Demorest ZL, Li J, Cedrone F, Tibebu R, Davison S, Ray EE, Daulhac A, Coffman A,
Yabandith A, Retterath A, Haun W, Baltes NJ, Mathis L, Voytas DF, Zhang F. (April 2015) Improving cold storage and
processing traits in potato through targeted gene knockout. Plant Biotechnol J. doi: 10.1111/pbi.12370.
Clasen, B.M, N.G. Moss, M.A. Chandler, A.G. Smith. 2011. Genetic Diversity Within and Among Populations of Common
Tansy (Tanacetum vulgar). Canadian J. Plant Biology 91:717-723.
Clayton JB, Johnson TJ, Huang H, Vangay P, Ward T, Travis DA, Long HT, Tuan BV, Minh VV, Glander KE, Knights D. The
modern human microbiome resembles captive primate dysbiosis. (under review).
Clayton, J.B., Danzeisen, J.L., Trent, A.M., Murphy, T., Johnson, T.J. Longitudinal characterization of Escherichia coli in
healthy non-human primates. Frontiers in Veterinary Science 1:24.
Cowperthwaite, M.C., Economo, E.P., Harcombe, W.R., Miller, E.L., & Meyers, L.A. 2008. A simple rule shapes phenotypic
evolution. PLoS: Computational Biology. 4(7):e1000110
Crawford, J.E., Riehle, M.M., Guelbeogo, W.M., Gneme, A., Sagnon, N., Vernick, K.D., Nielsen, R., and Lazzaro, B.P.
(2015). Reticulate Speciation and Barriers to Introgression in the Anopheles gambiae Species Complex. Genome Biol Evol
7, 3116-3131.
Curtin SJ, Michno JM, Campbell BW, Gil-Humanes J, Mathioni SM, Donohue RC, Kantar MB, Eamens AL, Meyers BC,
Voytas DF, Stupar RM. (2015) microRNA maturation and microRNA target gene expression regulation are severely
disrupted in soybean dicer-like1 double mutants. G3 (Bethesda) (accepted).
D. L. González, M. Angus, I. K. Tetteh, G. A. Bello, K. Padmanabhan, S. V. Pendse, S. Srinivas, J. Yu, F. Semazzi, V. Kumar,
and N. F. Samatova. On the data-driven inference of modulatory networks in climate science: an application to West
African rainfall. Nonlinear Processes in Geophysics Discussions 1: pp. 479-517. January 13, 2015.
Da-Hye Jung, Eun-Jung Kim, Eunok Jung, Romas J. Kazlauskas, Kwon-Young Choi, Byung-Gee Kim (2015) Production of p-
hydroxybenzoic acid from p-coumaric acid by Burkholderia glumae BGR1. Biotechnol. Bioeng., revisions in progress Nov
2015
Dale, Jennifer L., et al. "Multiple roles for Enterococcus faecalis glycosyltransferases (GTFs) in biofilm-associated
antibiotic resistance, cell envelope integrity, and conjugative transfer." Antimicrobial agents and chemotherapy (2015):
AAC-00344.
Danzeisen J, Clayton J, Huang H, Knights D, McComb B, Hayer S, Johnson T. Relationships between cecum, ileum and
litter bacterial microbiomes in a commercial turkey flock, and the impact of penicillin treatment on early bacterial
community establishment. Frontiers in Veterinary Science 2 (2015): 56.
Das, A. and Das, A. (2014) Delineation of polar localization domains of Agrobacterium tumefaciens type IV secretion
apparatus proteins VirB4 and VirB11. MicrobiologyOpen 3:793–802.
David M. Nedrud, Hui Lin, Gilsinia Lopez, Santosh K. Padhi, Graig A. Legatt, Romas J. Kazlauskas (2014) Uncovering
subtleties in serine hydrolases: a surprising residue substitution needed to convert Hevea brasiliensis hydroxynitrile
lyase into an esterase. Chem. Sci. 5, 4265-77; http://doi.org/10.1039/c4sc01544d.
6
DeHaan, LR; Van Tassel DL; Anderson, JA; Asselin, SR; Barnes, R; Baute, GJ; Cattani, DJ; Culman, S; Dorn, KM ; Hulke, BS;
Kantar, M; Larson, S; Marks, MD; Miller, AJ; Poland, J; Ravetta, DA; Rude, E; Ryan, MR; Wyse, DL; Zhang, X. (2015) A
Pipeline Strategy for Crop Domestication. Under Review at Crop Science.
Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda ML, de Visser JA, Fraser JS, Tawfik DS. Negative Epistasis and Evolvability
in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder. J Mol Biol. 427:2396-
409. PMID: 26004540
Der Sarkissian, C, Ermini, L, Schubert, M, Yang, M, Librado Sanz, P, Fumagalli, M, Jónsson, H, Albrechtsen, A, Vieira, FG,
Petersen, B, Ginolhac, A, Seguin-Orlando, A, Magnussen, K, Fagès, A, Gamba, C, Lorente, B, Steiner, C, Neuditschko, M,
Jagannathan, V, Feh, C, Greenblatt, CL, Alfarhan, AH, Alquraishi, SA, Al-Rasheid, KAS, Ludwig, A, Abramson, N,
Zimmermann, W, Schafberg, R, Tikhonov, A, Sicheritz-Ponten, T, Gilbert, MT, Willerslev, E, Marques-Bonet, T, Kahila Bar-
Gal, G, Ryder, O, McCue, ME, Rieder, R, Leeb, T, Slatkin, M, Orlando, L. Evolutionary genomics and conservation of the
endangered Przewalski’s horses. Current Biology in press.
Diaz A, Enomoto S, Romagosa A, Sreevatsan S, Nelson M, Culhane M, Torremorell M. Genome plasticity of triple-
reassortant H1N1 influenza A virus during infection of vaccinated pigs. J Gen Virol. 2015 Oct;96(10):2982-93. doi:
10.1099/jgv.0.000258. Epub 2015 Aug 5. PubMed PMID: 26251306.
Diaz A, Perez A, Sreevatsan S, Davies P, Culhane M, Torremorell M. Association between Influenza A Virus Infection and
Pigs Subpopulations in Endemically Infected Breeding Herds. PLoS One. 2015 Jun
15;10(6):e0129213.doi:10.1371/journal.pone.0129213. eCollection 2015. PubMed PMID: 26076494; PubMed Central
PMCID: PMC4468154.
Docherty, K.M., Borton, H., Espinosa, N., Gebhardt, M., Gil-Loaiza, J., Gutknecht, J.L.M., Maes, P.W., Mott, B.M., Parnell,
J., Purdy, G., Rodrigues, P.A., Stanish, L., Walser, O., and Gallery, R.E. 2015. Key edaphic properties largely explain
temporal and geographic variation in soil microbial communities across four biomes. PLoS One. journal.pone.0135352
Dodge AG, Carrasquillo K, Rivera L, Xu L, Wackett LP, Sadowsky MJ. Rapid method using two microbial enzymes for
detection of L-abrine in food as a marker for the toxic protein abrin. Appl Environ Microbiol. 2015 Mar;81(5):1610-5. doi:
10.1128/AEM.03492-14. Epub 2014 Dec 19. PubMed PMID: 25527549; PubMed Central PMCID: PMC4325171.
Dodge, A.G., K. Carrasquillo, L. Rivera, L. Xu, L.P. Wackett and M.J. Sadowsky (2015) A rapid detection method for L-
abrine in food as a marker for the toxic protein abrin using two microbial enzymes. Appl. Environ. Microbiol. 81: 1610-
1615.
Dorr C, Janik C, Weg M, Been RA, Bader J, Kang R, Ng B, Foran L, Landman SR, O'Sullivan MG, Steinbach M, Sarver AL,
Silverstein KA, Largaespada DA, Starr TK. Transposon Mutagenesis Screen Identifies Potential Lung Cancer Drivers and
CUL3 as a Tumor Suppressor. Mol Cancer Res. 2015 Aug;13(8):1238-47. doi: 10.1158/1541-7786.MCR-14-0674-T. Epub
2015 May 20.
Dos Santos LF, Clavijo MJ, Sreevatsan S, Rovira A, Moreira MA, Pieters M. Genotyping of Mycoplasma hyorhinis using
multiple-locus variable number tandem repeat analysis. J Microbiol Methods. 2015 Apr;111:87-92.
doi:10.1016/j.mimet.2015.02.003. Epub 2015 Feb 4. PubMed PMID: 25661497.
Dos Santos LF, Sreevatsan S, Torremorell M, Moreira MA, Sibila M, Pieters M. Genotype distribution of Mycoplasma
hyopneumoniae in swine herds from different geographical regions. Vet Microbiol. 2015 Feb 25;175(2-4):374-81.
doi:10.1016/j.vetmic.2014.11.018. Epub 2014 Dec 2. PubMed PMID: 25497236.
Drees J, Mertensotto M, Liu G, Panyam J, Leonard A, Augustin L, Schottel J, Saltzman D. Attenuated Salmonella enterica
Typhimurium reduces tumor burden in an autochthonous breast cancer model. Anticancer Res. 2015 Feb;35(2):843-9.
PubMed PMID: 25667465.
7
Drees JJ, Mertensotto MJ, Augustin LB, Schottel JL, Saltzman DA. Vasculature Disruption Enhances Bacterial Targeting of
Autochthonous Tumors. J Cancer. 2015;6(9):843-8. PubMed PMID: 26284135; PubMed Central PMCID: PMC4532981.
Drew, Jennifer, Yue, Chengyan, Anderson, Neil O., & Pardey, Philip G. (2015). Premiums and Discounts for Plant Patents
and Trademarks Used on Ornamental Plant Cultivars: A Hedonic Price Analysis. HortScience, 50(6), 879-887.
Dukowic-Schulze S, Harris A, Chen C (2015). Immunolocalization on whole anther chromosome spreads for male
meiosis.Methods Mol Biol. (in press)
Durvasula A, Kent TV, Hoffman PJ, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J 2015. ANGSD-wrapper. PeerJ PrePrints 3:
e1837.
E. C. Snell-Rood. Comment: Bringing biology back to biomimetics. In press, Nature. (Invited opinion piece)
E. Morton, J. Lynch, A. Froment, S. Lafosse, E. Heyer, M. Przeworski, R. Blekhman*, and L Ségurel*. Variation in rural
African gut microbiomes is strongly shaped by parasitism and diet. PLOS Genetics (accepted)
Eberle, C.A., B.M. Clasen, N. O. Anderson and A. G. Smith. 2012. A novel pollen tube growth assay utilizing a transmitting
tract-ablated Nicotiana tabacum style. Sexual Plant Reproduction 25:27-37.
Eberle, C.A., N.O. Anderson, B.M. Clasen, A.D. Hegeman, A.G. Smith. 2013. PELPIII the Class III Pistil-Specific Extensin-Like
Nicotiana tabacum protein is essential for interspecific incompatibility. The Plant J. 74:805-814.
Eckard, J.T., K.D. Glover, M. Mergoum, J.A. Anderson, and J.L. Gonzalez-Hernandez. 2015. Multiple Fusarium head blight
resistance loci mapped and pyramided onto elite spring wheat Fhb1 backgrounds using an IBD-based linkage approach.
Euphytica 204:63-79.
Eichten SR, Springer NM 2015. Minimal evidence for consistent changes in maize DNA methylation patterns following
environmental stress. Frontiers in Plant genetics and Genomics 6:308.
Ensemble learning methods for binary classification with multi-modality within the classes. A. Karpatne, A. Khandelwal,
and V. Kumar. Proceedings of the SIAM International Conference on Data Mining (SDM 2015). pp. 730-738. Vancouver,
Canada. April 30-May 2, 2015.
Epstein B, Sadowsky MJ, Tiffin P. Selection on horizontally transferred and duplicated genes in sinorhizobium (ensifer),
the root-nodule symbionts of medicago. Genome Biol Evol. 2015 May 19;7(5):1329-30. doi: 10.1093/gbe/evu246.
PubMed PMID: 25991814; PubMed Central PMCID: PMC4453054.
Espeset, A, C. Roy and E. C. Snell-Rood. The evolution of costly ornamentation in the face of anthropogenic changes in
nutrients. In revision, Evolution.
F. Yu, J. Lu, X. Liu, E. Gazave, D. Chang, S. Raj, H. Hunter-Zinck, R. Blekhman, L. Arbiza, C. Van Hout, A. Morrison, A. D.
Johnson, J. Bis, L. A. Cupples, B. M. Psaty, D. Muzny, J. Yu, R. A. Gibbs, A. Keinan, A. G. Clark, E. Boerwinkle. (2015)
Population genomics analysis of 962 whole genomes of humans reveals natural selection in non-coding regions. PLOS
One, 25;10(3):e0121644.
Fan K-T, Rendahl A, Chen W-P, Freund D, Gray W, Cohen JD, Hegeman A Proteome scale-protein turnover analysis using
high resolution mass spectrometric data from stable-isotope labeled plants. Journal of Proteome Research (accepted
pending revision 10/5/15)
Faris, J.D., Zhang, Z., Garvin, D.F., and Xu, S.S. 2014. Molecular and comparative mapping of genes governing spike
compactness inherited from wild emmer wheat. Molecular Genetics and Genomics 289:641-651.
Fernandez C.W. and P.G. Kennedy. 2015. Moving beyond the black-box: fungal traits, community structure, and carbon
sequestration in forest soils. 205:1378-1380.
8
Fernandez, C.W. and P.G. Kennedy. Revisting the ‘Gadgil Effect’: do interguild fungal interactions control carbon cycling
in forest soils? New Phytologist, in press.
Figueroa, M., Castell-Miller, C.V., Li, F., Hulbert, S.H., Bradeen, J.M. 2015. Pushing the boundaries of resistance: Insights
from Brachypodium-rust interactions. Frontiers in Plant Sciences, doi: 10.3389/fpls.2015.00558
Figueroa, M., Manning, V.A., Pandelova, I., Ciuffetti L.M. 2015. Persistence of the host-selective toxin Ptr ToxB in the
apoplast. Molecular Plant-Microbe Interactions doi: 10.1094/MPMI-05-15-0097-R
Figueroa, M., Moscou, M., Kianian, S., Li, F., Castell-Miller, C.V., Larson, D., Ayliffe, M., Garvin, D., Vogel, J.P.
Identification of resistance factors against rust fungi: leveraging genetic and genomic tools in Brachypodium - rust fungi
pathosystems. 2015. Submitted to Borlaug Global Rust Initiative Workshop, Sydney Australia.
Figueroa, M; Gordon, S; Castell-Miller, C., Li, F; Filichkin, S; Moscou, M; Vogel, J.P; Mockler, TC; Garvin, D; Pfender, W.
2015. The Brachypodium-Puccinia graminis system: solving a puzzle to uncover the underlying mechanisms of non-host
resistance and plant immunity. Plant and Animal Genome Conference XXIII San Diego, CA.
Flowers JM, Hazzouri KM, Pham GM, Rosas U, Bahmani T, Khraiwesh B, Nelson DR, Jijakli K, Abdrabu R, Harris EH,
Lefebvre PA, Hom EF, Salehi-Ashtiani K, Purugganan MD. Whole-Genome Resequencing Reveals Extensive Natural
Variation in the Model Green Alga Chlamydomonas reinhardtii. Plant Cell. 2015 Sep;27(9):2353-69. doi:
10.1105/tpc.15.00492. Epub 2015 Sep 21. PubMed PMID: 26392080.
Frank, Kristi L., et al. "Evaluation of the Enterococcus faecalis Biofilm-Associated Virulence Factors AhrC and Eep in Rat
Foreign Body Osteomyelitis and In Vitro Biofilm-Associated Antimicrobial Resistance." PloS one 10.6 (2015).
G Atluri, M Steinbach, KO Lim, V Kumar, A MacDonald. Connectivity cluster analysis for discovering discriminative
subnetworks in schizophrenia. Human brain mapping 36 (2), 756-767, 2015.
Gadgil, M. and Hu, W-S. Cell line development for biomanufacturing processes. Biotechnology, (Wiley) (accepted)
Gao, L., J Kielsmeirer-Cook, P Bajgain, X, Zhang, S. Chao M.N. Rouse, and J.A. Anderson. 2015. Development of
genotyping by sequencing (GBS) and array derived SNP markers for stem rust resistance gene Sr42. Mol. Breeding
35:207.
Gardner, N., R. Felsheim and A.G. Smith. 2009. Production of male- and female-sterile plants through reproductive tissue
ablation. J. Plant Physiol. 166: 871-881.
Garvin, D.F., Porter, H., Blankenheim, Z.J., Chao, S., and Dill-Macky, R. 2015. A spontaneous segmental deletion from
chromosome arm 3DL enhances Fusarium head blight resistance in wheat. Genome. doi.org/10.1139/gen-2015-0088.
Gaut BS, Diez CM, Morrell PL 2015. Genomics and the contrasting dynamics of annual and perennial domestication.
Trends in Genetics
GD Weiblen, J P Wenger, KJ Craft, MA ElSohly,Z Mehmedic, EL Treiber, & MD Marks (2015) Gene duplication and
divergence affecting drug content in Cannabis sativa. New Phytologist. DOI: 10.1111/nph.13562
Gentzbittel L, Andersen SU, Ben C, Rickauer M, Stougaard J, Young ND (2015) Naturally occuring diversity helps to reveal
genes of adaptive importance in legumes. Frontiers in Plant Science, 6: 269. doi: 10.3389/fpls.2015.00269
Ghosh S, LaPara TM, Sadowsky MJ. Transformation of tetracycline by TetX and its subsequent degradation in a
heterologous host. FEMS Microbiol Ecol. 2015 Jun;91(6). pii: fiv059. doi: 10.1093/femsec/fiv059. Epub 2015 Jun 1.
PubMed PMID: 26038239.
Gibson, S. I. (2015) Promoting an active form of learning out-of-class via online “study questions” leads to higher than
expected exam scores in General Biology. PeerJ 3:e1322
9
Godden SM, Wells S, Donahue M, Stabel J, Oakes JM, Sreevatsan S, Fetrow J. Effect of feeding heat-treated colostrum on
risk for infection with Mycobacterium avium ssp. paratuberculosis, milk production, and longevity in Holstein dairy cows.
J Dairy Sci. 2015 Aug;98(8):5630-41. doi: 10.3168/jds.2015-9443. PMID: 26074228.
Gordon, S. P., Tseng, E.,Salamov, A., Zhang, J., Meng, X., Zhao, Z., Kang, D., Underwood, J.,Grigoriev, I., Figueroa, M.,
Schilling, J.S., Chen, F., Wang, Z. 2015. Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA
Sequencing. PloSONE. doi:10.1371/journal.pone.0132628
Gordon, S.P., Priest, H., Des Marais, D., Schackwitz, W., Figueroa, M., Martin, J., Bragg, J., Tyler, L., Lee, C., Bryant, D.,
Wang, W., Messing, J., Manzaneda, A., Barry, K., Garvin, D.F., Budak, H., Tuna, M., Mitchell-Olds, T., Pfender, W.F.,
Juenger, T., Mockler, T., and Vogel, J.P. 2014. Genome diversity in Brachypodium distachyon: deep sequencing of highly
diverse inbred lines. Plant Journal 79:361-374.
Graebner RC, Wise M, Cuesta-Marcos A, Geniza M, Blake T, Blake VC, Butler J, Chao S, Hole DJ, Horsley R, Jaiswal P,
Obert D, Smith KP, Ullrich S, Hayes PM. 2015. Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E)
Pathway in Barley. PLoS ONE 10(7): e0133767. doi:10.1371/journal.pone.0133767
Graham D, Becker C, Doan A, Goel G, Villablanca E, Knights D, Mok A, Ng A, Doench J, Root D, Clish C, Xavier RJ.
Functional Genomics Identifies Negative Regulatory Nodes Controlling Phagocyte Oxidative Burst. Nature
Communications 6 (2015).
Graybosch, R., Bockleman, H.E., Garland-Campbell, K.A., Garvin, D.F., and Regassa, T. 2014. Wheat. In Smith, S., Diers,
B., and Carver, B. (eds.): Yield gains in major U.S. field crops. American Society of Agronomy, Madison, WI. 487 pp.
Grossenbacher, D. L., R. Briscoe Runquist, E. E. Goldberg, and Y. Brandvain. 2015. Geographic range size is predicted by
plant mating system. Ecology Letters 18: 706-713.
Guma Cintron, Y., Bandyopadhay, Hu, W-‐‐S., Nadathur, G. Transcriptomic analysis of cobalt stress in the marine yeast
Debaryomyces hansenii, FEMS Yeast Research, (Accepted)
Guo, L., Breakspear, A., Zhao, G., Gao, L., Kistler, H.C., Xu, J.R., and Ma, L.J. 2015. Conservation and divergence of the
cAMP-PKA pathway in two plant pathogenic fungi, Fusarium graminearum and F. verticillioides. Molecular Plant
Pathology doi: 10.1111/mpp.12272.
Haase, N., T. Beissinger, C. Hirsch, B. Vaillancourt, S. Deshpande, K. Barry, C.R. Buell, S. Kaeppler, N. de Leon. 2015.
Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked
Segregant Analysis Sequencing and Traditional Linkage Analysis. Genes Genomes and Genetics. 5:1593-1602.
Han D, Nam SI, Ha HK, Kim H, Sadowsky MJ, Lee YK, Hur HG. Bacterial Biogeography Influenced by Shelf-Basin Exchange
in the Arctic Surface Sediment at the Chukchi Borderland. Environ Microbiol. 2015 Sep 28. doi: 10.1111/1462-
2920.13064. [Epub ahead of print] PubMed PMID: 26411339.
Harcombe, W.R. & Bull, J.J. 2005. Impact of phages on a two-species bacterial community. Applied and Environmental
Microbiology 71, 5254-5259.
Harcombe, W.R. & Hoffmann, A. 2004. Wolbachia effects in Drosophila melanogaster: in search of fitness benefits.
Journal of Invertebrate Pathology 87, 45-50.
Harcombe, W.R. 2010. Novel cooperation experimentally evolved between species. Evolution. 64(7) 2166-2172.
Harcombe, W.R. Delaney, N.F., Leiby, N., Klitgord, N. & Marx, C.J. 2013. The ability of flux balance analysis to predict
evolution of central metabolism scales with the initial distance to the optimum. PLoS Computional Biology.
9(6):e1003091.
10
Harcombe, W.R., Riehl, W., Dukovski, I., Granger, B.R. Betts, A., Lang, A.H. Bonilla, G., Kar, A., Leiby, N., Mehta, P., Marx,
C.J., Segre, D. 2014 Predicting the spatio-temporal dynamics of microbial community metabolism. Cell Reports
7(4):1104-1115.
Harcombe, W.R., Springman, R. & Bull, J.J. 2009. Partial conservation of compensatory evolution in phages deleted for a
DNA metabolism gene. BMC Evolutionary Biology. 9(1):106
Hargreaves ML, Shaw KM, Dobbins G, Snippes Vagnone PM, Harper JE, Boxrud D, Lynfield R, Aziz M, Price LB, Silverstein
KA, Danzeisen JL, Youmans B, Case K, Sreevatsan S, Johnson TJ. Clonal dissemination of Enterobacter cloacae harboring
blaKPC-3 in the upper midwestern United States. Antimicrob Agents Chemother. 2015 Oct 5. pii: AAC.01291-15. [Epub
ahead of print] PubMed PMID: 26438492.
Hargreaves ML, Shaw KM, Dobbins G, Snippes Vagnone PM, Harper JE, Boxrud D, Lynfield R, Aziz M, Price LB, Silverstein
KA, Danzeisen JL, Youmans B, Case K, Sreevatsan S, Johnson TJ. Clonal dissemination of Enterobacter cloacae harboring
blaKPC-3 in the upper midwestern United States. Antimicrob Agents Chemother. 2015 Oct 5. pii: AAC.01291-15.
He SL, Yang Y, Morrell PL, Yi TS 2015. Nucleotide sequence diversity and linkage disequilibrium of four nuclear loci in
foxtail millet (Setaria italica). PLoS One 10: e0137088.
Heesung Eum, Romas J. Kazlauskas, Hyun-Joon Ha (2014) Molecular basis for the enantioselectivity of Burkholderia
cepacia lipase toward γ-butyrolactone primary alcohols. Adv Synth Catal. 356, 3585-99;
http://doi.org/10.1002/adsc.201400510
Heisel T, Podgorski H, Staley CM, Knights D, Sadowsky MJ, Gale CA. Complementary Amplicon- Based Genomic
Approaches For the Study of Fungal Communities in Humans. PLoS One 2015 Feb 23;10(2).
Heisel T, Podgorski H, Staley CM, Knights D, Sadowsky MJ, Gale CA. Complementary amplicon-based genomic
approaches for the study of fungal communities in humans. PLoS One. 2015 Feb 23;10(2):e0116705. doi:
10.1371/journal.pone.0116705. eCollection 2015. PubMed PMID: 25706290; PubMed Central PMCID: PMC4338280.
Heisel, T.J., Li, C.Y., Grey, K.M., Gibson, S.I. (2013) Mutations in HISTONE ACETYLTRANSFERASE1 affect sugar response
and gene expression in Arabidopsis. Front. Plant Sci. 4, 245
Hiblot J, Bzdrenga J, Champion C, Chabriere E, Elias M. Crystal structure of VmoLac, a tentative quorum quenching
lactonase from the extremophilic crenarchaeon Vulcanisaeta moutnovskia. Scientific Reports. 2015; 5:8372. PMID:
25670483
Hirsch C, Springer NM, Hirsch CN. 2015. Genomic limitations to RNAseq expression profiling. Plant Journal 84: 491–503.
Hirsch, C.D., C.R. Buell, C.N. Hirsch. A Toolbox of Potato Genetic and Genomic Resources. American Journal of Potato
Research. (in press).
Hirsch, C.D., N. Springer, C.N. Hirsch. 2015. Genomic Limitations to RNAseq Expression Profiling. The Plant Journal.
84(3):491-503.
Hofstad, A.N., T. Nussbaumer, E. Akhunov, S. Shin, K.G. Kugler, H.C. Kistler, K.F.X. Mayer, and G.J. Muehlbauer.
Examining the transcriptional response of the wheat Fhb1 gene to Fusarium graminearum infection and deoxynivalenol
treatment. The Plant Genome (In press).
Hollander, J, EC Snell-Rood, S Foster. 2015. Editorial: New frontiers in phenotypic plasticity and evolution. Heredity, in
press.
Holt, Jonathan F., et al. "Enterococcus faecalis 6-phosphogluconolactonase is required for both commensal and
pathogenic interactions with Manduca sexta." Infection and immunity 83.1 (2015): 396-404.
11
Hong, S.-B., Peebles, C., Shanks, J.V., San, K.-Y., Gibson, S.I. (2006) Expression of the Arabidopsis feedback-insensitive
anthranilate synthase holoenzyme and tryptophan decarboxylase genes in Catharanthus roseus hairy roots. J.
Biotechnol. 122, 28-38
Hong, S.-B., Peebles, C.A.M., Shanks, J.V., San, K.-Y., Gibson, S.I. (2006) Terpenoid indole alkaloid production by
Catharanthus roseus hairy roots induced by Agrobacterium tumefaciens harboring rol ABC genes. Biotechnol. Bioeng.
93, 386-390
Huang, Y., Li, C.Y., Biddle, K.D., Gibson, S.I. (2008) Identification, cloning and characterization of sis7 and sis10 sugar-
insensitive mutants of Arabidopsis. BMC Plant Biol. 8, 104
Huang, Y., Li, C.Y., Pattison, D.L., Gray, W., Park, S., Gibson. S.I. (2010) SUGAR INSENSITIVE3, a RING E3 ligase, is a new
player in plant sugar response. Plant Physiol. 152, 1889-1900
Huang, Y., Li, C.Y., Qi, Y., Park, S., Gibson, S.I. (2014) SIS8, a putative mitogen-activated protein kinase kinase kinase,
regulates sugar resistant seedling development in Arabidopsis. Plant J. 77, 577-588
Hui Lin, Michael Travisano, Romas J. Kazlauskas (2015) Experimental evolution of Trichoderma citrinoviride for faster
deconstruction of cellulose. PLoS ONE, revised manuscript submitted Oct 2015.
I.B. Tikh, M. Held and C. Schmidt-Dannert (2014) BioBrickTM compatible vector system for protein expression in
Rhodobacter sphaeroides. Appl. Microb. Biotechnol. 98(7):3111-9.
I.B. Tikh, M.B. Quin and C. Schmidt-Dannert (2014) A tale of two reductases: extending the bacteriochlorophyll
biosynthetic pathway in E. coli. PLoS One. 9(2):e89734.
J. Tung, L. B. Barreiro, M. B. Burns^, J.-C. Grenier, J. Lynch^, L. Grieneisen, J. Altmann, S. C. Alberts, R. Blekhman, and E.
A. Archie. (2015) Social networks predict gut microbiome composition in wild baboons. eLife, 16;4.
J.K. Dozier, S.L. Khatwani, J.W. Wollack, Y.C. Wang, C. Schmidt-Dannert, M.D. Distefano (2014) Engineering protein
farnesyltransferase for enzymatic protein labeling applications. Bioconjug Chem. 25(7):1203-12.
Jan von Langermann, David M. Nedrud, Romas J. Kazlauskas (2014) Improving the catalytic efficiency of hydroxynitrile
lyase toward aromatic hydroxynitriles by copying active site residues from an esterase that accepts aromatic esters.
ChemBioChem 15, 1931-8
Jang J, Di DY, Han D, Unno T, Lee JH, Sadowsky MJ, Hur HG. Dynamic changes in the population structure of Escherichia
coli in the Yeongsan River basin of South Korea. FEMS Microbiol Ecol. 2015 Nov;91(11). pii: fiv127. doi:
10.1093/femsec/fiv127. Epub 2015 Oct 20. PMID: 26490749.
Jeon JM, Lee HI, Sadowsky MJ, Sugawara M, Chang WS. Characterization of a Functional Role of the Bradyrhizobium
japonicum Isocitrate Lyase in Desiccation Tolerance. Int J Mol Sci. 2015 Jul 22;16(7):16695-709. doi:
10.3390/ijms160716695. PubMed PMID: 26204840; PubMed Central PMCID: PMC4519974.
Johnson, K.C., Yongky, A., Vishwanathan, N., Jacob, N.M., Jayapal, K.P., Goudar, C.T., Karypis, G., Hu, (2014) W-S.
Exploring the transcriptome space of a recombinant BHK cell line through next generation sequencing. Biotechnol.
Bioeng. 111, 770-781. (DOI: 10.1002/bit.25135)
Johnson, T.J. Greater Ciprofloxacin Tolerance as a Possible Selectable Phenotype Underlying the Pandemic Spread of the
H30 Subclone of Sequence Type 131. Antimicrobial Agents and Chemotherapy XX:XXXX.
Johnson, T.J., Singer, R.S., Isaacson, R.E., Danzeisen, J.L., Lang, K., Kobluk, K., Rivet, B., Borewicz, K., Frye, J.G., Englen, M.,
Anderson, J., and Davies, P.R. In Vivo transmission of an IncA/C plasmid in Escherichia coli depends on tetracycline
12
concentration, and acquisition of the plasmid results in a variable cost of fitness. Applied and Environmental
Microbiology 81:3561-70.
Jordan, NR; Dorn, KM ; Runck, B; Ewing, P; Williams, A; Anderson, KA; Felice, L; Haralson, K; Goplen, J; Altendorf, K;
Fernandez, A; Phippen, W; Sedbrook, J; Marks, MD; Wolf, KE; Wyse, DL; Johnson, G. (2015) Sustainable
commercialization of Field Pennycress: a strategy for sustainable intensification of agriculture in central North America.
Under review at Elementa
JR Becker, C Pons, HD Nguyen, M Costanzo, C Boone, CL Myers, Anja-Katrin Bielinsky. Genetic Interactions Implicating
Postreplicative Repair in Okazaki Fragment Processing. PLoS Genet 11 (11), e1005659.
Jun Huang, Bryan J. Jones, Romas J. Kazlauskas (2015) Stabilization of an α/β-hydrolase by introducing proline residues:
salicylic binding protein 2 from tobacco. Biochemistry 54, 4330–41; http://doi.org/10.1021/acs.biochem.5b00333
Kandil MM, Trigo C, Koskinen WC, Sadowsky MJ. Isolation and Characterization of a Novel Imidacloprid-Degrading
Mycobacterium sp. Strain MK6 from an Egyptian Soil. J Agric Food Chem. 2015 May 20;63(19):4721-7. doi:
10.1021/acs.jafc.5b00754. Epub 2015 May 12. PubMed PMID: 25932751.
Kang Y, Sakuroglu M, Krom N, Stanton-Geddes J, Wang M, Lee Y-C, Young ND, Udvard M (2015) Genome-wide
assocation of drought-related and biomass traits with HapMap SNPs in Medicago truncatula. Plant Cell Environ. doi:
10.1111/pce.12520.
Kang, X., Li, W., Zhou, Y., and Ni, M. (2013). A WRKY transcription factor recruits SYG1-like protein SHB1 to activate gene
expression and seed cavity enlargement. PLoS Genetics 9(3): e1003347.
Katagiri, F., Canelon-Suarez, D., Griffin, K., Petersen, J., Meyer, R. K., Siegle, M., and Mase, K. (2015) Design and
Construction of an Inexpensive Homemade Plant Growth Chamber. PLOS ONE 10, e0126826.
Kelly, A.C., Clear, R.M., O’Donnell, K., McCormick, S., Turkington, T.K., Tekauz, A., Gilbert, J., Kistler, H.C., Busman, M.,
and Ward, T.J., 2015. Diversity of fusarium head blight populations and trichothecene toxin types reveals regional
differences in pathogen composition and temporal dynamics. Fungal Genetics and Biology
doi:10.1016/j.fgb.2015.05.016
Khodursky A, Guzman EC, Hanawalt PC. Thymineless Death Lives On: New Insights into a Classic Phenomenon. Annual
review of microbiology 2015, Aug. 7; 69.
Khoruts A, Sadowsky MJ, Hamilton MJ. Development of fecal microbiota transplantation suitable for mainstream
medicine. Clin Gastroenterol Hepatol. 2015 Feb;13(2):246-50. doi: 10.1016/j.cgh.2014.11.014. Epub 2014 Nov 20.
Review. PubMed PMID: 25460566.
Kishore, G.M., Ruff, T.G., Arondel, V.J.M.A., Gibson, S.I., Somerville, C.R. (2010). Altered linolenic and linoleic acid
content in plants. Patent #: US7790959
Kistler, H.C. and Broz, K. 2015. Cellular compartmentalization of secondary metabolism. Frontiers in Microbiology 6:68
doi:10.3389/fmicb.2015.00068.
KM Dorn, JD Fankhauser, DL Wyse, MD Marks (2015) A draft genome of field pennycress (Thlaspi arvense) provides tools
for the domestication of a new winter biofuel crop DNA Research doi: 10.1093/dnares/dsu045
Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra D, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak
JM, Huang H, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ. Complex host genetics influence the
microbiome in inflammatory bowel disease. Genome Medicine 6(12), 107.
13
Knoblauch, M., Vendrell, M., de Leau, E., Paterlini, A., Knox, K., Ross-Elliot, T., Reinders, A., Brockman, S. A., Ward, J. M.,
and Oparka, K. (2015) Multispectral Phloem-mobile probes:properties and applications. Plant Physiol. 167: 1121-1120.
Koets AP, Eda S, Sreevatsan S. The within host dynamics of Mycobacterium avium ssp. paratuberculosis infection in
cattle: where time and place matter. Vet Res. 2015 Jun 19;46:61. doi: 10.1186/s13567-015-0185-0. PubMed PMID:
26092382; PubMed Central PMCID: PMC4473847.
Kono TJY, Fu F, Mohammadi M, Hoffman PJ, Liu C, Muehlbauer GJ, Stupar RM, Tiffin P, Smith KP, Fay JC, Morrell PL 2015.
The role deleterious substitutions in crop genomes. bioRxiv
Kreiser M, Giblin C, Murphy R, Fiesel P, Braun L, Johnson G, Wyse D, Cohen JD Conversion of indole-3-butyric acid to
indole-3-acetic acid in shoot tissue of hazelnut (Corylus) and elm (Ulmus). J Plant Growth Regulation (Revision submitted
10/2/15)
Krumholz EW, Libourel IGL (2015) Sequence-Based Network Completion Reveals the Integrality of Missing Reactions in
Metabolic Networks. J Biol Chem 290 (31), 19197-19207
Kudirkien, E., Bager, R.J., Johnson, T.J., Bojesen, A.M. Chaperone-usher fimbriae in a diverse selection of Gallibacterium
genomes. BMC Genomics 15:1093.
Lan Chun C, Kahn CI, Borchert AJ, Byappanahalli MN, Whitman RL, Peller J, Pier C, Lin G, Johnson EA, Sadowsky MJ.
Prevalence of toxin-producing Clostridium botulinum associated with the macroalga Cladophora in three Great Lakes:
growth and management. Sci Total Environ. 2015 Apr 1;511:523-9. doi: 10.1016/j.scitotenv.2014.12.080. Epub 2015 Jan
8. PubMed PMID: 25577739.
Lang, K., and Johnson, T.J. Transcriptome modulations due to A/C2 plasmid acquisition. Plasmid XX:XXXX
LaPara, T., Madson, M., Borchardt, S., Lang, K., and Johnson, T.J. Multiple Discharges of Treated Municipal Wastewater
Have a Small Effect on the Quantities of Numerous Antibiotic Resistance Determinants in the Upper Mississippi River.
Environmental Science and Technology XX:XXXX.
Le, H., Vishwanathan, N., Jacob, N. M., Gadgil, M. and Hu, W.-S. (2015) Cell Line Development for Biomanufacturing
Processes: Recent Advances and An Outlook. Biotechnol. Lett., 37,1553-1564.
Lebarbenchon C, Pedersen JC, Sreevatsan S, Ramey AM, Dugan VG, Halpin RA, Ferro PJ, Lupiani B, Enomoto S, Poulson
RL, Smeltzer M, Cardona CJ, Tompkins SM, Wentworth DE, Stallknecht DE, Brown JD. H7N9 influenza A virus in turkeys in
Minnesota. J Gen Virol. 2015 Feb;96(Pt 2):269-76. doi: 10.1099/vir.0.067504-0. Epub 2014 Oct 28. PubMed PMID:
25351723; PubMed Central PMCID: PMC4298677.
LeBlanc, N., Kinkel, L.L. and Kistler, H.C. 2015. Soil fungal communities respond to grassland plant community richness
and soil edaphics. Molecular Ecology 70: 188-195. doi:10.1007/s00248-014-0531-1
Leiby, N.L., Harcombe, W.R., Marx, C.J. 2012. Multiple long-term, experimentally-evolved population of Escherichia coli
acquire dependence upon citrate as an iron chelator for optimal growth on glucose. BMC Evolutionary Biology. 12:151.
Levar CE, Chan CH, Mehta-Kolte MG, Bond DR. 2014. An inner membrane cytochrome required only for reduction of
high redox potential extracellular electron acceptors. MBio 5:e02034.
Li J, Dukowic-Schulze S, Lindquist IE, Farmer AD, Kelly B, Li T, Smith AG, Retzel EF, Mudge J, Chen C (2015). The plant-
specific protein FEHLSTART controls male meiotic entry, initializing meiotic synchronization in Arabidopsis. Plant J. Doi:
10.1111/tpj.13026.
14
Li J, Stoddard TJ, Demorest ZL, Lavoie PO, Luo S, Clasen BM, Cedrone F, Ray EE, Coffman AP, Daulhac A, Yabandith A,
Retterath AJ, Mathis L, Voytas DF, D'Aoust MA, Zhang F. (2015). Multiplexed, targeted gene editing in Nicotiana
benthamiana for glyco-engineering and monoclonal antibody production. Plant Biotechnology Journal.
Li Q, Eichten SR, Hermanson PJ, Zaunbrecher V, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess
D, Richman TA, Kaeppler SM, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Jeddeloh JA, Springer NM. 2014.
Genetic perturbation of the maize methylome. Plant Cell 26:4602-4616.
Li Q, Song J, West PT, Zynda G, Eichten SR, Vaughn MW, Springer NM. 2015. Examining the causes and consequences of
context-specific differential DNA methylation in maize. Plant Physiology 168(4):1262-1274.
Li Q, Suzuki M, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J, Richmond T, Rosenbaum H,
Burgess D, Springer NM, Greally JM. 2015. Post-conversion targeted capture of modified cytosines in mammalian and
plant genomes. Nucleic Acids Research 43(12):e81.
Li X, Harwood VJ, Nayak B, Staley C, Sadowsky MJ, Weidhaas J. A novel microbial source tracking microarray for
pathogen detection and fecal source identification in environmental systems. Environ Sci Technol. 2015 Jun
16;49(12):7319-29. doi: 10.1021/acs.est.5b00980. Epub 2015 May 27. PubMed PMID: 25970344.
Li, C.Y., Leopold, A.L., Sander, G.W., Shanks, J.V., Zhao, L., Gibson, S.I. (2013) The ORCA2 transcription factor plays a key
role in regulation of the terpenoid indole alkaloid pathway. BMC Plant Biol. 13, 155
Li, C.Y., Leopold, A.L., Sander, G.W., Shanks, J.V., Zhao, L., Gibson, S.I. (2015) CrBPF1 overexpression alters transcript
levels of terpenoid indole alkaloid biosynthetic and regulatory genes. Front. Plant Sci. 6, 818
Li, J., S. Dukowic-Schulze1 I.E. Lindquist, A.D. Farmer, B. Kelly, T. Li, Al.G. Smith, E.F. Retzel, J Mudge and C. Chen. 2015.
The plant-specific protein FEHLSTART controls male meiotic entry, initializing meiotic synchronization in Arabidopsis.
Plant J, DOI: 10.1111/tpj.13026.
Li, Q, J. Gent, G. Zynda, J. Song, I. Makarevitch, C.D. Hirsch, C.N. Hirsch, R.K. Dawe, T. Madzima, K. McGinnis, D. Lisch, R.
Schmitz, M. Vaughn, N. Springer. RNA-directed DNA methylation enforces boundaries between heterochromatin and
euchromatin in the maize genome. PNAS. (in press).
Li, X., S. Shin, S. Heinen, R. Dill-Macky, F. Berthiller, T. Clemente, S. McCormick and G.J. Muehlbauer. 2015. Transgenic
wheat expressing a barley UDP-glucosyltransferase detoxifies deoxynivalenol and provides high levels of Fusarium head
blight resistance. Molecular Plant-Microbe Interactions (In press).
Liang, C, JLM Gutknecht, and TC Balser (2015) Microbial lipid and amino sugar responses to long-term simulated global
environmental changes in a California annual grassland. Frontiers in Microbiology 6: 385.
Liang, J., Lofgren, L., Ma, Z., Ward, T.J. and Kistler, H.C. 2015. Population subdivision of Fusarium graminearum from
barley and wheat in the upper Midwestern United States at the turn of the century. Phytopathology (In press).
Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fummagalli M, Yang MA, Gamba C, Ginolhac
A, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover C, Lorente B, Nedoluzhko A, Boulougina E, Neuditschko M,
Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Sicheritz-Ponten T, Popov R, Alekseev AN, Rubin E,
McCue ME, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J,
Prokhortchouk E, Orlando L. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to
subarctic environments. PNAS in press.
Lin, R., Glazebrook, J., Katagiri, F., Orf, J.H., and Gibson, S.I. Identification of differentially expressed genes between
developing seeds of different soybean cultivars. Genomics Data 6:92-98. doi:10.1016/j.gdata.2015.08.005 (2015).
15
Lin, R., Glazebrook, J., Katagiri, F., Orf, J.H., Gibson, S.I. (2015) Identification of differentially expressed genes between
developing seeds of different soybean cultivars. Genom. Data 6, 92-98
Linhares LL, Yang M, Sreevatsan S, Munoz-Zanzi CA, Torremorell M, Davies PR. The effect of anatomic site and age on
detection of Staphylococcus aureus in pigs. J Vet Diagn Invest. 2015 Jan;27(1):55-60. doi: 10.1177/1040638714559598.
PubMed PMID: 25525138.
Liu Y, Wang Z, Liu J, Levar C, Edwards MJ, Babauta JT, Kennedy DW, Shi Z, Beyenal H, Bond DR, Clarke TA, Butt JN,
Richardson DJ, Rosso KM, Zachara JM, Fredrickson JK, Shi L. 2014. A trans-outer membrane porin-cytochrome protein
complex for extracellular electron transfer by Geobacter sulfurreducens PCA. Env Microbiol Rep 6:776–785.
Liu, C., Tan, C., Zheng, H., Yang, M., Xu, Z., Wang, X., Wei, L., Tang, B., Liu, F., Zhang, Y., Ding, Y., Tang, X., Wu, B., Chen,
H., Johnson, T.J. Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain
PCN033. BMC Genomics XX:XXXX.
Livne, S., Lor, V.S., Nir, I., Eliaz, N., Aharoni, A., Olszewski, N.E., Eshed, Y., and Weiss, D. (2015). Uncovering DELLA-
Independent Gibberellin Responses by Characterizing New Tomato procera Mutants. The Plant cell 27, 1579-1594.
Lor, V.S., and Olszewski, N.E. (2015). GA signalling and cross-talk with other signalling pathways. Essays Biochem 58, 49-
60.
Lorenz, A. and K.P. Smith. 2015. Adding genetically distant individuals to training populations reduces genomic
prediction accuracy in barley. Crop Sci. doi: 10.2135/cropsci2014.12.0827
Lowder LG, Zhang D, Baltes NJ, Paul JW, Tang X, Zheng X, Voytas DF, , Hsieh T, Zhang Y, Qi Y. (August 25, 2015) A
CRISPR/Cas9 toolbox for gene editing and transcriptional regulation. Plant Physiology.
LT MacNeil, C Pons, HE Arda, GE Giese, CL Myers, AJM Walhout. Transcription Factor Activity Mapping of a Tissue-
Specific In Vivo Gene Regulatory Network. Cell Systems 1 (2), 152-162.
Lu Y, Samac DA, Glazebrook J, Ishimaru CA. Complete genome sequence of Clavibacter michiganensis subsp. insidiosus
R1-1 using PacBio single-molecule realtime technology.Genome Announcements 3(3):e00396-15.
doi:10.1128/genomeA.00396-15 (2015).
Lu Y., Hatsugai N., Katagiri F., Ishimaru C., and Glazebrook, J. Putative Serine Protease Effectors of Clavibacter
michiganensis Induce a Hypersensitive Response in the Apoplast of Nicotiana Species. Mol. Plant-Microbe Int. in press
(2015).
Lu, Y., D. A. Samac, J. Glazebrook, and C. A. Ishimaru. 2015. Complete genome sequence of Clavibacter michiganensis
subsp. insidiosus R1-1 using PacBio Single-Molecule Real-Time Technology. Genome Announce. 3(3):e00396-15.
doi:10.1128/genomeA.00396-15.
Lu, Y., Hatsugai, N., Katagiri, F., Ishimaru, C. A., Glazebrook, J. (2015) “Putative Serine Protease Effectors of Clavibacter
michiganensis Induce a Hypersensitive Response in the Apoplast of Nicotiana Species” Mol Plant Microbe Interact, Epub
ahead of print.
Lu, Y., N. Hatsugai, F. Katagiri, C. A. Ishimaru, and J. Glazebrook. 2015. Putative serine protease effectors of Clavibacter
michiganensis induce a hypersensitive response in the apoplast of Nicotiana species. Mol. Plant Microbe Inter. 28:1216-
1226 http://dx.doi.org/10.1094/MPMI-02-15-0036-R
Luo S, Li J, Stoddard TJ, Baltes NJ, Demorest ZL, Clasen BM, Coffman A, Retterath A, Mathis L, Voytas DF, Zhang F. (2015).
Non-transgenic Plant Genome Editing Using Purified Sequence-Specific Nucleases. Molecular Plant.
16
Lusk BG, Badalamenti JP, Parameswaran P, Bond DR, Torres CI. 2015. Draft Genome Sequence of the Gram-Positive
Thermophilic Iron Reducer Thermincola ferriacetica Strain Z-0001T. Genome Announc 3.
M. B. Burns, J. Lynch, T. K. Starr, D. Knights, and R. Blekhman. (2015) Virulence genes are a signature of the microbiome
in the colorectal tumor microenvironment. Genome Medicine, 24; 7(1):55.
M.B. Quin and C. Schmidt-Dannert (2014) Designer microbes for biosynthesis. Curr. Opin. Biotechnol. 29C:55-61 (ePub
ahead of print).
M.B. Quin, C. Flynn and C. Schmidt-Dannert (2014) Traversing the fungal terpenome. Nat. Prod. Rep. 31:1449-1473.
Makarevitch I, Waters AJ, West PT, Stitzer M, Ross-Ibarra J, Springer NM. 2015. Transposable elements contribute to
activation of maize genes in response to abiotic stress. PLoS Genetics 11:e1004915.
Makarevitch, I., A. Waters, P. West, M. Stitzer, C. Hirsch, J. Ross-Ibarra, N. Springer. 2015. Transposable elements
contribute to activation of maize genes in response to abiotic stress. PLoS Genetics. 11(1):e1004915.
Martinez-Vaz B, Denny R, Sadowsky M, Young ND (2015) An alternative approach to “Identification of Unknowns”:
designing a protocol to verify the identities of nitrogen fixing bacteria. Journal Microbiology and Biology Education, In
press.
McCue ME, Geor RJ, Shultz NE. Equine Metabolic Syndrome: a complex disease influenced by genetics and the
environment. Journal of Equine Veterinary Science 35 (5) (2015): 367-375.
McGaugh, S.E., C.-H. Kuo, D. Reding, E. Addis, L.E.Flagel, F. J. Janzen, A. Broniwoski, T. Schwartz. 2015 Rapid molecular
evolution across amniotes of IIS/TOR network. Proceedings of the National Academy of Sciences. 112: 7055-7060.
McGaugh, S.E., C.-H. Kuo, D. Reding, E. Addis, L.E.Flagel, F. J. Janzen, A. Broniwoski, T. Schwartz. Rapid molecular
evolution across amniotes of IIS/TOR network. Proceedings of the National Academy of Sciences. 112: 7055-7060.
McGinnis, E. E., M. H. Meyer and A. G. Smith. 2010. Sweet and Sour: A Scientific and Legal Look at Herbicide-Tolerant
Sugar Beet. Plant Cell 22: 1653-1657. (10.1105/tpc.110.077198).
McGinnis, E.E., A.G. Smith, M.H. Meyer. 2014. A post-floral initiation chilling treatment controls dichogamy sequence in
Carex pensylvanica. Hort Tech 24:301-306.
McGinnis, E.E., M. Meyer and A.G. Smith. 2012. Analysis of U.S. Genetically Engineered Crop Regulation and Litigation.
Crop Sci. 52:991-1002.
McNally, R. R., C. A. Ishimaru and D. K. Malvick. 2015. Novel PCR-mediated assay for detection, identification and
quantification of Clavibacter michiganensis subsp. nebraskensis. Phytopathology 105(Suppl. ):S4.94.
McNeil, K.J. and A.G. Smith. 2009. A glycine-rich protein that facilitates exine formation during tomato pollen
development. Planta 231: 793-808.
Medema, M, et al. (2015) Minimum information about a biosynthetic gene cluster. Nat. Chem. Biol. 11:625-631.
Mertensotto MJ, Drees JJ, Augustin LB, Schottel JL, Saltzman DA. Expression of periplasmic chaperones in Salmonella
Typhimurium reduces its viability in vivo. Curr Microbiol. 2015 Mar;70(3):433-5. PubMed PMID: 25432864.
Meulemans J, Ward T, Knights D. Syntax and Semantics of Coding in Python. Hydrocarbon and Lipid Microbiology
Protocols (2015).
Michael Kantar, Catrin Tyl, Kevin Dorn, Xiaofei Zhang, Jacob Jungers, Joe Kaser, Rachel Schendel, James Eckberg, Bryan
Runck, Mirko Bunzel, Nick Jordan, Robert Stupar, M. David Marks, James Anderson, Gregg Johnson, Craig Sheaffer,
17
Tonya Schoenfuss, Baraem Ismail, George Heimpel, and Donald Wyse (0000) Perennial Grain and Oilseed Crops. Annu.
Rev. Plant Biol. doi: 10.1146/annurev-arplant-043015-112311
Michno JM, Wang X, Liu J, Curtin SJ, Kono TJ, Stupar RM. (2015) CRISPR/Cas mutagenesis of soybean and Medicago
truncatula using a new web-tool and a modified Cas9 enzyme. GM Crops Food (in press).
Millett, B.P., Gao, L., Iorizzo, M., Carputo, D., and Bradeen, J.M. 2015. Potato tuber blight resistance phenotypes
correlate with RB transgene transcript levels in an age-dependent manner. Phytopathology dx.doi.org/10.1094/PHYTO-
10-14-0291-R.
Mitri, C., Bischoff, E., Takashima, E., Williams, M., Eiglmeier, K., Pain, A., Guelbeogo, W.M., Gneme, A., Brito-Fravallo, E.,
Holm, I., et al. (2015). An Evolution-Based Screen for Genetic Differentiation between Anopheles Sister Taxa Enriches for
Detection of Functional Immune Factors. PLoS Pathog 11, e1005306.
Mitri, C., Markianos, K., Guelbeogo, W.M., Bischoff, E., Gneme, A., Eiglmeier, K., Holm, I., Sagnon, N., Vernick, K.D., and
Riehle, M.M. (2015). The kdr-bearing haplotype and susceptibility to Plasmodium falciparum in Anopheles gambiae:
genetic correlation and functional testing. Malaria journal 14, 391.
Moche, M., Gutknecht, J., Schulz, E., Langer, U., and Rinklebe, J. (2015) Monthly dynamics of microbial community
structure and their controlling factors in three floodplain soils. Soil Biology and Biochemistry 90: 169-178
Mohammadi, M., A. Budde, R. Horsley, S. Ullrich, T. Blake, P. Hayes, D. Hole, D. Obert, B. Cooper, S. Chao, and K.P. Smith.
2015. A genome-wide association study of malting quality across eight U.S. barley breeding programs. Theor. Appl.
Genet. 128:705-721. DOI 10.1007/s00122-015-2465-5
Mohammadi, M., Tiede, T., and Smith K.P. 2015. PopVar: A genome-wide procedure for predicting genetic variance and
correlated response in bi-parental breeding populations Crop Sci. - doi:10.2135/cropsci2015.01.0030
Montassier E, Al-Ghalith GA, Ward T, Corvec S, Potel G, Moreau P, de la Cochetiere MF, Batard E , Knights D.
Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection. (under review).
Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, des Varannes SB, Massart S, Moreau P, Potel G, de La Cochetiere MF,
Batard E and Knights D. Chemotherapy-driven Dysbiosis in the Intestinal Microbiome. Alimentary Pharmacology &
Therapeutics 42.5 (2015): 515-528.
Moore M, Ostry M, Hegeman AD, and Martin AC (2015) Inhibition of Ophiognomonia clavigignenti-juglandacearum by
Juglans species bark extracts, Plant Dis, 99 (3): 401-408.
Mujic A., Durall D. M, Spatafora J. W., P.G. Kennedy. Competitive avoidance not edaphic specialization drives vertical
niche partitioning of sister species of ectomycorrhizal fungi. New Phytologist, in press.
Mulukutla, B., Yongky, A, Daoutidis, P. and Hu, W.-S. (2014) Bistability in glycolysis pathway as a physiological switch in
energy metabolism. Plos One, 9(6), e98756. Doi:10.1371.
Muñoz-Amatriaín, M., S. Lonardi, M.C. Luo, K. Madishetty, J.T. Svensson, M.J. Moscou, S. Wanamaker, T. Jiang, A.
Kleinhofs, G.J. Muehlbauer, R.P Wise, N. Stein, Y. Ma, E. Rodriguez, D. Kudrna, P.R. Bhat, S. Chao, P. Condamine, S.
Heinen, J. Resnik, R. Wing, H.N. Witt, M. Alpert, M. Beccuti, S. Bozdag, F. Cordero, H. Mirebrahim, R. Ounit, Y. Wu, F.
You, J. Zheng, H. Šimková, J. Doležel J. Grimwood, J. Schmutz, D. Duma, L. Altschmied, T. Blake, P. Bregitzer, L. Cooper,
M. Dilbirligi, A. Falk, L. Feiz, A. Graner, P. Gustafson, P.M. Hayes, P. Lemaux, J. Mammadov, and T.J. Close. 2015.
Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome. The Plant J. 84:216-227.
Murren, C. J., J. R. Auld, H. Callahan, C. Ghalambor, C. A. Handelsman, M. A. Heskel, J. G. Kingsolver, H. J. Maclean, J.
Masel, H. Maughan, D. W. Pfennig, R. A. Relyea, S. Seiter, E. Snell-Rood, U. K. Steiner, and C. D. Schlichting. 2015.
Perspective: Revisiting the costs and limits to phenotypic plasticity. In press, Heredity. doi: 10.1038/hdy.2015.8
18
Mutlu, B.R., K. Hirschey, L.P. Wackett, and A. Aksan (2015) Optimization of aging, drying and storage conditions for
biocatalytic silica gel. J.Sol-Gel Sci. Technol. 74: 823-833. DOI 1007/s10971-015-3690-8.
Mutlu, B.R., S. Yeom, L.P. Wackett, and A. Aksan (2015) Modelling and optimization of a bioremediation system utilizing
silica gel encapsulated whole-cell biocatalyst. Chem. Eng. J. 259: 574-580.
Narożna D, Pudełko K, Króliczak J, Golińska B, Sugawara M, Mądrzak CJ, Sadowsky MJ. Survival and Competitiveness of
Bradyrhizobium japonicum Strains 20 Years after Introduction into Field Locations in Poland. Appl Environ Microbiol.
2015 Aug 15;81(16):5552-9. doi: 10.1128/AEM.01399-15. Epub 2015 Jun 5. PubMed PMID: 26048934; PubMed Central
PMCID: PMC4510166.
Nelson MI, Wentworth DE, Das SR, Sreevatsan S, Killian ML, Nolting JM, Slemons RD, Bowman AS. Evolutionary Dynamics
of Influenza A Viruses in US Exhibition Swine. J Infect Dis. 2015 Aug 4. pii: jiv399. [Epub ahead of print] PubMed PMID:
26243317.
Nelson MS, Sadowsky MJ. Secretion systems and signal exchange between nitrogen-fixing rhizobia and legumes. Front
Plant Sci. 2015 Jul 1;6:491. doi: 10.3389/fpls.2015.00491. eCollection 2015. Review. PubMed PMID: 26191069; PubMed
Central PMCID: PMC4486765.
Nguyen N., D. Smith, K. Peay, P. G. Kennedy. 2015. Parsing ecological signal from noise in next-generation amplicon
sequencing. New Phytologist, 205:1389-1393.
Nguyen N.H., Song Z., Bates S.T., Branco S., Tedersoo L., Menke J., Schilling J.S., P.G. Kennedy. FUNGuild: An open
annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology, in press.
O’Quin, K. and S.E. McGaugh. 2015. The genetic bases of troglomorphy in Astyanax: How far we have come and where
do we go from here? in Biology and Evolution of the Mexican Cavefish. eds Alex Keene, Masato Yoshizawa, and Suzanne
McGaugh. Elsevier, in press
O’Rourke, J.A., Fu, F., Bucciarelli, B., Yang, S.S., Samac, D.A., Lamb, J.F.S., Monteros, M., Graham, M.A., Gronwald, J.W.,
Krom, N., Li, J., Dai, X., Zhao, P.X., and Vance, C.P. 2015. The Medicago sativa Gene Index 1.2: Using a web-accessible
gene expression atlas to investigate gene expression differences between two Medicago sativa subspecies. BMC
Genomics 16:502.
O’Sullivan, D.J. 2015. The Contribution of Bifidobacteria to an Optimally Functioning Human Gut Microbiota. Sixth
International Conference on Food Factors, Seoul, Korea
Omolo, M.A, Wong, Z-Z., Mergan, A.K., Hastings, J.C., Le, N.C., Reiland, H.A. Case, K.A., and D.J. Baumler. 2014.
Antimicrobial properties of chili peppers. J. Infectious Diseases and Therapy. 2:145.
Osborn MJ, Gabriel R, Webber BR, DeFeo AP, McElroy AN, Jarjour J, Starker CG, Wagner JE, Joung JK, Voytas DF, von
Kalle C, Schmidt M, Blazar BR, Tolar J. (Feb. 2015) Fanconi Anemia Gene Editing by the CRISPR/Cas9 System. Human
Gene Therapy. 26(2):114-126.
Ostrer L, Hamann BL, Khodursky A: Perturbed states of the bacterial chromosome: a thymineless death case study.
Frontiers in Microbiology 2015, 24; 6: 363 .
Pannell, J. R., J. R. Auld, Y. Brandvain, M. Burd, J. W. Busch, P-O Cheptou, J. K. Conner, E. E. Goldberg, A-G Grant, D. L.
Grossenbacher, S. M. Hovick, B. Igic, S. Kalis, T. Petanidou, A. M.Randle, R. Rubio de Casas, A. Pauw, J. C. Vamosi and A.
A. Winn. 2015. The scope of Baker’s law. New Phytologist 208: 656–667.
Pardey, Philip G., Chan-Kang, Connie, Beddow, Jason M., & Dehmer, Steven P. (2015). Long-run and Global R&D Funding
Trajectories: The U.S. Farm Bill in a Changing Context. American Journal of Agricultural Economics, 97(5), 1312-1323. doi:
10.1093/ajae/aav035
19
Peebles, C.A.M., Gibson, S.I., Shanks, J.V., San, K.-Y. (2007) Characterization of an ethanol-inducible promoter system in
Catharanthus roseus hairy roots. Biotechnol. Prog. 23, 1258-1260
Peebles, C.A.M., Gibson, S.I., Shanks, J.V., San, K.-Y. (2007) Long-term maintenance of a transgenic Catharanthus roseus
hairy root line. Biotechnol. Prog. 23, 1517-1518
Peebles, C.A.M., Hong, S.-B., Gibson, S.I., Shanks, J.V., San, K.-Y. (2006) Effects of terpenoid precursor feeding on
Catharanthus roseus hairy roots over-expressing the alpha or the alpha and beta subunits of anthranilate synthase.
Biotechnol. Bioeng. 93, 534-540
Pei, D., Hill-Clemons, C., Carissimo, G., Yu, W., Vernick, K.D., and Xu, J. (2015). Draft Genome Sequences of Two Strains of
Serratia spp. from the Midgut of the Malaria Mosquito Anopheles gambiae. Genome Announc 3.
Petersen JL, Mickelson JR, Valberg SJ, McCue ME. Genome-wide SNP data shows little differentiation between the
Appaloosa and other American stock horse breeds. Animal Genetics Article first published online: 22 MAY 2015 DOI:
10.1111/age.12301.
Pfennig, D.W., Harcombe, W.R. & Pfennig, K.S. 2001. Evolution of mimicry in snakes. Nature 410, 323.
Pfennig, D.W., Harper, G.R., Brumo, A.F., Harcombe, W.R. & Pfennig, K.S. 2007. Population differences in predation on
Batesian mimics in allopatry with their model: selection against mimics is strongest when they are common. Behavioral
Ecology and Sociobiology 61, 505-511.
Piotrowski JS, Okada H, Lu F, Li SC, Hinchman L, Ranjan A, Smith DL, Kigbee AJ, Ulbrich A, Coon JJ, Deshpande R,
Bukhman YV, McIlwain S, Ong IM, Myers CL, Boone C, Landick R, Ralph J, Kabbage M, Ohya Y. Plant-derived antifungal
agent poacic acid targets β-1,3-glucan. PNAS 2015 Mar 24;112(12):E1490-7.
Plucain, J. Hindre, T., Le Gac M., Tenaillon, O., Cruvioller, S., Medigue, C., Leiby. N., Harcombe, W.R., Marx, C.J., Lenski,
R., Schnedier, D. 2014. Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.
Science 343(6177):1366-1369.
Poets AM, Fang Z, Clegg MT, Morrell PL 2015. Barley landraces are characterized by geographically heterogeneous
genomic origins. Genome Biol 16: 173.
Poets AM, Mohammadi M, Seth K, Wang H, Kono TJY, Fang Z, Muehlbauer GJ, Smith KP, Morrell PL 2015. The effects of
both recent and long-term selection and genetic drift are readily evident in North American barley breeding populations.
bioRxiv
Pons C, Costanzo M, Boone C, Myers CL. Systems Genetics - linking genotypes and phenotypes: Computational
paradigms for analyzing genetic interaction networks. Cambridge University Press 2015.
Poynter JN, Bestrashniy JR, Silverstein KA, Hooten AJ, Lees C, Ross JA, Tolar J. Cross platform analysis of methylation,
miRNA and stem cell gene expression data in germ cell tumors highlights characteristic differences by tumor histology.
BMC Cancer. 2015 Oct 23;15:769. doi: 10.1186/s12885-015-1796-6.
Quandt, A.C., Bushley, K. E., and Spatafora, J.W. 2015. The genome of the truffle-parasite Tolypocladium
ophioglossoides and the evolution of antifungal peptiabiotics. BMC Genomics, 16:553.
Quin MB, Michel SN, C. Schmidt-Dannert (2015) Moonlighting Metals: Insights into Regulation of Cyclization Pathways in
Fungal Δ(6) -Protoilludene Sesquiterpene Synthases. Chembiochem. 16(15):2191-9.
Quin, K. and S.E. McGaugh. 2015. The genetic bases of troglomorphy in Astyanax: How far we have come and where do
we go from here? in Biology and Evolution of the Mexican Cavefish. eds Alex Keene, Masato Yoshizawa, and Suzanne
McGaugh. Elsevier, in press
20
R. Blekhman, J. K. Goodrich, K. Huang, Q. Sun, R. Bukowski, A. Keinan, R. E. Ley, D. Gevers, and A. G. Clark. (2015) Host
genetic variation impacts microbiome composition across human body sites. Genome Biology 16:191
Radian, A., K.A. Aukema, A. Aksan, L.P. Wackett (2015) A silica gel for enhanced activity and hypochlorite-protection of
cyanuric acid hydrolase in a recombinant E. coli. mBio doi:10.1128/mBio.01477-15.
Ramdani, G., Naissant, B., Thompson, E., Breil, F., Lorthiois, A., Dupuy, F., Cummings, R., Duffier, Y., Corbett, Y.,
Mercereau-Puijalon, O., et al. (2015). cAMP-Signalling Regulates Gametocyte-Infected Erythrocyte Deformability
Required for Malaria Parasite Transmission. PLoS Pathog 11, e1004815.
Raschke, A., Ibañez, C., Ullrich, K.K., Anwer, M.U., Becker, S., Glöckner, A., Trenner, J., Denk, K., Saal, B., Sun, X., Ni, M.,
Davis, S.J., Delker, C., Quint, M. (2015). Natural variants of ELF3 affect thermomorphogenesis by transcriptionally
modulating PIF4-dependent auxin response genes. BMC Plant Biol. 15:197. doi: 10.1186/s12870-015-0566-6.
Redmond, S.N., Eiglmeier, K., Mitri, C., Markianos, K., Guelbeogo, W.M., Gneme, A., Isaacs, A.T., Coulibaly, B., Brito-
Fravallo, E., Maslen, G., et al. (2015). Association mapping by pooled sequencing identifies TOLL 11 as a protective factor
against Plasmodium falciparum in Anopheles gambiae. BMC Genomics 16, 779.
Reiland, H.A. Omolo, M.A, Johnson, T.J., and D.J. Baumler. 2014. A survey of Escherichia coli O157:H7 virulence factors:
The first 25 years and 13 genomes. Advances in Microbiology. 4:7.
Reinders, A., Ward, J. M. (2015) Investigating polymorphisms in MATP (SLC45A2) using sucrose transporters as a model.
Mol. Med. Rep. 12:1393-1398.
Response-Guided Community Detection: Application to Climate Index Discovery. G. A. Bello, M. Angus, N. Pedemane, J.
K. Harlalka, F. H. M. Semazzi, V. Kumar, and N. F. Samatova. European Conference on Machine Learning and Principles
and Practice of Knowledge Discovery in Databases. Porto, Portugal. September 7-11, 2015.
Rodrigues, A.F., Formas-Liveira, A.S., Bandeira, V., Alves, P.M., Hu, W-S. and Coroadinha, A.S., Metabolic pathways
recruited in the production of a recombinant enveloped virus: mining targets for process and cell engineering. Metabolic
Eng. (accepted).
Romas J. Kazlauskas (2016) Chapter 5. Hydrolysis and formation of carboxylic acid derivatives in Organic Synthesis using
Biocatalysis, Goswami, A, Stewart, J. S. Eds., pp 127–48; http://doi.org/10.1016/B978-0-12-411518-7.00005-6
Roux, M.E., Rasmussen, M.W., Palma, K., Lolle, S., Regué, A.M., Bethke, G., Glazebrook, J., Zhang, W., Sieburth, L.,
Larsen, M.R., Mundy, J., and Petersen, M. The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4
and immune receptor SUMM2. The EMBO Journal, 34:593-608. doi: 10.15252/embj.201488645 (2015).
S.E. Bloch and C. Schmidt-Dannert (2014) Construction of a chimeric biosynthetic pathway for the de novo biosynthesis
of rosmarinic acid in Escherichia coli. ChemBiochem 15:2393-401.
Sakkos, J.K., D.P. Kieffer, B.R. Mutlu, L.P. Wackett and A. Aksan (2015) Design of a silica encapsulation platform using a
model hydrocarbon degrader Pseudomonas sp. NCIB 9816. Biotechnol. Bioeng., doi: 10.1002/bit.25821.
Samac, D.A., Schraber, S., and Barclay, S. 2015. A mineral seed treatment for control of seedling diseases of alfalfa
suitable for organic production systems. Plant Dis. 99:614-620.
Samuel, L., X. Li, A. Hu, N. Todt, J. Yang, X. Li, X. Yu, G.J. Muehlbauer, M.C.P. Timmermans, J. Yu, P.S. Schnable, and M.J.
Scanlon. Genetic control of morphometric diversity in the maize shoot apical meristem. Nature Communications (In
press).
Schlatter, D.C., Bakker, M.G., Bradeen, J.M., and Kinkel, L.L. 2015. Plant community richness and microbial interactions
structure bacterial communities in soil. Ecology 96:134-142.
21
Schlichting, CD, Josh R. Auld, Hilary Callahan, Cameron K. Ghalambor, Corey A. Handelsman, Mary A. Heskel, Joel G.
Kingsolver, Heidi J. Maclean, Joanna Masel, Heather Maughan, David W. Pfennig, Rick A. Relyea, Sarah Seiter, Emilie
Snell-Rood, Ulrich K. Steiner, and Courtney J. Murren. Detecting costs of plasticity. In revision.
Schmidt, J, E Schulz, B Michalzik, F Buscot, and JLM Gutknecht (2015) Carbon input and crop-related changes in microbial
biomarker levels strongly affect the turnover and composition of soil organic carbon. Soil Biology and Biochemistry 85:
39-50.
Schroeder, J. I., Bethke, P. C., Gassmann, W. and Ward, J. M. (2015) Chapter 3. Membrane Transport. In Biochemistry
and Molecular Biology of Plants. Eds. Buchanan, Gruissem, Jones. American Society of Plant Biologists.
Schürner, H., J.L. Seffernick, A. Grzybkowska, A. Dybala-Defratyka, L.P. Wackett, and M. Elsner (2015) Characteristic
isotope fractionation patterns in s-triazine degradation have their origin in multiple protonation sites in the s-triazine
hydrolase TrzN. Environ. Sci. Technol. 49: 3490-3498.
Sedghifar, A., Y. Brandvain, P. L. Ralph, and G. Coop. 2015. The spatial mixing of genomes in secondary contact zones.
Genetics. 201: 243 – 261.
Seffernick, J.L. and L.P. Wackett (2015) Ancient and recent evolution converge for the biodegradation of cyanuric acid
and related triazines. Appl. Environ. Microbiol. (invited review).
Shi Y-F, Wang D-I, Wang C, Culler AH, Kreiser MA, Suresh J, Cohen JD, Pan J, Baker B, and Liu J-Z Loss of GSNOR1 function
leads to compromised auxin signaling and polar auxin transport. Molecular Plant 8:1350-1365 (2015)
Siobhan M. Brady, S. M., Burow, M., Busch, W., Carlborg, O., Denby, K.J., Glazebrook, J., Hamilton, E.S., Harmer, S.L.,
Haswell, E.S., Maloof, J.N., Springer, N., and Kliebenstein, D.J. Reassess the t-Test: Interact with All Your Data via ANOVA.
The Plant Cell 27: 2088-2094 doi:10.1105/tpc.15.00238 (2015).
Smanski MJ, Schlatter DC, Kinkel LL (2015) Leveraging ecological theory to guide natural product discovery. J. Ind.
Micribiol. Biotechnol. DOI 10.1007/s10295-015-1683-9.
Smanski MJ, Zhou H, Claesen J, Shen B, Fischbach M, Voigt CA (2015) Synthetic biology to access and expand nature’s
chemical diversity. Nat. Rev. Microbiol. Accepted.
Smith A.G. and B.M. Clasen. 2011. Development of seedless taxa of popular invasive landscape plants. Combined
Proceedings International Plant Propagators’ Society 60: 69-77.
Smith, A.G., C.A. Eberle, N.O. Anderson, B.M. Clasen, A.D. Hegeman. 2013. The transmitting tissue of Nicotiana tabacum
is not essential to pollen tube growth, and its ablation can reverse prezygotic interspecific barriers. Plant Reprod 26:339-
350.
Snell-Rood, E. C. and M. Steck. 2015. The development of movement-behavioral syndromes in cabbage white butterflies.
Frontiers in Ecology and Evolution 3: article 21. DOI=10.3389/fevo.2015.00021
Snell-Rood, E. C., E. Swanson, and R. L. Young. 2015. Developmental timing as a constraint on the evolution of plasticity.
In press, Heredity. doi: 10.1038/hdy.2015.47
Snell-Rood, E. C., E. Swanson, and S. Jaumann. 2015. Insects as a model system to understand the evolutionary
implications of innovation. Pp 459-477 In: AB Kaufman & JC Kaufman (eds), Animal Creativity and Innovation, Academic
Press, Amsterdam.
Snell-Rood, E. C., M. Burger, Q. Hutton, and A. P. Moczek. Parental investment, developmental buffering, and the
accumulation of genetic variation: a case study with dung beetles. In press, Evolutionary Ecology.
22
Snell-Rood, E. C., R. Cothran, A. Espeset, P. Jeyasingh, S. Hobbie, N. Morehouse. 2015. Life history evolution in the
anthropocene: effects of increasing nutrients on traits and tradeoffs. Evolutionary Applications 8: 635–649. DOI:
10.1111/eva.12272
Sokol, K.A., and Olszewski, N.E. (2015). The Putative Eukaryote-Like O-GlcNAc Transferase of the Cyanobacterium
Synechococcus elongatus PCC 7942 Hydrolyzes UDP-GlcNAc and Is Involved in Multiple Cellular Processes. Journal of
Bacteriology 197, 354-361.
Song Z, Vail A, Sadowsky MJ, Schilling JS. Influence of Hyphal Inoculum potential on the Competitive Success of Fungi
Colonizing Wood. Microb Ecol. 2015 May;69(4):758-67. doi: 10.1007/s00248-015-0588-5. Epub 2015 Mar 8. PubMed
PMID: 25750000.
Song Z., Schlatter D., Kennedy P.G., Kinkel L.L., Kistler H.C., Nguyen N., Bates, S.T. (2015) Effort versus Reward: Preparing
Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils. PLoS ONE 10:
e0127234.
Song, Z., Schlatter, D., Kennedy. P., Kinkel, L.L., Kistler, H.C., Nguyen, N., Bates, S.T. 2015. Effort versus reward: preparing
samples for fungal community characterization in high-throughput sequencing surveys of soils. PLoS ONE doi:
10.1371/journal.pone.0127234.
Spanic, V., M.N. Rouse, J.A. Kolmer, and J.A. Anderson. 2015. Leaf and stem seedling rust resistance in wheat cultivars
grown in Croatia. Euphytica 203:437–448.
Spatafora, J.W. and Bushley, K.E. 2015. Phylogenomics and evolution of secondary metabolism in plant-associated
fungi. Current Opinion in Plant Biology, 26-37-44.
Spatio-temporal Data Mining for Climate Data: Advances, Challenges, and Opportunities. J.H. Faghmous and V. Kumar. In
W. Chu, Ed. Data Mining and Knowledge Discovery for Big Data: Methodologies, Challenges, and Opportunities. pp. 83-
116. Springer, 2014.
Springer NM, McGinnis KM. 2015. Paramutation in evolution, population genetics and breeding. Semin Cell Dev Biol.
doi: 10.1016/j.semcdb.2015.08.010.
Springer NM. 2015. Transposable elements: Microbiomes in the genomes. Nature Plants 1:15004.
Sreekanta, S., Bethke, G., Hatsugai, N., Tsuda, K., Thao, A., Wang, L., Katagiri, F., and Glazebrook, J. (2015) “The receptor-
like cytoplasmic kinase PCRK1 contributes to pattern-triggered immunity against Pseudomonas syringae in Arabidopsis
thaliana” New Phtol doi: 10.1111/nph.13345.
Sreekanta, S., Bethke, G., Hatsugai, N., Tsuda, K., Thao, A., Wang, L., Katagiri. F., and Glazebrook, J. The Receptor-Like
Cytoplasmic Kinase PCRK1 Contributes to Pattern-Triggered Immunity against Pseudomonas syringae in Arabidopsis
thaliana. New Phytologist, 207:78-90 doi: 10.1111/nph.13345 (2015).
Sreekanta, S., Haruta, M., Minkoff, B.B, and Glazebrook, J. Functional Characterization of PCRK1, a Putative Protein
Kinase With a Role in Immunity. Plant Signaling and Behavior 10(10): e1063759. doi:10.1080/15592324.2015.1063759
(2015).
Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ. Evaluation of water sampling methodologies for
amplicon-based characterization of bacterial community structure. J Microbiol Methods. 2015 Jul;114:43-50. doi:
10.1016/j.mimet.2015.05.003. Epub 2015 May 6. PubMed PMID: 25956022.
Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ. High-throughput functional screening reveals low
frequency of antibiotic resistance genes in DNA recovered from the Upper Mississippi River. J Water Health. 2015
Sep;13(3):693-703. doi: 10.2166/wh.2014.215. PubMed PMID: 26322755.
23
Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ. Species sorting and seasonal dynamics primarily shape
bacterial communities in the Upper Mississippi River. Sci Total Environ. 2015 Feb 1;505:435-45. doi:
10.1016/j.scitotenv.2014.10.012. Epub 2014 Oct 21. PubMed PMID: 25461045.
Staley C, Johnson D, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ. Frequencies of heavy metal resistance are
associated with land cover type in the Upper Mississippi River. Sci Total Environ. 2015 Apr 1;511:461-8. doi:
10.1016/j.scitotenv.2014.12.069. Epub 2015 Jan 6. PubMed PMID: 25569582.
Steffenson, B., Figueroa, M., Kianian, S., Hokanson, K., Bradeen, J.M. 2015. The University of Minnesota Stakman-
Borlaug Center (SBC) for Sustainable Plant Health: Ongoing support for rust research and education. Submitted to
Borlaug Global Rust Initiative Workshop, Sydney Australia.
Stelpflug, S., R. Sekhon, B. Vaillancourt, C. Hirsch, C.R. Buell, N. de Leon, S. Kaeppler. 2015. An expanded maize gene
expression atlas based on RNA-sequencing and its use to explore root development. The Plant Genome.
doi:10.3835/plantgenome2015.04.0025.
Stephen CS, LaBelle EV, Brantley SL, Bond DR. 2014. Abundance of the multiheme c-type cytochrome OmcB increases in
outer biofilm layers of electrode-grown Geobacter sulfurreducens. PLoS ONE 9:e104336.
Subramanian, K., Owens, D.J., Raju, R., Firpo, M., O’Brien, T.D., Verfaillie, C.M. and Hu, W-S. (2014) Spheroid culture for
enhanced differentiation of human embryonic stem cells to hepatocyte-like cells. Stem Cell Dev., 23:124-31.
Sun, X., Kang, X., and Ni, M. (2012). Hypersensitive to Red and Blue 1 and its modification by Protein Phosphatase 7 are
implicated in the control of Arabidopsis stomatal aperture. PLoS Genetics 8(5): e1002674 .
Swanson, E., A. Espeset, I. Mikati, I. Bolduc, R. Kulhanek, W. A. White, S. Kenzie, and E. C. Snell-Rood. Nutrition shapes
life history evolution across species: a case study in butterflies. In review, PNAS.
Tavakol, E., R. Okagaki, G. Verderio, V. Shariati, A. Hussien, H. Bilgic, M.J. Scanlon, N.R. Todt, T.J. Close, A. Druka, R.
Waugh, B. Steuernagel, R. Ariyadasa, A. Himmelbach, N. Stein, G.J. Muehlbauer* and L. Rossini*. 2015. The barley
Uniculme4 gene encodes a BOP-like protein that controls tillering, and proximal-distal leaf patterning. Plant Physiology
168:164-174. *Indicates co-last authors.
Taylor, M. R., Reinders, A., Ward, J. M. (2015) Transport Function of Rice Amino Acid Permeases (AAPs). Plant Cell and
Physiology 56: 1355-1363
Thompson, A.M., J. Yu, M.C.P. Timmermans, P. Schnable, J.C. Crants, M.J. Scanlon¬¬, and G.J. Muehlbauer. 2015.
Diversity of maize shoot apical meristem architecture and its relationship to plant morphology. G3 5:819-827.
Tivendale ND, Cohen JD Analytical history of auxin. J. Plant Growth Regulation 34:708–722 (2015)
Uhlen, K., J.A Dieseth, S. Koga, U. Böcker, B.O. Hoel, and J.A Anderson. 2015 Variation in gluten quality parameters of
spring wheat varieties of different origin grown in contrasting environments. J. Cereal Sci. 62:110-116.
Unno T, Choi JH, Hur HG, Sadowsky MJ, Ahn YT, Huh CS, Kim GB, Cha CJ. Changes in human gut microbiota influenced by
probiotic fermented milk ingestion. J Dairy Sci. 2015 Jun; 98(6):3568-76. doi: 10.3168/jds.2014-8943. Epub 2015 Apr 8.
PubMed PMID: 25864056.
Unno T, Choi JH, Hur HG, Sadowsky MJ, Ahn YT, Huh CS, Kim GB, Cha CJ. Changes in human gut microbiota influenced by
probiotic fermented milk ingestion. J Dairy Sci. 2015 Jun;98(6):3568-76. doi: 10.3168/jds.2014-8943. Epub 2015 Apr 8.
PubMed PMID: 25864056.
24
Unno T, Kim J, Kim Y, Nguyen SG, Guevarra RB, Kim GP, Lee JH, Sadowsky MJ. Influence of seawater intrusion on
microbial communities in groundwater. Sci Total Environ. 2015 Nov 1;532:337-43. doi: 10.1016/j.scitotenv.2015.05.111.
Epub 2015 Jun 14. PubMed PMID: 26081736.
Vail AW, Wang P, Uefuji H, Samac DA, Vance CP, Wackett LP, Sadowsky MJ. Biodegradation of atrazine by three
transgenic grasses and alfalfa expressing a modified bacterial atrazine chlorohydrolase gene. Transgenic Res. 2015
Jun;24(3):475-88. doi: 10.1007/s11248-014-9851-7. Epub 2014 Nov 29. PubMed PMID: 25432082.
Vail, A.W., P. Wang, H. Uefuji, D.A. Samac, C.P. Vance, L.P. Wackett, and M.J. Sadowsky (2015) Biodegradation of
atrazine by three transgenic grasses and alfalfa expressing a modified bacterial atrazine chlorohydrolase gene.
Transgenic Res. 24:475-488.
Vail, A.W., Wang, P., Uefuji, H., Samac, D.A., Vance, C.P., Wackett, L.P., and Sadowsky, M.J. 2015. Biodegradation of
atrazine by three transgenic grasses and alfalfa expressing a modified bacterial atrazine chlorohydrolase gene.
Transgenic Res. 24:475-488.
"Vangay P, Ward T, Gerber J, Knights D. Antibiotics, Pediatric Dysbiosis, and Disease.
Cell Host and Microbe 17 (5), 553-564."
Varga, E., Wiesenberger, G., Hametner, C., Ward, T. J., Dong, Y., Schöfbeck, D., McCormick, S., Broz, K., Stückler, R.,
Schuhmacher, R., Krska, R., Kistler, H. C., Berthiller, F. and Adam, G. 2015. New tricks of an old enemy: Isolates of
Fusarium graminearum produce a novel type A trichothecene mycotoxin. Environmental Microbiology doi:
10.1111/1462-2920.12718.
Vishwanathan N., Le H.T.N., Jacob N.M., Tsao Y.-S., Ng S.-W., Loo B.L.W., Liu Z., Kantardjeiff A. and Hu W.-S. (2014)
Transcriptome dynamics of transgene amplification in Chinese hamster ovary cells, Biotechnol. Bioeng, 111, 518–528.
(doi:10.1002/bit.25117).
Vishwanathan, N., Le, H., Le, T. and Hu, W-S. (2014) Advancing Biopharmaceutical process science through
transcriptome analysis. Curr. Opinion Biotechnol., 30,113-119.
Vishwanathan, N., Yongky, A., Johnson, K., Fu, H-Y.,Jacob, N., Le, H., Yusufi, F.N.K., Lee, D.Y. and Hu, W-S. (2015) Global
insight into the Chinese hamster and CHO cell transcriptome. Biotechnol. Bioeng., DOI10.1002/bit. 25513.
Wanzala SI, Nakavuma J, Travis DA, Kia P, Ogwang S, Sreevatsan S. Draft Genome Sequences of Mycobacterium bovis BZ
31150 and Mycobacterium bovis B2 7505, Pathogenic Bacteria Isolated from Archived Captive Animal Bronchial Washes
and Human Sputum Samples in Uganda. Genome Announc. 2015 Oct 8;3(5). pii: e01102-15. doi:
10.1128/genomeA.01102-15. PubMed PMID: 26450718; PubMed Central PMCID: PMC4599077.
Ward T, Larson J, Lynch J, Sidiropoulos D, Blekhman R, Fink R, Knights D. BugBase predicts community-wide microbiome
phenotypes. (under review).
Weeks A.R., Turelli M., Harcombe W.R., Reynolds K.T., & Hoffmann A.A. 2007. From parasite to mutualist: Rapid
evolution of Wolbachia in natural populations of Drosophila. PLoS: Biology. 17:5
Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J,
Khoruts A, Knight R, Sadowsky MJ. Dynamic changes in short- and long-term bacterial composition following fecal
microbiota transplantation for recurrent Clostridium difficile infection. Microbiome. 2015 Mar 30;3:10. doi:
10.1186/s40168-015-0070-0. eCollection 2015. PubMed PMID: 25825673; PubMed Central PMCID: PMC4378022.
Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J,
Khoruts A, Knight R, Sadowsky MJ. Dynamic changes in short- and longterm bacterial composition following fecal
microbiota transplantation for recurrent Clostridium difficile infection. Microbiome 2015, 3:10.
25
Weingarden AR, Chen C, Zhang N, Graiziger CT, Dosa PI, Steer CJ, Shaughnessy MK, Johnson JR, Sadowsky MJ, Khoruts A.
Ursodeoxycholic Acid Inhibits Clostridium difficile Spore Germination and Vegetative Growth, and Prevents the
Recurrence of Ileal Pouchitis Associated With the Infection. J Clin Gastroenterol. 2015 Oct 17. [Epub ahead of print]
PubMed PMID: 26485102.
Wilson MB, Brinkman D, Spivak M, Gardner G, Cohen JD Regional variation in composition and antimicrobial activity of
U.S. propolis against Paenibacillus larvae and Ascopheara apis. Journal of Invertebrate Pathology 124:44-50 (2015)
Wolf TM, Mugisha L, Shoyama FM, O'Malley MJ, Flynn JL, Asiimwe B, Travis DA, Singer RS, Sreevatsan S. Noninvasive test
for tuberculosis detection among primates. Emerg Infect Dis. 2015 Mar;21(3):468-70. doi: 10.3201/eid2103.140052.
PubMed PMID: 25695329; PubMed Central PMCID: PMC4344255.
Wolf TM, Sreevatsan S, Singer RS, Lipende I, Collins A, Gillespie TR, Lonsdorf EV, Travis DA. Noninvasive Tuberculosis
Screening in Free-Living Primate Populations in Gombe National Park, Tanzania. Ecohealth. 2015 Sep 29. [Epub ahead of
print] PubMed PMID: 26419483.
Wolf, V.C., A. Gassmann, B.M. Clasen, A.G. Smith, C. Müller. 2012. Genetic and chemical variation of Tanacetum vulgare
in plants of native and invasive origin. Biological Control. 61:240-245.
Wongphatcharachai M, Staley C, Wang P, Moncada KM, Sheaffer CC, Sadowsky MJ. Predominant populations of
indigenous soybean-nodulating Bradyrhizobium japonicum strains obtained from organic farming systems in Minnesota.
J Appl Microbiol. 2015 May;118(5):1152-64. doi: 10.1111/jam.12771. Epub 2015 Mar 23. PubMed PMID: 25660818.
Wongphatcharachai M, Wang P, Staley C, Chun CL, Ferguson JA, Moncada KM, Sheaffer CC, Sadowsky MJ. Site-specific
distribution and competitive ability of indigenous bean-nodulating rhizobia isolated from organic fields in Minnesota. J
Biotechnol. 2015 Nov 20;214:158-68. doi: 10.1016/j.jbiotec.2015.09.009. Epub 2015 Sep 25. PubMed PMID: 26403588.
X. Chen, J. H. Faghmos, A. Khandelwal, and V. Kumar.Clustering Dynamic Spatio-Temporal Patterns in the Presence of
Noise and Missing Data. 24th International Joint Conference on Artificial Intelligence (IJCAI-15). Buenos Aires, Argentina.
July 25-31, 2015.
X. Chen, Y. Yao, S. Shi, V. Kumar, and J. Faghmous. Online change point detection for remote sensing time series. Fifth
International Workshop on Climate Informatics, Boulder, CO. September 24-25, 2015.
Xiao Y, Sun Q, Kang X, Chen C, Nin M (2015). SHORT HYPOCOTYL UNDER BLUE1 or HAIKU2 mixexpression alters canola
and Arabidopsis seed development. New Phytologist. DOI: 10.1111/nph.13632.
Xiao, Y., Sun, Q., Kang, X., Chen, C., and Ni, M. (2015). SHORT HYPOCOTYL UNDER BLUE1 or HAIKU2 mixexpression alters
canola and Arabidopsis seed development. New phytologist doi: 10.1111/nph.13632.
Yeom, S., B. Mutlu, A. Aksan, and L.P. Wackett (2015) Bacterial cyanuric acid hydrolases for water treatment. Appl.
Environ. Microbiol. 81:6660-6668.
Yohe S, Hauge A, Bunjer K, Kemmer T, Bower M, Schomaker M, Onsongo G, Wilson J, Erdmann J, Zhou Y, Deshpande A,
Spears MD, Beckman K, Silverstein KA, Thyagarajan B. Clinical validation of targeted next-generation sequencing for
inherited disorders. Arch Pathol Lab Med. 2015 Feb;139(2):204-10. doi: 10.5858/arpa.2013-0625-OA.
Yongky, A., Lee, J., Le, T., Mulukutla, B.C., Daoutidis, P. and Hu, W-S. (2015) Mechanism for multiplicity of steady states
with distinct cell concentration in continuous culture of mammalian Cells. Biotechnol. Bioeng.. 112,1437-1445.
Yongky, A., Mulukutla, B, Grimm, S., Daoutidis, P. and Hu, W.-S. (2015) Multiplicity of steady states in glycolysis and shift
of metabolic State in cultured mammalian cells. Plos One, 10(3):e0121561. DOI:10.1371/journal.pone.0121561.
26
You, L., Samac, D.A., Glazebrook, J., and Ishimaru, C.A. 2015. Complete genome sequence of Clavibacter michiganensis
subsp. insidiosus R1-1 using PacBio Single-Molecule Real-Time Technology. Genome Announc. 3: e00396-15.
Young ND, Zhou P, Silverstein KAT (2016) Exploring structural variants in environmentally-sensitive gene families.
Current Opinion in Plant Biology (In press).
Yu P, Lor P, Ludwig-Müller J, Hegeman AD**, and Cohen JD (2015) Quantitative evaluation of IAA conjugate pools in
Arabidopsis thaliana, Planta, 241(2): 539-48.
Yu P, Lor P, Ludwig-Müller J, Hegeman AD, Cohen JD Quantitative evaluation of IAA conjugate pools in Arabidopsis
thaliana. Planta 241:539-548 (2015)
Zacharoff L, Chan CH, Bond DR. 2016. Reduction of low potential electron acceptors requires the CbcL inner membrane
cytochrome of Geobacter sulfurreducens. Bioelectrochemistry 107:7–13.
Zhang, N, S Wan, J Guo, G Han, JLM Gutknecht, B Schmid, L Yu, W Liu, J Bi, Z Wang, and K Ma (2015) Precipitation
modifies the effects of warming and nitrogen addition on soil microbial communities in northern Chinese grasslands. Soil
Biology and Biochemistry. 89: 12-23.
Zhang, X., A. Sallam, L. Gao, T. Kantarski, J. Poland, L. DeHaan, D. Wyse, and J. Anderson. 2015. Establishment and
optimization of genomic selection to accelerate the domestication and improvement of intermediate wheatgrass
(Thinopyrum intermedium) using recurrent selection. The Plant Genome. In press. doi:
10.3835/plantgenome2015.07.0059
Zhang, X., S.Haring, J.-B. Ohm, L.R. DeHaan, and J.A. Anderson. 2015. Towards the understanding of end-use quality in
intermediate wheatgrass (Thinopyrum intermedium): high-molecular-weight glutenin subunits, protein polymerization,
and mixing characteristics. J. Cereal Sci. 88:81-88.
Zhao, L., Fu, H., Zhou, W. and Hu, W-S. (2015) Advances in process analytical tools for cell culture bioprocesses. Eng. Life
Sci., (DOI 10.1007/elsc.201500006).
Zhong, S., Ali, S., Leng, Y., Wang, R., Garvin, D.F. 2015. Brachypodium distachyon-Cochliobolus sativus pathosystem is a
new model for studying plant-fungal interactions in cereal crops. Phytopathology 105:482-489.
Zlesak, D., Clark, A., Bradeen, J., and Hokanson, S. 2015. Determining the association of SCAR marker ND5E and
resistance to race 8 of Diplocarpon rosae Wolf in a diverse group of landscape roses. Acta Hort 1064:79-86.