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1 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.

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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

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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:

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Dodge, A.G., K. Carrasquillo, L. Rivera, L. Xu, L.P. Wackett and M.J. Sadowsky (2015) A rapid detection method for L-

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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

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Dos Santos LF, Clavijo MJ, Sreevatsan S, Rovira A, Moreira MA, Pieters M. Genotyping of Mycoplasma hyorhinis using

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Dos Santos LF, Sreevatsan S, Torremorell M, Moreira MA, Sibila M, Pieters M. Genotype distribution of Mycoplasma

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Drees J, Mertensotto M, Liu G, Panyam J, Leonard A, Augustin L, Schottel J, Saltzman D. Attenuated Salmonella enterica

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Drees JJ, Mertensotto MJ, Augustin LB, Schottel JL, Saltzman DA. Vasculature Disruption Enhances Bacterial Targeting of

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Drew, Jennifer, Yue, Chengyan, Anderson, Neil O., & Pardey, Philip G. (2015). Premiums and Discounts for Plant Patents

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Eberle, C.A., B.M. Clasen, N. O. Anderson and A. G. Smith. 2012. A novel pollen tube growth assay utilizing a transmitting

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Epstein B, Sadowsky MJ, Tiffin P. Selection on horizontally transferred and duplicated genes in sinorhizobium (ensifer),

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Fan K-T, Rendahl A, Chen W-P, Freund D, Gray W, Cohen JD, Hegeman A Proteome scale-protein turnover analysis using

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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

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Lefebvre PA, Hom EF, Salehi-Ashtiani K, Purugganan MD. Whole-Genome Resequencing Reveals Extensive Natural

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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

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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

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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.

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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.,

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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-

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Harcombe, W.R. & Bull, J.J. 2005. Impact of phages on a two-species bacterial community. Applied and Environmental

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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

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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

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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.

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