Hungate, E. A., Earley, E. J., Boussy, I. A., Turissini, D. A., Ting, C. T., Moran, J. R., … Jones, C. D. (2013). A locus in Drosophila sechellia affecting tolerance of a host plant toxin. Genetics195(3), 1063-1075. DOI: 10.1534/genetics.113.154773

Huang, Y., Hu, Y., Jones, C. D., Macleod, J. N., Chiang, D. Y., Liu, Y., … Liu, J. (2013). A robust method for transcript quantification with rna-seq data. Journal of Computational Biology20(3), 167-187. DOI: 10.1089/cmb.2012.0230

Sarris, P. F., Trantas, E. A., Baltrus, D. A., Bull, C. T., Wechter, W. P., Yan, S., … Goumas, D. E. (2013). Comparative Genomics of Multiple Strains of Pseudomonas cannabina pv. alisalensis, a Potential Model Pathogen of Both Monocots and Dicots. PLoS ONE8(3), [e59366]. DOI: 10.1371/journal.pone.0059366

Creighton, C. J., Morgan, M., Gunaratne, P. H., Wheeler, D. A., Gibbs, R. A., Robertson, G., … Sofia, H. J. (2013). Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature499(7456), 43-49. DOI: 10.1038/nature12222

Reinhardt, J. A., Wanjiru, B. M., Brant, A. T., Saelao, P., Begun, D. J., & Jones, C. D. (2013). De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences. PLoS Genetics9(10), [e1003860]. DOI: 10.1371/journal.pgen.1003860

Hu, Y., Huang, Y., Du, Y., Orellana, C. F., Singh, D., Johnson, A. R., … Liu, J. (2013). DiffSplice: The genome-wide detection of differential splicing events with RNA-seq. Nucleic Acids Research41(2). DOI: 10.1093/nar/gks1026

Cox, C. E., Jones, C. D., Wares, J. P., Castillo, K. D., Mcfield, M. D., & Bruno, J. F. (2013). Genetic testing reveals some mislabeling but general compliance with a ban on herbivorous fish harvesting in Belize. Conservation Letters6(2), 132-140. DOI: 10.1111/j.1755-263X.2012.00286.x

Getz, G., Gabriel, S. B., Cibulskis, K., Lander, E., Sivachenko, A., Sougnez, C., … Levine, D. A. (2013). Integrated genomic characterization of endometrial carcinoma. Nature497(7447), 67-73. DOI: 10.1038/nature12113

Roach, J. M., Racioppi, L., Jones, C. D., & Masci, A. M. (2013). Phylogeny of Toll-Like Receptor Signaling: Adapting the Innate Response. PLoS ONE8(1), [e54156]. DOI: 10.1371/journal.pone.0054156

Lundberg, D. S., Yourstone, S., Mieczkowski, P., Jones, C. D., & Dangl, J. L. (2013). Practical innovations for high-throughput amplicon sequencing. Nature Methods10(10), 999-1002. DOI: 10.1038/nmeth.2634

Ligon, L. S., Rigel, N. W., Romanchuk, A., Jones, C. D., & Braunstein, M. (2013). Suppressor analysis reveals a role for secY in the secA2-dependent protein export pathway of mycobacteria. Journal of Bacteriology195(19), 4456-4465. DOI: 10.1128/JB.00630-13

Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., … Kling, T. (2013). The cancer genome atlas pan-cancer analysis project. Nature Genetics45(10), 1113-1120. DOI: 10.1038/ng.2764

Reinhardt, J. A., & Jones, C. D. (2013). Two rapidly evolving genes contribute to male fitness in Drosophila. Journal of Molecular Evolution77(5-6), 246-259. DOI: 10.1007/s00239-013-9594-8


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