January 1, 2018

Radovich, M., Pickering, C. R., Felau, I., Ha, G., Zhang, H., Jo, H., . . . Zmuda, E. (2018). The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell, 33(2), 244-258. doi:10.1016/j.ccell.2018.01.003

Wang, J. R., Holt, J., Mcmillan, L., & Jones, C. D. (2018). FMLRC: Hybrid long read error correction using an FM-index. BMC Bioinformatics, 19(1). doi:10.1186/s12859-018-2051-3

Paredes, S. H., Gao, T., Law, T. F., Finkel, O. M., Mucyn, T., Teixeira, P. J., . . . Castrillo, G. (2018). Design of synthetic bacterial communities for predictable plant phenotypes. PLOS Biology, 16(2). doi:10.1371/journal.pbio.2003962



January 1, 2017

Poe, J. C., Jia, W., Su, H., Anand, S., Rose, J. J., Tata, P. V., . . . Sarantopoulos, S. (2017). An aberrant NOTCH2-BCR signaling axis in B cells from patients with chronic GVHD. Blood,130(19), 2131-2145. doi:10.1182/blood-2017-05-782466

Abeshouse, A., Adebamowo, C., Adebamowo, S. N., Akbani, R., Akeredolu, T., Ally, A., . . . Zmuda, E. (2017). Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell, 171(4), 950-965. doi:10.1016/j.cell.2017.10.014

Pan, J. W., Mclaughlin, J., Yang, H., Leo, C., Rambarat, P., Okuwa, S., . . . Volkan, P. C. (2017). Comparative analysis of behavioral and transcriptional variation underlying CO2 sensory neuron function and development in Drosophila. Fly, 11(4), 239-252. doi:10.1080/19336934.2017.1344374

Pan, J. W., Li, Q., Barish, S., Okuwa, S., Zhao, S., Soeder, C., . . . Volkan, P. C. (2017). Patterns of transcriptional parallelism and variation in the developing olfactory system of Drosophila species. Scientific Reports, 7(1). doi:10.1038/s41598-017-08563-0

Robertson, A. G., Shih, J., Yau, C., Gibb, E. A., Oba, J., Mungall, K. L., . . . Zmuda, E. (2017). Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell, 32(2), 204-220. doi:10.1016/j.ccell.2017.07.003

Raphael, B. J., Hruban, R. H., Aguirre, A. J., Moffitt, R. A., Yeh, J. J., Stewart, C., . . . Zenklusen, J. C. (2017). Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell, 32(2), 185-203. doi:10.1016/j.ccell.2017.07.007

O’Keeffe, K. R., Carbone, I., Jones, C. D., & Mitchell, C. E. (2017). Plastic potential: How the phenotypes and adaptations of pathogens are influenced by microbial interactions within plants. Current Opinion in Plant Biology, 38, 78-83. doi:10.1016/j.pbi.2017.04.014

Farshidfar, F., Zheng, S., Gingras, M., Newton, Y., Shih, J., Robertson, A. G., . . . Zmuda, E. (2017). Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH -Mutant Molecular Profiles. Cell Reports, 19(13), 2878-2880. doi:10.1016/j.celrep.2017.06.008

Ally, A., Balasundaram, M., Carlsen, R., Chuah, E., Clarke, A., Dhalla, N., . . . Laird, P. W. (2017). Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell, 169(7), 1327-1341. doi:10.1016/j.cell.2017.05.046

Sze, S., Pimsler, M. L., Tomberlin, J. K., Jones, C. D., & Tarone, A. M. (2017). A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics, 18(S4). doi:10.1186/s12864-017-3735-1

Burk, R. D., Chen, Z., Saller, C., Tarvin, K., Carvalho, A. L., Scapulatempo-Neto, C., . . . Mutch, D. (2017). Integrated genomic and molecular characterization of cervical cancer. Nature, 543(7645), 378-384. doi:10.1038/nature21386

Cherniack, A. D., Shen, H., Walter, V., Stewart, C., Murray, B. A., Bowlby, R., . . . Zuna, R. E. (2017). Integrated Molecular Characterization of Uterine Carcinosarcoma. Cancer Cell,31(3), 411-423. doi:10.1016/j.ccell.2017.02.010

Fishbein, L., Leshchiner, I., Walter, V., Danilova, L., Robertson, A. G., Johnson, A. R., . . . Zmuda, E. (2017). Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma. Cancer Cell, 31(2), 181-193. doi:10.1016/j.ccell.2017.01.001

Barish, S., Li, Q., Pan, J. W., Soeder, C., Jones, C., & Volkan, P. C. (2017). Transcriptional profiling of olfactory system development identifies distal antenna as a regulator of subset of neuronal fates. Scientific Reports, 7, 40873. doi:10.1038/srep40873

Walsh, D. M., McCullough, S. D., Yourstone, S., Jones, S. W., Cairns, B. A., Jones, C. D., … Diaz-Sanchez, D. (2017). Alterations in airway microbiota in patients with PAO2/FiO2 ratio ≤ 300 after burn and inhalation injury. PLoS ONE12(3), [e0173848]. DOI: 10.1371/journal.pone.0173848

Zhang, C., Lu, X., Zhu, Z., Hu, Y., Singh, D., Jones, C., … Liu, Y. (2017). REC: Fast sparse regression-based multicategory classification. Statistics and its Interface10(2), 175-185. DOI: 10.4310/SII.2017.v10.n2.a2

Castrillo, G., Teixeira, P. J. P. L., Paredes, S. H., Law, T. F., De Lorenzo, L., Feltcher, M. E., … Dangl, J. L. (2017). Root microbiota drive direct integration of phosphate stress and immunity. Nature543(7646), 513-518. DOI: 10.1038/nature21417



January 1, 2016

Welch, J. D., Williams, L. A., DiSalvo, M., Brandt, A. T., Marayati, R., Sims, C. E., … Jones, C. D. (2016). Selective single cell isolation for genomics using microraft arrays. Nucleic Acids Research44(17), 8292-8301. DOI: 10.1093/nar/gkw700

Campbell, J. D., Alexandrov, A., Kim, J., Wala, J., Berger, A. H., Pedamallu, C. S., . . . Meyerson, M. (2016). Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nature Genetics, 48(6), 607-616. doi:10.1038/ng.3564

Ceccarelli, M., Barthel, F., Malta, T., Sabedot, T., Salama, S., Murray, B., . . . Zmuda, E. (2016). Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell, 164(3), 550-563. doi:10.1016/j.cell.2015.12.028

Linehan, W. M., Spellman, P. T., Ricketts, C. J., Creighton, C. J., Fei, S. S., Davis, C., . . . Zuna, R. (2016). Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. New England Journal of Medicine, 374(2), 135-145. doi:10.1056/nejmoa1505917

Li, Q., Barish, S., Okuwa, S., Maciejewski, A., Brandt, A. T., Reinhold, D., … Volkan, P. C. (2016). A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity. PLoS Genetics12(1), [e1005780]. DOI: 10.1371/journal.pgen.1005780



January 1, 2015

Boothby, T. C., Tenlen, J. R., Smith, F. W., Wang, J. R., Patanella, K. A., Nishimura, E. O., . . . Goldstein, B. (2015). Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proceedings of the National Academy of Sciences, 112(52), 15976-15981. doi:10.1073/pnas.1510461112

Black, J. L., Harrell, J. C., Leisner, T. M., Fellmeth, M. J., George, S. D., Reinhold, D., … Parise, L. V. (2015). CIB1 depletion impairs cell survival and tumor growth in triple-negative breast cancer. Breast Cancer Research and Treatment152(2), 337-346. DOI: 10.1007/s10549-015-3458-4

Brat, D. J., Verhaak, R. G. W., Aldape, K. D., Yung, W. K. A., Salama, S. R., Cooper, L. A. D., … Zhang, J. (2015). Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. New England Journal of Medicine372(26), 2481-2498. DOI: 10.1056/NEJMoa1402121

Lawrence, M. S., Sougnez, C., Lichtenstein, L., Cibulskis, K., Lander, E., Gabriel, S. B., … The Cancer Genome Atlas Network (2015). Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature517(7536), 576-582. DOI: 10.1038/nature14129

Dworkin, I., & Jones, C. D. (2015). Evolutionary genetics: You are what you evolve to eat. Current Biology25(8), R341-R344. [11776]. DOI: 10.1016/j.cub.2015.01.044

Miller, C. N., Steele, S. P., Brunton, J. C., Jenkins, R. J., Lovullo, E. D., Taft-Benz, S. A., … Kawula, T. H. (2015). Extragenic suppressor mutations in ΔripA disrupt stability and function of LpxA. BMC Microbiology14(1), [336]. DOI: 10.1186/s12866-014-0336-x

Wang, J. R., & Jones, C. D. (2015). Fast alignment filtering of nanopore sequencing reads using locality-sensitive hashing. In Proceedings – 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 127-130). [7359668] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/BIBM.2015.7359668

Akbani, R., Akdemir, K. C., Aksoy, B. A., Albert, M., Ally, A., Amin, S. B., … The Cancer Genome Atlas Network (2015). Genomic Classification of Cutaneous Melanoma. Cell161(7), 1681-1696. DOI: 10.1016/j.cell.2015.05.044

Zhou, S., Jones, C., Mieczkowski, P., & Swanstrom, R. (2015). Primer ID validates template sampling depth and greatly reduces the error rate of next-generation sequencing of HIV-1 genomic RNA populations. Journal of Virology89(16), 8540-8555. DOI: 10.1128/JVI.00522-15

Lebeis, S. L., Paredes, S. H., Lundberg, D. S., Breakfield, N., Gehring, J., McDonald, M., … Dangl, J. L. (2015). Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science349(6250), 860-864. DOI: 10.1126/science.aaa8764

Abeshouse, A., Ahn, J., Akbani, R., Ally, A., Amin, S., Andry, C. D., … Zmuda, E. (2015). The Molecular Taxonomy of Primary Prostate Cancer. Cell163(4), 1011-1025. DOI: 10.1016/j.cell.2015.10.025



January 1, 2014

Miller, C. N., Steele, S. P., Brunton, J. C., Jenkins, R. J., Lovullo, E. D., Taft-Benz, S. A., . . . Kawula, T. H. (2014). Extragenic suppressor mutations in ΔripA disrupt stability and function of LpxA. BMC Microbiology, 14(1). doi:10.1186/s12866-014-0336-x

Parfenov, M., Pedamallu, C. S., Gehlenborg, N., Freeman, S. S., Danilova, L., Bristow, C. A., . . . Yarbrough, W. G. (2014). Characterization of HPV and host genome interactions in primary head and neck cancers. Proceedings of the National Academy of Sciences, 111(43), 15544-15549. doi:10.1073/pnas.1416074111

Romanchuk, A., Jones, C. D., Karkare, K., Moore, A., Smith, B. A., Jones, C., … Baltrus, D. A. (2014). Bigger is not always better: Transmission and fitness burden of ~1MB Pseudomonas syringae megaplasmid pMPPla107. Plasmid73, 16-25. DOI: 10.1016/j.plasmid.2014.04.002

Weinstein, J. N., Akbani, R., Broom, B. M., Wang, W., Verhaak, R. G. W., McConkey, D., … Eley, G. (2014). Comprehensive molecular characterization of urothelial bladder carcinoma. Nature507(7492), 315-322. DOI: 10.1038/nature12965

Collisson, E. A., Campbell, J. D., Brooks, A. N., Berger, A. H., Lee, W., Chmielecki, J., … Cheney, R. (2014). Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network. Nature511(7511), 543-550. DOI: 10.1038/nature13385

Baltrus, D. A., Yourstone, S., Lind, A., Guilbaud, C., Sands, D. C., Jones, C. D., … Dangl, J. L. (2014). Draft genome sequences of a phylogenetically diverse suite of Pseudomonas syringae strains from multiple source populations. Genome Announcements2(1), [e01195-13]. DOI: 10.1128/genomeA.01195-13

Guo, X., Zheng, S., Dang, H., Pace, R. G., Stonebraker, J. R., Jones, C. D., … Voynow, J. A. (2014). Genome reference and sequence variation in the large repetitive central Exon of human MUC5AC. American Journal of Respiratory Cell and Molecular Biology50(1), 223-232. DOI: 10.1165/rcmb.2013-0235OC

Jabara, C. B., Hu, F., Mollan, K. R., Williford, S. E., Menezes, P., Yang, Y., … Lemon, S. M. (2014). Hepatitis C Virus (HCV) NS3 sequence diversity and antiviral resistance-associated variant frequency in HCV/HIV coinfection. Antimicrobial Agents and Chemotherapy58(10), 6079-6092. DOI: 10.1128/AAC.03466-14

Davis, C., Ricketts, C. J., Wang, M., Yang, L., Cherniack, A., Shen, H., . . . Sofia, H. (2014). The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell,26(3), 319-330. doi:10.1016/j.ccr.2014.07.014

Agrawal, N., Akbani, R., Aksoy, B. A., Ally, A., Arachchi, H., Asa, S. L., … Zou, L. (2014). Integrated Genomic Characterization of Papillary Thyroid Carcinoma. Cell159(3), 676-690. DOI: 10.1016/j.cell.2014.09.050

Yourstone, S. M., Lundberg, D. S., Dangl, J. L., & Jones, C. D. (2014). MT-Toolbox: Improved amplicon sequencing using molecule tags. BMC Bioinformatics15(1), [284]. DOI: 10.1186/1471-2105-15-284

Zhao, L., Saelao, P., Jones, C. D., & Begun, D. J. (2014). Origin and spread of de novo genes in Drosophila melanogaster populations. Science343(6172), 769-772. DOI: 10.1126/science.1248286

Reinhardt, J. A., Kolaczkowski, B., Jones, C. D., Begun, D. J., & Kern, A. D. (2014). Parallel geographic variation in Drosophila melanogaster. Genetics197(1), 361-373. DOI: 10.1534/genetics.114.161463

Bartoli, C., Berge, O., Monteil, C. L., Guilbaud, C., Balestra, G. M., Varvaro, L., … Morris, C. E. (2014). The Pseudomonas viridiflava phylogroups in the P.syringae species complex are characterized by genetic variability and phenotypic plasticity of pathogenicity-related traits. Environmental Microbiology16(7), 2301-2315. DOI: 10.1111/1462-2920.12433

Mucyn, T. S., Yourstone, S., Lind, A. L., Biswas, S., Nishimura, M. T., Baltrus, D. A., … Grant, S. R. (2014). Variable Suites of Non-effector Genes Are Co-regulated in the Type III Secretion Virulence Regulon across the Pseudomonas syringae Phylogeny. PLoS Pathogens10(1), [e1003807]. DOI: 10.1371/journal.ppat.1003807



January 1, 2013

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



January 1, 2012

Huang, Y., Hu, Y., Jones, C. D., MacLeod, J. N., Chiang, D. Y., Liu, Y., … Liu, J. (2012). A Robust method for transcript quantification with RNA-seq data. In Research in Computational Molecular Biology – 16th Annual International Conference, RECOMB 2012, Proceedings (Vol. 7262 LNBI, pp. 127-147). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 7262 LNBI). DOI: 10.1007/978-3-642-29627-7_12

Pfennig, K. S., Allenby, A., Martin, R. A., Monroy, A., & Jones, C. D. (2012). A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.). Molecular Ecology Resources12(5), 909-917. DOI: 10.1111/j.1755-0998.2012.03150.x

Hammerman, P. S., Voet, D., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., … Shen, R. (2012). Comprehensive genomic characterization of squamous cell lung cancers. Nature489(7417), 519-525. DOI: 10.1038/nature11404

Muzny, D. M., Bainbridge, M. N., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., … Thomson., E. (2012). Comprehensive molecular characterization of human colon and rectal cancer. Nature487(7407), 330-337. DOI: 10.1038/nature11252

Kohl, K. P., Jones, C. D., & Sekelsky, J. (2012). Evolution of an MCM complex in flies that promotes meiotic crossovers by blocking BLM helicase. Science338(6112), 1363-1365. DOI: 10.1126/science.1228190

Leichty, A. R., Pfennig, D. W., Jones, C. D., & Pfennig, K. S. (2012). Relaxed genetic constraint is ancestral to the evolution of phenotypic plasticity. Integrative and Comparative Biology52(1), 16-30. DOI: 10.1093/icb/ics049



January 1, 2011

Jabara, C. B., Jones, C. D., Roach, J., Anderson, J. A., & Swanstrom, R. (2011). Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proceedings of the National Academy of Sciences, 108(50), 20166-20171. doi:10.1073/pnas.1110064108

Earley, E. J., & Jones, C. D. (2011). Next-Generation Mapping of Complex Traits with Phenotype-Based Selection and Introgression. Genetics, 189(4), 1203-1209. doi:10.1534/genetics.111.129445

Singh, D., Orellana, C. F., Hu, Y., Jones, C. D., Liu, Y., Chiang, D. Y., . . . Prins, J. F. (2011). FDM: A graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics, 27(19), 2633-2640. doi:10.1093/bioinformatics/btr458

Baltrus, D. A., Nishimura, M. T., Romanchuk, A., Chang, J. H., Mukhtar, M. S., Cherkis, K., . . . Dangl, J. L. (2011). Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates. PLoS Pathogens, 7(7). doi:10.1371/journal.ppat.1002132

Sawyer, J. M., Glass, S., Li, T., Shemer, G., White, N. D., Starostina, N. G., . . . Goldstein, B. (2011). Overcoming Redundancy: An RNAi Enhancer Screen for Morphogenesis Genes in Caenorhabditis elegans. Genetics, 188(3), 549-564. doi:10.1534/genetics.111.129486

Baltrus DA, Romanchuk A, Nishmura M, Roach J, Jones CD, Dangl JD. Whole genome sequencing of a clade of Pseudomonads reveals complex interplay between effector repertoire and host utilization. PLoS Pathogens [accepted pending minor revision].



January 1, 2010

Anderson, J. A., Ping, L., Dibben, O., Jabara, C. B., Arney, L., Kincer, L., . . . Swanstrom, R. (2010). HIV-1 Populations in Semen Arise through Multiple Mechanisms. PLoS Pathogens,6(8). doi:10.1371/journal.ppat.1001053

Temple, B. R., Jones, C. D., & Jones, A. M. (2010). Evolution of a Signaling Nexus Constrained by Protein Interfaces and Conformational States. PLoS Computational Biology,6(10). doi:10.1371/journal.pcbi.1000962



January 1, 2009

Earley, EJ, and B Wolford (2009) Mechanosensation diversity across and within Drosophila species. DIS 92: 119-122.

Friedman, E. J., Temple, B. R., Hicks, S. N., Sondek, J., Jones, C. D., & Jones, A. M. (2009). Prediction of Protein-Protein Interfaces on G-Protein β Subunits Reveals a Novel Phospholipase C β2 Binding Domain. Journal of Molecular Biology, 392(4), 1044-1054. doi:10.1016/j.jmb.2009.07.076

Faddah, D. A., Ganko, E. W., Mccoach, C., Pickrell, J. K., Hanlon, S. E., Mann, F. G., . . . Vision, T. J. (2009). Systematic Identification of Balanced Transposition Polymorphisms in Saccharomyces cerevisiae. PLoS Genetics, 5(6). doi:10.1371/journal.pgen.1000502

Dworkin, I., & Jones, C. D. (2009). Genetic Changes Accompanying the Evolution of Host Specialization in Drosophila sechellia. Genetics, 181(2), 721-736. doi:10.1534/genetics.108.093419

Reinhardt, J. A., Baltrus, D. A., Nishimura, M. T., Jeck, W. R., Jones, C. D., & Dangl, J. L. (2008). De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Research, 19(2), 294-305. doi:10.1101/gr.083311.108