Todd Wylie  Wylie_T@kids.wustl.edu

Assistant Professor of Pediatrics
Laboratory Medicine

phone: (314) 454-4525

Clinical Interests

I have over 20 years experience in large-scale genomics, applying biology, informatics, and analytic skills to a wide range of scientific research. I am highly experienced in the technology development and informatics operations of a large genome center. Early in my career, I contributed to the International Human Genome Sequencing Consortium that sequenced and mapped the first human genome [PMID: 11237011]. Subsequently, I contributed to the sequencing and analysis of other landmark model organisms, including mouse, macaque, platypus, soybean, zebrafish, toxoplasma, and numerous parasitic and free-living nematode species. I contributed to the sequencing and publication of the first human cancer genome [PMID: 18987736], a patient with acute myeloid leukemia, as well as subsequent projects involving sequence data from human cancers. I worked 9 years in the area of technology development at The McDonnell Genome Institute (MGI) under Dr. Elaine R. Mardis, managing a small, agile group of bioinformaticians. This role required being the informatics/analysis "glue" between the development wet lab, bioinformatics team, testing and training, and other collaborative groups at the institute. As such, I have extensive experience handling and analyzing high throughput sequencing data as produced by multiple next-generation sequencing platforms. Prior to joining the Department of Pediatrics, I directed Dr. George Weinstock’s microbial computing group, focusing on software development and analysis for the study of human and microbial genomes. I also have an extensive background in targeted sequence capture, transcriptomics, and the analysis of whole exome data. My colleagues and I recently developed a comprehensive targeted sequence capture panel called ViroCap [PMID: 26395152], designed to enrich nucleic acid from DNA and RNA viruses. This tool will greatly enhance the study of eukaryotic DNA and RNA viruses and takes us closer to using high-throughput sequencing as a comprehensive viral diagnostic tool.

Education

  • B.S., Southern Illinois University Edwardsville1995

Training

  • Introduction to UNIX Programming, University of Missouri St. Louis (UMSL), St. Louis, MO1997 - 1997
  • Advanced UNIX Programming, University of Missouri St. Louis (UMSL), St. Louis, MO1997 - 1997
  • Introduction to C Programming, University of Missouri St. Louis (UMSL), St. Louis, MO1998 - 1998
  • Introduction to Perl RegExes for Bioinformaticians, Practical Innovation at BioCon2003 - 2003
  • Introduction to Dreamweaver MX, Washington University School of Medicine, St. Louis, MO2003 - 2003
  • Advanced Dreamweaver MX, Washington University School of Medicine, St. Louis, MO2003 - 2003
  • SynaMatix Training Program, Washington University School of Medicine, St. Louis, MO2006 - 2006
  • Perl Master Class: Intermediate Perl, Stonehenge Consulting Services2006 - 2006
  • Ensembl Workshop: Ensembl Core API / BioMart Web Services, Washington University School of Medicine, St. Louis, MO2007 - 2007
  • Big Nerd Ranch Cocoa Bootcamp, Big Nerd Ranch2008 - 2008
  • Early Access Training for Pacific Biosciences RS Platform, Pacific Biosciences2010 - 2010
  • Complete Genomics Data Training, Washington University School of Medicine, St. Louis, MO2010 - 2010
  • Pacific Biosciences Bioinformatics Workshop, Washington University School of Medicine, St. Louis, MO2012 - 2012
  • Computing for Data Analysis, Johns Hopkins Bloomberg School of Medicine2013 - 2013
  • Python for Genomic Data Science, John Hopkins University2016 - 2016

Recent Publications view all (47)


  1. Wylie KM, Blanco-Guzman M, Wylie TN, Lawrence SJ, Ghobadi A, DiPersio JF, Storch GA. High-throughput sequencing of cerebrospinal fluid for diagnosis of chronic Propionibacterium acnes meningitis in an allogeneic stem cell transplant recipient. Transpl Infect Dis. 2016;18(2):227-33. doi:10.1111/tid.12512  PMID:26895706  
  2. Rowley AH, Wylie KM, Kim KY, Pink AJ, Yang A, Reindel R, Baker SC, Shulman ST, Orenstein JM, Lingen MW, Weinstock GM, Wylie TN. The transcriptional profile of coronary arteritis in Kawasaki disease. BMC Genomics. 2015;16(1):1076. doi:10.1186/s12864-015-2323-5  PMCID:PMC4683744  PMID:26679344  
  3. Solga AC, Pong WW, Kim KY, Cimino PJ, Toonen JA, Walker j, Wylie T, Magrini V, Griffith M, Griffith OL, Ly A, Ellisman MH, Mardis ER, Gutmann DH. RNA Sequencing of Tumor-associated microglia reveals CcI5 as a stromal chemokine critical for neurofibromatosis-1 glioma growth. Neoplasia. 2015;17(10):776-88. doi:10.1016/j.neo.2015.10.002  PMCID:PMC4656811  PMID:26585233  
  4. Wylie TN, Wylie KM, Herter BN, Storch GA. Enhanced virome sequencing using targeted sequence capture. Genome Res. 2015. doi:10.1101/gr.191049.115  PMID:26395152  
  5. Rodriguez M, Hogan PG, Satola SW, Crispell E, Wylie T, Gao H, Sodergren E, Weinstock GM, Burnham CA, Fritz SA. Discriminatory Indices of Typing Methods for Epidemiologic Analysis of Contemporary Staphylococcus aureus Strains. Medicine (Baltimore). 2015;94(37):e1534. doi:10.1097/MD.0000000000001534  PMID:26376402  
  6. Wylie TN, Wylie KM, Buller RS, Cannella M, Storch GA. Development and Evaluation of an Enterovirus D68 Real-Time Reverse Transcriptase PCR Assay. J Clin Microbiol. 2015;53(8):2641-7. doi:10.1128/JCM.00923-15  PMCID:PMC4508392  PMID:26063859  
  7. Griffith M, Griffith OL, Smith SM, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK. Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015;11(7):e1004274. doi:10.1371/journal.pcbi.1004274  PMCID:PMC4497734  PMID:26158448  
  8. Farrell JJ, Ikladios O, Wylie KM, O'Rourke LM, Lowery KS, Cromwell JS, Wylie TN, Melendez EL, Makhoul Y, Sampath R, Bonomo RA, Storch GA. Enterovirus D68-associated acute respiratory distress syndrome in adult, United States, 2014. Emerg Infect Dis. 2015;21(5):914-6. doi:10.3201/eid2105.142033  PMCID:PMC4412249  PMID:25897542  
  9. Solga AC, Pong WW, Walker J, Wylie T, Magrini V, Apicelli AJ, Griffith M, Griffith OL, Kohsaka S, Wu GF, Brody DL, Mardis ER, Gutmann DH. RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease. Glia. 2015;63(4):531-48. doi:10.1002/glia.22754  PMCID:PMC4331255  PMID:25258010  
  10. Wylie KM, Wylie TN, Orvedahl A, Buller RS, Herter BN, Magrini V, Wilson RK, Storch GA. Genome sequence of enterovirus D68 from St. Louis, Missouri, USA. Emerg Infect Dis. 2015;21(1):184-6. doi:10.3201/eid2101.141605  PMCID:PMC4285240  PMID:25532062  
  11. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014;158(4):929-44. doi:10.1016/j.cell.2014.06.049  PMCID:PMC4152462  PMID:25109877  
  12. Carl MA, Ndao IM, Springman AC, Manning SD, Johnson JR, Johnston BD, Burnham CA, Weinstock ES, Weinstock GM, Wylie TN, Mitreva M, Abubucker S, Zhou Y, Stevens HJ, Hall-Moore C, Julian S, Shaikh N, Warner BB, Tarr PI. Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Clin Infect Dis. 2014;58(9):1211-8. doi:10.1093/cid/ciu084  PMCID:PMC3982840  PMID:24647013  
  13. Turabelidze G, Lawrence SJ, Gao H, Sodergren E, Weinstock GM, Abubucker S, Wylie T, Mitreva M, Shaikh N, Gautom R, Tarr PI. Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis. J Clin Microbiol. 2013;51(12):3950-4. doi:10.1128/JCM.01930-13  PMCID:PMC3838074  PMID:24048526  
  14. Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45(10):1113-20. doi:10.1038/ng.2764  PMCID:PMC3919969  PMID:24071849  
  15. Gutmann DH, McLellan MD, Hussain I, Wallis JW, Fulton LL, Fulton RS, Magrini V, Demeter R, Wylie T, Kandoth C, Leonard JR, Guha A, Miller CA, Ding L, Mardis ER. Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma. Genome Res. 2013;23(3):431-9. doi:10.1101/gr.142604.112  PMCID:PMC3589532  PMID:23222849  
  16. Klco JM, Spencer DH, Lamprecht TL, Sarkaria SM, Wylie T, Magrini V, Hundal J, Walker J, Varghese N, Erdmann-Gilmore P, Lichti CF, Meyer MR, Townsend RR, Wilson RK, Mardis ER, Ley TJ. Genomic impact of transient low-dose decitabine treatment on primary AML cells. Blood. 2013;121(9):1633-43. doi:10.1182/blood-2012-09-459313  PMCID:PMC3587326  PMID:23297133  
  17. Pong WW, Walker J, Wylie T, Magrini V, Luo J, Emnett RJ, Choi J, Cooper ML, Griffith M, Griffith OL, Rubin JB, Fuller GN, Piwnica-Worms D, Feng X, Hambardzumyan D, DiPersio JF, Mardis ER, Gutmann DH. F11R is a novel monocyte prognostic biomarker for malignant glioma. PLoS One. 2013;8(10):e77571. doi:10.1371/journal.pone.0077571  PMCID:PMC3795683  PMID:24147027  
  18. Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O'Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, Hundal J, Cook LL, Swift GW, Reed JP, Alldredge PA, Wylie TN, Walker JR, Watson MA, Heath SE, Shannon WD, Varghese N, Nagarajan R, Payton JE, Baty JD, Kulkarni S, Klco JM, Tomasson MH, Westervelt P, Walter MJ, Graubert TA, DiPersio JF, Ding L, Mardis ER, Wilson RK. The origin and evolution of mutations in acute myeloid leukemia. Cell. 2012;150(2):264-78. doi:10.1016/j.cell.2012.06.023  PMCID:PMC3407563  PMID:22817890  
  19. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487(7407):330-7. doi:10.1038/nature11252  PMCID:PMC3401966  PMID:22810696  
  20. Human Microbiome Project Consortium. A framework for human microbiome research. Nature. 2012;486(7402):215-21. doi:10.1038/nature11209  PMCID:PMC3377744  PMID:22699610  
  21. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-14. doi:10.1038/nature11234  PMCID:PMC3564958  PMID:22699609  
  22. Matsushita H, Vesely MD, Koboldt DC, Rickert CG, Uppaluri R, Magrini VJ, Arthur CD, White JM, Chen YS, Shea LK, Hundal J, Wendl MC, Demeter R, Wylie T, Allison JP, Smyth MJ, Old LJ, Mardis ER, Schreiber RD. Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature. 2012;482(7385):400-4. doi:10.1038/nature10755  PMCID:PMC3874809  PMID:22318521  
  23. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011;474(7353):609-15. doi:10.1038/nature10166  PMCID:PMC3163504  PMID:21720365  
  24. Duncavage EJ, Magrini V, Becker N, Armstrong JR, Demeter RT, Wylie T, Abel HJ, Pfeifer JD. Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue. J Mol Diagn. 2011;13(3):325-33. doi:10.1016/j.jmoldx.2011.01.006  PMCID:PMC3077736  PMID:21497292  
  25. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O'Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, Swift GW, Reed JP, Alldredge PA, Wylie T, Walker J, Kalicki J, Watson MA, Heath S, Shannon WD, Varghese N, Nagarajan R, Westervelt P, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Wilson RK. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010;363(25):2424-33. doi:10.1056/NEJMoa1005143  PMCID:PMC3201818  PMID:21067377  
  26. Ramsingh G, Koboldt DC, Trissal M, Chiappinelli KB, Wylie T, Koul S, Chang LW, Nagarajan R, Fehniger TA, Goodfellow P, Magrini V, Wilson RK, Ding L, Ley TJ, Mardis ER, Link DC. Complete characterization of the microRNAome in a patient with acute myeloid leukemia. Blood. 2010;116(24):5316-26. doi:10.1182/blood-2010-05-285395  PMCID:PMC3012545  PMID:20876853  
  27. Fehniger TA, Wylie T, Germino E, Leong JW, Magrini VJ, Koul S, Keppel CR, Schneider SE, Koboldt DC, Sullivan RP, Heinz ME, Crosby SD, Nagarajan R, Ramsingh G, Link DC, Ley TJ, Mardis ER. Next-generation sequencing identifies the natural killer cell microRNA transcriptome. Genome Res. 2010;20(11):1590-604. doi:10.1101/gr.107995.110  PMCID:PMC2963822  PMID:20935160  
  28. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, Meyer RJ, Schindler JK, Pohl CS, Wallis JW, Shi X, Lin L, Schmidt H, Tang Y, Haipek C, Wiechert ME, Ivy JV, Kalicki J, Elliott G, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson MA, Baty J, Heath S, Shannon WD, Nagarajan R, Link DC, Walter MJ, Graubert TA, DiPersio JF, Wilson RK, Ley TJ. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009;361(11):1058-66. doi:10.1056/NEJMoa0903840  PMCID:PMC3201812  PMID:19657110  
  29. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009;25(17):2283-5. doi:10.1093/bioinformatics/btp373  PMCID:PMC2734323  PMID:19542151  
  30. Martin J, Abubucker S, Wylie T, Yin Y, Wang Z, Mitreva M. Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. Nucleic Acids Res. 2009;37(Database issue):D571-8. doi:10.1093/nar/gkn744  PMCID:PMC2686480  PMID:18940860  
  31. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, Pohl C, Smith S, Hawkins A, Abbott S, Locke D, Hillier LW, Miner T, Fulton L, Magrini V, Wylie T, Glasscock J, Conyers J, Sander N, Shi X, Osborne JR, Minx P, Gordon D, Chinwalla A, Zhao Y, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson M, Baty J, Ivanovich J, Heath S, Shannon WD, Nagarajan R, Walter MJ, Link DC, Graubert TA, DiPersio JF, Wilson RK. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008;456(7218):66-72. doi:10.1038/nature07485  PMCID:PMC2603574  PMID:18987736  
  32. Wylie T, Martin J, Abubucker S, Yin Y, Messina D, Wang Z, McCarter JP, Mitreva M. NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics. 2008;9:525. doi:10.1186/1471-2164-9-525  PMCID:PMC2588608  PMID:18983679  
  33. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008;453(7192):175-83. doi:10.1038/nature06936  PMCID:PMC2803040  PMID:18464734  
  34. Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER. Whole-genome sequencing and variant discovery in C. elegans. Nat Methods. 2008;5(2):183-8. doi:10.1038/nmeth.1179  PMID:18204455  
  35. Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222-34. doi:10.1126/science.1139247  PMID:17431167  
  36. Mitreva M, Wendl M, Martin J, Wylie T, Yin Y, Parkinson J, Blaxter M, Waterston RH, McCarter JP. Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species Genome Biol.. 2006;7(8):75. PMCID:PMC1779591  
  37. Mitreva M, McCarter JP, Arasu P, Hawdon J, Martin J, Dante M, Wylie T, Xu J, Stajich JE, Kapulkin W, Clifton SW, Waterston RH, Wilson RK. Investigating hookworm genomes by comparative analysis of two Ancylostoma species. BMC Genomics. 2005;6:58. doi:10.1186/1471-2164-6-58  PMCID:PMC1112591  PMID:15854223  
  38. Mitreva M, Jasmer DP, Appleton J, Martin J, Dante M, Wylie T, Clifton SW, Waterston RH, McCarter JP. Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages. Mol Biochem Parasitol. 2004;137(2):277-91. doi:10.1016/j.molbiopara.2004.05.015  PMID:15383298  
  39. Mitreva M, McCarter JP, Martin J, Dante M, Wylie T, Chiapelli B, Pape D, Clifton SW, Nutman TB, Waterston RH. Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Res. 2004;14(2):209-20. doi:10.1101/gr.1524804  PMCID:PMC327096  PMID:14762059  
  40. Wylie T, Martin JC, Dante M, Mitreva MD, Clifton SW, Chinwalla A, Waterston RH, Wilson RK, McCarter JP. Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res. 2004;32(Database issue):D423-6. doi:10.1093/nar/gkh010  PMCID:PMC308745  PMID:14681448  
  41. Li L, Brunk BP, Kissinger JC, Pape D, Tang K, Cole RH, Martin J, Wylie T, Dante M, Fogarty SJ, Howe DK, Liberator P, Diaz C, Anderson J, White M, Jerome ME, Johnson EA, Radke JA, Stoeckert CJ Jr, Waterston RH, Clifton SW, Roos DS, Sibley LD. Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database. Genome Res. 2003;13(3):443-54. doi:10.1101/gr.693203  PMCID:PMC430278  PMID:12618375  
  42. McCarter JP, Mitreva MD, Martin J, Dante M, Wylie T, Rao U, Pape D, Bowers Y, Theising B, Murphy CV, Kloek AP, Chiapelli BJ, Clifton SW, Bird DM, Waterston RH. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol. 2003;4(4):R26. PMCID:PMC154577  PMID:12702207  
  43. Shoemaker R, Keim P, Vodkin L, Retzel E, Clifton SW, Waterston R, Smoller D, Coryell V, Khanna A, Erpelding J, Gai X, Brendel V, Raph-Schmidt C, Shoop EG, Vielweber CJ, Schmatz M, Pape D, Bowers Y, Theising B, Martin J, Dante M, Wylie T, Granger C. A compilation of soybean ESTs: generation and analysis. Genome. 2002;45(2):329-38. PMID:11962630  
  44. Clark MD, Hennig S, Herwig R, Clifton SW, Marra MA, Lehrach H, Johnson SL, Group tW, WU-GSCnEST Group. An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library. Genome Res. 2001;11(9):1594-602. doi:10.1101/gr.186901  PMCID:PMC311136  PMID:11544204  
  45. Akopyants NS, Clifton SW, Martin J, Pape D, Wylie T, Li L, Kissinger JC, Roos DS, Beverley SM. A survey of the Leishmania major Friedlin strain V1 genome by shotgun sequencing: a resource for DNA microarrays and expression profiling. Mol Biochem Parasitol. 2001;113(2):337-40. PMID:11295190  
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