About

HEADSHOT I'm Todd Wylie, an Assistant Professor at Washington University School of Medicine (St. Louis, MO). 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.

Research

Listed below are several vignettes related to my contributions to science, in reverse chronological order. Please click here for a full list of publications.

Microbial Genomics

I took the opportunity to participate in a large consortium, the Human Microbiome Project (HMP), whose aim was to identify what constitutes a "normal" human microbiome. By sequencing microbial communities from 300 individuals sampled at multiple body sites, the range of normal flora in a large cohort was described. This study of healthy individuals can now serve as a reference point for studies of the human microbiota and its association with disease. Involvement in the HMP led to my joining the lab of one of project’s PIs, Dr. George Weinstock, as Director of Microbial Genomics Computing. I led a team that provided informatics infrastructure for research analysts and augmented the analytic capabilities of the lab. Areas of applied research included: microbial assembly and annotation, comparative genomics, automating analytic workflows, R&D support, and updating and extending older pipelines. Administrative duties included overseeing data submission to archives/repositories, web site development, and grant writing. I also interfaced with PIs and colleagues in clinical collaborations, which ultimately led to the formation of a new Pediatric Microbial Genomics group in the Department of Pediatrics, and my faculty position thereof. The Pediatric Microbial Genomics group focuses on improving medical practice through the application of high-throughput multi-omics data and associated computational methods in the clinic. My colleagues and I have recently developed a comprehensive targeted sequence capture panel called ViroCap, 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.

Selected Publications

  • Enhanced virome sequencing using targeted sequence capture. PMID: 26395152
  • Development and Evaluation of an Enterovirus D68 Real-Time Reverse Transcriptase PCR Assay. PMID: 26063859
  • Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. PMID: 24647013
  • Human Microbiome Project Consortium. A framework for human microbiome research. PMID: 22699610
  • Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. PMID: 22699609

Technology Development

My analytical work on early next-generation sequencing data provided the background needed to manage a small group of bioinformaticians in the context of technology development. As the Manager of Application Programming and Development for the Technology Development group under Dr. Elaine Mardis, I oversaw several areas of bioinformatics development: performing ad hoc and high priority analyses; analysis workflow and pipeline development (e.g. sncRNA, RNA-seq, and targeted sequencing analysis automation); evaluation/feedback of data produced by early-access and cutting edge technologies; contributing written word and data visualization to presentations, publications, and grants. I contributed analyses, experience, and suggestions to the sequencing and publication of the first human cancer genome, a patient with acute myeloid leukemia (AML), as well as subsequent projects analyzing sequence data from human cancers. Much of my group’s effort was in the emerging area of cancer genomics. My group formulated approaches for assessing custom and whole exome targeted sequence capture platforms, while troubleshooting early-access capture products. We also engineered workflows for comparing coverage/efficiency among multiple commercial exome capture kits. My group was responsible for providing analysis support and tool development for AML methylation studies. I collaborated with a team of oncologists and research biologists to formulate an approach to miRNA generation and analysis from cancer patient specimens. My team also provided analysis, insight, and workflows for an innovative, exploratory project aimed at creating personalized breast cancer vaccines based on epitope binding efficacy, as predicted in silico from underlying SNV mutations from tumor/normal pairs.

Selected Publications

  • DNMT3A mutations in acute myeloid leukemia. PMID: 21067377
  • Next-generation sequencing identifies the natural killer cell microRNA transcriptome. PMID: 20935160
  • Recurring mutations found by sequencing an acute myeloid leukemia genome. PMID: 19657110
  • DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. PMID: 18987736

Computational Biology

The advent of next-generation sequencing technologies dramatically increased genomic data throughput well beyond the capabilities of the computational tools current at the time. As such, I was a charter member of a team of "CompBio" analysts responsible for handling and assessing NGS data. Our foci included: reviewing, testing, and application of cutting edge sequence alignment algorithms, developing coverage modeling algorithms for NGS alignment data, variant calling, and proposing best practices in data handling/assessment of high-throughput data, as imposed by emerging NGS technologies. Our group was one of the first to sequence and evaluate a multicellular organism (C. elegans) using NGS technology. During this time, I greatly increased my proficiency in creating, analyzing, and manipulating large data sets, while expanding my understanding of core bioinformatics algorithms, applications, and data repositories. Our team also developed computational methods for genome assembly appraisal (e.g. platypus, macaque), as well as software to guide draft genome assembly with cDNA sequences. Many of the approaches formulated to handle NGS data would go on to be incorporated into the center’s automated analysis pipeline, the Genome Modeling System. Several of my CompBio colleagues went on to found Cofactor Genomics.

Selected Publications

  • Genome Modeling System: A Knowledge Management Platform for Genomics. PMID: 26158448
  • Genome analysis of the platypus reveals unique signatures of evolution. PMID: 18464734
  • Whole-genome sequencing and variant discovery in C. elegans. PMID: 18204455
  • Evolutionary and biomedical insights from the rhesus macaque genome. PMID: 17431167

The Human Genome and Model Organisms

My earliest work in genomics involved sequencing and analyzing expressed sequence tags (ESTs) from multiple model organisms--e.g. human, mouse, chicken, soybean, zebrafish, toxoplasma, and numerous parasitic and free-living nematode species. Under Dr. Marco A. Marra, I contributed to the management of a research laboratory (15+ technicians) specializing in large-scale cDNA sequencing, at the time the largest provider of open-access EST data in the world. During this time, I became fluent in Unix/Linux operating systems and associated programming languages, as well as core bioinformatics applications. I helped define the analysis pipeline and methods used to process ~6 million ESTs from over 90 species and co-authored over 2.3 million ESTs submitted to NCBI’s dbEST repository. I filled a key analysis role as a member of the Parasitic Nematode EST Project team, which entailed the sequencing, cataloging, and comparative analysis of ESTs from over 30 species of free-living and parasitic nematode species. I was lead software engineer for Nematode Net. Designing this site combined many disparate aspects of my skill set: biology, database administration, programming, and web design. I also implemented NemaPath software, which provides information about the presence, absence and composition of enzymatic pathways in given organisms based on transcript data, while providing higher-order comparisons across clades and hosts. These activities were formative in building skills and knowledge related to genomics, bioinformatics, and transcriptome analysis.

Selected Publications

  • NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. PMID: 18983679
  • Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. PMID: 14681448
  • A compilation of soybean ESTs: generation and analysis. PMID: 11962630
  • An encyclopedia of mouse genes. PMID: 9988271

Publications (49)

I periodically update this page with my publications, listed in reverse chronological order. You may also visit My NCBI Bibliography for a list of indexed publications.

indicates first, co-first, or corresponding author

Chandrasekaran S, Burnham CD, Warner BB, Tarr PI, Wylie TN. Carriage of Cronobacter sakazakii in the very preterm infant gut. Clin Infect Dis. 2018 Jan 31. doi: 10.1093/cid/ciy062. [Epub ahead of print] PubMed PMID: 29394356
Wylie KM, Wylie TN, Storch GA. Genome Sequence of Enterovirus D68 from St. Louis, Missouri, USA, 2016. Genome announcements. 2017; 5(9). PMID: 28254971, PMCID: PMC5334578
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 Apr;18(2):227-33. doi: 10.1111/tid.12512. Epub 2016 Mar 31. PubMed PMID: 26895706.
Rowley AH, Wylie KM, Kim KY, Pinku 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 Dec 18;16:1076. doi: 10.1186/s12864-015-2323-5. PubMed PMID: 26679344; PubMed Central PMCID: PMC4683744.
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 Ccl5 as a Stromal Chemokine Critical for Neurofibromatosis-1 Glioma Growth. Neoplasia. 2015 Oct;17(10):776-88. doi: 10.1016/j.neo.2015.10.002. PubMed PMID: 26585233; PubMed Central PMCID: PMC4656811.
Wylie TN, Wylie KM, Herter BN, Storch GA. Enhanced virome sequencing using targeted sequence capture. Genome Res. 2015 Dec;25(12):1910-20. doi: 10.1101/gr.191049.115. Epub 2015 Sep 22. PubMed PMID: 26395152; PubMed Central PMCID: PMC4665012.
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 Sep;94(37):e1534. doi: 10.1097/MD.0000000000001534. PubMed PMID: 26376402; PubMed Central PMCID: PMC4635816.
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 Jul 9;11(7):e1004274. doi: 10.1371/journal.pcbi.1004274. eCollection 2015 Jul. PubMed PMID: 26158448; PubMed Central PMCID: PMC4497734.
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 Aug;53(8):2641-7. doi: 10.1128/JCM.00923-15. Epub 2015 Jun 10. PubMed PMID: 26063859; PubMed Central PMCID: PMC4508392.
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 May;21(5):914-6. doi: 10.3201/eid2105.142033. PubMed PMID: 25897542; PubMed Central PMCID: PMC4412249.
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 Jan;21(1):184-6. doi: 10.3201/eid2101.141605. PubMed PMID: 25532062; PubMed Central PMCID: PMC4285240.
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 Apr;63(4):531-48. doi: 10.1002/glia.22754. Epub 2014 Sep 24. PubMed PMID: 25258010; PubMed Central PMCID: PMC4331255.
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 Aug 14;158(4):929-44. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7. PubMed PMID: 25109877; PubMed Central PMCID: PMC4152462.
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 May;58(9):1211-8. doi: 10.1093/cid/ciu084. Epub 2014 Mar 18. PubMed PMID: 24647013; PubMed Central PMCID: PMC3982840.
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 Oct 11;8(10):e77571. doi: 10.1371/journal.pone.0077571. eCollection 2013. PubMed PMID: 24147027; PubMed Central PMCID: PMC3795683.
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 Oct;45(10):1113-20. doi: 10.1038/ng.2764. PubMed PMID: 24071849; PubMed Central PMCID: PMC3919969.
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 Dec;51(12):3950-4. doi: 10.1128/JCM.01930-13. Epub 2013 Sep 18. PubMed PMID: 24048526; PubMed Central PMCID: PMC3838074.
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 Feb 28;121(9):1633-43. doi: 10.1182/blood-2012-09-459313. Epub 2013 Jan 7. PubMed PMID: 23297133; PubMed Central PMCID: PMC3587326.
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 Mar;23(3):431-9. doi: 10.1101/gr.142604.112. Epub 2012 Dec 5. PubMed PMID: 23222849; PubMed Central PMCID: PMC3589532.
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 Jul 20;150(2):264-78. doi: 10.1016/j.cell.2012.06.023. PubMed PMID: 22817890; PubMed Central PMCID: PMC3407563.
Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252. PubMed PMID: 22810696; PubMed Central PMCID: PMC3401966.
Human Microbiome Project Consortium. A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209. PubMed PMID: 22699610; PubMed Central PMCID: PMC3377744.
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234. PubMed PMID: 22699609; PubMed Central PMCID: PMC3564958.
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 Feb 8;482(7385):400-4. doi: 10.1038/nature10755. PubMed PMID: 22318521; PubMed Central PMCID: PMC3874809.
Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. Erratum in: Nature. 2012 Oct 11;490(7419):298. PubMed PMID: 21720365; PubMed Central PMCID: PMC3163504.
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 May;13(3):325-33. doi: 10.1016/j.jmoldx.2011.01.006. PubMed PMID: 21497292; PubMed Central PMCID: PMC3077736.
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 Dec 16;363(25):2424-33. doi: 10.1056/NEJMoa1005143. Epub 2010 Nov 10. PubMed PMID: 21067377; PubMed Central PMCID: PMC3201818.
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 Nov;20(11):1590-604. doi: 10.1101/gr.107995.110. Epub 2010 Oct 8. PubMed PMID: 20935160; PubMed Central PMCID: PMC2963822.
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 Dec 9;116(24):5316-26. doi: 10.1182/blood-2010-05-285395. Epub 2010 Sep 28. PubMed PMID: 20876853; PubMed Central PMCID: PMC3012545.
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 Sep 10;361(11):1058-66. doi: 10.1056/NEJMoa0903840. Epub 2009 Aug 5. PubMed PMID: 19657110; PubMed Central PMCID: PMC3201812.
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 Sep 1;25(17):2283-5. doi: 10.1093/bioinformatics/btp373. Epub 2009 Jun 19. PubMed PMID: 19542151; PubMed Central PMCID: PMC2734323.
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 Nov 6;456(7218):66-72. doi: 10.1038/nature07485. PubMed PMID: 18987736; PubMed Central PMCID: PMC2603574.
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 Nov 4;9:525. doi: 10.1186/1471-2164-9-525. PubMed PMID: 18983679; PubMed Central PMCID: PMC2588608.
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 Jan;37(Database issue):D571-8. doi: 10.1093/nar/gkn744. Epub 2008 Oct 21. PubMed PMID: 18940860; PubMed Central PMCID: PMC2686480.
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 May 8;453(7192):175-83. doi: 10.1038/nature06936. Erratum in: Nature. 2008 Sep 11;455(7210):256. Nefedov, Mikhail [added]; de Jong, Pieter J [added]. PubMed PMID: 18464734; PubMed Central PMCID: PMC2803040.
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 Feb;5(2):183-8. doi: 10.1038/nmeth.1179. Epub 2008 Jan 20. PubMed PMID: 18204455.
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 Apr 13;316(5822):222-34. PubMed PMID: 17431167.
Mitreva M, Wendl MC, Martin J, Wylie T, Yin Y, Larson A, Parkinson J, 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):R75. PubMed PMID: 26271136; PubMed Central PMCID: PMC1779591.
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 Apr 26;6:58. PubMed PvMID: 15854223; PubMed Central PMCID: PMC1112591.
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 Oct;137(2):277-91. PubMed PMID: 15383298.
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 Feb;14(2):209-20. PubMed PMID: 14762059; PubMed Central PMCID: PMC327096.
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 Jan 1;32(Database issue):D423-6. PubMed PMID: 14681448; PubMed Central PMCID: PMC308745.
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. Epub 2003 Mar 31. PubMed PMID: 12702207; PubMed Central PMCID: PMC154577.
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 Mar;13(3):443-54. PubMed PMID: 12618375; PubMed Central PMCID: PMC430278.
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 Apr;45(2):329-38. PubMed PMID: 11962630.
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 Sep;11(9):1594-602. PubMed PMID: 11544204; PubMed Central PMCID: PMC311136.
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 Apr 6;113(2):337-40. PubMed PMID: 11295190.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J; International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921. Erratum in: Nature 2001 Jun 7;411(6838):720. Szustakowki, J [corrected to Szustakowski, J]. Nature 2001 Aug 2;412(6846):565. PubMed PMID: 11237011. Full Author List
Marra M, Hillier L, Kucaba T, Allen M, Barstead R, Beck C, Blistain A, Bonaldo M, Bowers Y, Bowles L, Cardenas M, Chamberlain A, Chappell J, Clifton S, Favello A, Geisel S, Gibbons M, Harvey N, Hill F, Jackson Y, Kohn S, Lennon G, Mardis E, Martin J, Mila L, McCann R, Morales R, Pape D, Person B, Prange C, Ritter E, Soares M, Schurk R, Shin T, Steptoe M, Swaller T, Theising B, Underwood K, Wylie T, Yount T, Wilson R, Waterston R. An encyclopedia of mouse genes. Nat Genet. 1999 Feb;21(2):191-4. PubMed PMID: 9988271.

Abstracts (51)

I periodically update this page with abstracts from presentations and conferences.

indicates speaker/presenter

Todd N. Wylie, Gregory A. Storch, Kristine M. Wylie. MAGPIE: A lightweight computational pipeline for detection of viral reads from complex metagenomic sequencing data. International Human Microbiome Consortium Congress 2016. Houston, Texas. November 9-11, 2016.
Richard Buller, Maria Cannella, Todd Wylie, Kristine Wylie, Amruta Padhye, Anthony Orvedahl, Angeliki Margoni, Gregory Storch. Development and Evaluation of a RT-PCR Assay for the Detection of Enterovirus D68. 31st Clinical Virology Symposium and Annual Meeting of the Pan American Society for Clinical Virology, Daytona Beach, Florida, 2015.
Kristine M. Wylie, Todd N. Wylie, Brandi N. Herter, Anthony Orvedahl, Richard Buller, Vincent Magrini, Richard K. Wilson, Gregory A. Storch. Enhanced virome sequencing with capture enrichment and its application to the EV-D68 outbreak. International Human Microbiome Consortium (IHMC): International Human Microbiome Congress, Luxembourg City, Luxembourg, 2015.
Todd N. Wylie, Kristine M. Wylie, Brandi N. Herter, Gregory A. Storch. ViroCap: enhanced virome sequencing through solution-based capture enrichment. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2015.
Anne H Rowley, Kristine Wylie, Kwang-Youn A Kim, Adam J Pink, Rebecca Reindel, Susan C Baker, Stanford T Shulman, Amy Yang, Jan M Orenstein, Mark W Lingen, George Weinstock, Todd Wylie. Deep RNA Sequencing Reveals a Transcriptional Profile of Cytotoxic T Lymphocyte Activation, Antigen Presentation, Immunoglobulin Production, and Type I Interferon Response in Kawasaki Disease Arteritis. Eleventh International Kawasaki Disease Symposium, Honolulu, Hawaii, 2015.
Maze Ndukum-Ndonwi, Brenda Kwambana, Hongyu Gao, Kathie A. Mihindukulasuriya, Kristine M. Wylie, Yanjiao Zhou, Todd Wylie, Susanna Siebert, Erica Sodergren, Saha Samir, Nierman Bill, Lucero Luluth, Adrian Peter, Martin Antonio, George M. Weinstock. Impact of Pneumococcal Vaccination on the Pediatric Nasopharyngeal Microbiome in the First Year of Life. 2nd Annual Global Health and Infectious Disease Conference and Symposium, Washington University School of Medicine, St. Louis, Missouri, 2014.
Robert S. Fulton, Kym Pepin, Veena Bhonagiri, Aye Wollam, Brandi Herter, Todd Wylie, Kristine Wylie, Makedonka Mitreva, and Richard Wilson. Facilitating Microbial Community Characterization by High Throughput Next Generation Sequencing of Reference Genomes. 2nd Annual Global Health and Infectious Disease Conference and Symposium, Washington University School of Medicine, St. Louis, Missouri, 2014.
Yanjiao Zhou, Makedonka Mitreva, Robert Fulton, Brandi Herter, Vincent Magrini, John Martin, Kathie Mihindukulasuriya, Bruce A. Rosa, Gregory A. Storch, Phillip I. Tarr, Kristine M. Wylie, Todd N. Wylie, Richard K. Wilson. Application of genomic and metagenomic approaches in infectious diseases. 2nd Annual Global Health and Infectious Disease Conference and Symposium, Washington University School of Medicine, St. Louis, Missouri, 2014.
Francisco M. De La Vega, Mehul Rathod, Richard Littin, Len Trigg, Todd Wylie, Susanna Siebert, Nelson B. Freimer, Wesley C. Waren, George M. Weinstock, and John G. Cleary. Scalable variant identification and imputation across large multigenerational pedigrees from high-throughput sequencing data. Biology of Genomes Cold Spring Harbor Laboratory (CSHL), CSHL, New York, 2013.
Jason Walker, Todd Wylie, Vincent Magrini, Sean McGrath, Malachi Griffith, Christopher Maher, Jasreet Hundal, Winnie W. Pong, Ryan Demeter, Amy Ly, David H. Gutmann, Richard K. Wilson, Elaine Mardis. Transcriptome Modeling: A high throughput analysis framework for RNA-seq and cDNA Capture. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2013.
Malachi Griffith, Obi L. Griffith, Scott Smith, Jason Walker, Allison Regier, Nathan Dees, Chris Miller, Gabriel Sanderson, Feiyu Du, Adam Coffman, Thomas Mooney, Mark Burnett, David Morton, Todd Wylie, Matthew Ellis, Govindan Ramaswamy, Benjamin Tan, Vincent Magrini, David Larson, Li Ding, David Dooling, Timothy J. Ley, Rick K. Wilson, Elaine R. Mardis. Clinical cancer sequencing and integrated analysis of whole genomes, exomes and transcriptomes. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2013.
David H. Spencer, Jeffery M. Klco, Tamara Lamprecht, Todd Wylie, Vince Magrini, Jasreet Hundal, Jason Walker, Nobish Varghese, Matthew Meyer, Petra Gilmore, Reid Townsend, Elaine Mardis, Timothy J. Ley. In vitro decitabine treatment demonstrates heterogeneous changes in methylation and gene expression in primary AML samples. 54th ASH Annual Meeting and Exposition, Atlanta, Georgia, 2012.
Maria Trissal, David H Spencer, Jessica Silva, Todd Wylie, Jasreet Hundal, Sean McGrath, Vincent Magrini, Giridharan Ramsingh, Richard J Wilson, Timothy J. Ley, and Daniel C. Link. Dysregulation of the Imprinted DLK1-DIO3 Locus in Promyelocytic Leukemia. 54th ASH Annual Meeting and Exposition, Atlanta, Georgia, 2012.
Jason Walker, Vincent Magrini, Todd Wylie, Sean D. McGrath, Don Conrad, Joseph Dougherty, Richard K. Wilson, and Elaine R. Mardis. Single-Molecule, Real-Time (SMRT) DNA sequencing facilitates long trinucleotide repeat characterization. Biology of Genomes Cold Spring Harbor Laboratory (CSHL), CSHL, New York, 2012.
EJ Duncavage, R Demeter, T Wylie, V Magrini, J Pfeifer. Genomic Characterization of Merkel Cell Polyomavirus Integration Sites in Merkel Cell Carcinoma. USCAP 2012 Annual Meeting Vancouver, BC, Canada, 2012.
Robert Fulton, Ryan Demeter, Vincent Magrini, Michael McLellan, Daniel Koboldt, Li Ding, Todd Wylie, Michelle O’Laughlin, Rachel Maupin, Elaine R. Mardis, Richard K. Wilson. Variant Validation, Extension, and Interpretation Methods at The Genome Institute at Washington University. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2012.
Vincent Magrini, Jason Walker, Todd Wylie, Sean McGrath, Amy Ly, Jasreet Hundal, Ryan Demeter, Laura Gottschalk, Khaing Soe, Nathan Sander, Lisa Cook, Erica Sodergren, Wes Warren, George Weinstock, Richard K. Wilson, Elaine R. Mardis. Combinatorial Data Sets: Pragmatic Applications Derived from Multiple Sequencing Technologies. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2012.
Jasreet Hundal & Todd Wylie, Vincent Magrini, Jason Walker, Maria Trissal, Sean D. McGrath, Jessica Silva, Giridharan Ramsingh, Todd A. Fehniger, Daniel Link, Timothy J. Ley, Richard K. Wilson, Elaine R. Mardis. Automated Profiling of Small RNA Molecules in Acute Myeloid Leukemia Using High- Throughput Next Generation Sequencing. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2012.
Todd A. Fehniger, Todd Wylie, Elizabeth Germino, Jeffrey W Leong, Vincent J Magrini, Sunita Koul, Catherine R Keppel, Stephanie E Schneider, Daniel C Koboldt, Ryan P Sullivan, Michael E Heinz, Seth D Crosby, Rakesh Nagarajan, Giridharan Ramsingh, Daniel C. Link, Timothy J Ley, Elaine R Mardis. The NK Cell MicroRNA Transcriptome Defined by Next-Generation Sequencing Identifies IL- 15-Signaled Alterations In Mature MiR-223 Expression, and MiR-223 as a Potential Regulator of Murine Granzyme B. 53rd ASH Annual Meeting and Exposition, Orlando, Florida, 2011.
Timothy J. Ley, Li Ding, Matthew J. Walter, Michael D. McLellan, Tamara Lamprecht, David E. Larson, Cyriac Kandoth, Jacqueline E. Payton, Jack Baty, John S. Welch, Christopher C. Harris, Cheryl F. Lichti, R. Reid Townsend, Robert S. Fulton, David J. Dooling, Daniel C. Koboldt, Heather Schmidt, Qunyuan Zhang, John R. Osborne, Ling Lin, Michelle O’Laughlin, Joshua F. McMichael, Kim D. Delehaunty, Sean D. McGrath, Lucinda A. Fulton, Vincent J. Magrini, Tammi L. Vickery, Jasreet Hundal, Lisa L. Cook, Joshua J. Conyers, Gary W. Swift, Jerry P. Reed, Patricia A. Alldredge, Todd Wylie, Jason Walker, Joelle Kalicki-Veizer, Mark A. Watson, Sharon Heath, William D. Shannon, Nobish Varghese, Rakesh Nagarajan, Peter Westervelt, Michael H. Tomasson, Daniel C. Link, Timothy A. Graubert, John F. DiPersio, Elaine R. Mardis, Richard K. Wilson. Mutations In the DNA Methyltransferase Gene DNMT3A Are Highly Recurrent In Patients with Intermediate Risk Acute Myeloid Leukemia, and Predict Poor Outcomes. 53rd ASH Annual Meeting and Exposition, Orlando, Florida, 2011.
John S. Welch, David Larson, Li Ding, Michael D. McLellan, Tamara Lamprecht, Cyriac Kandoth, Jacqueline E. Payton, Jack Baty, Christopher C. Harris, Cheryl F. Lichti, Robert S. Fulton, David J. Dooling, Daniel C Koboldt, Heather Schmidt, Qunyuan Zhang, John R. Osborne, Ling Lin, Michelle O’Laughlin, Joshua F. McMichael, Kim D. Delehaunty, Sean D. McGrath, Lucinda A. Fulton, Vincent J Magrini, Tammi L. Vickery, Todd Wylie, Jason Walker, Peter Westervelt, Michael H. Tomasson, Mark A. Watson, Sharon Heath1, William D. Shannon, Rakesh Nagarajan, Daniel C. Link, Timothy Graubert, John F. DiPersio, Elaine R. Mardis, Richard K. Wilson, Timothy J Ley. Complete Sequencing and Comparison of 12 Normal Karyotype M1 AML Genomes with 12 t(15;17) Positive M3-APL Genomes. 53rd ASH Annual Meeting and Exposition, Orlando, Florida, 2011.
V. Magrini, T. Wylie, S. McGrath, A. Ly, J. Walker, J. Hundal, E. R. Mardis. Leveraging the worm: an evaluation of third-generation sequencing technology. Biology of Genomes Cold Spring Harbor Laboratory (CSHL), CSHL, New York, 2011.
Ryan Demeter, Dan Koboldt, Li Ding, Jason Walker, Todd Wylie, Richard K. Wilson, Elaine R. Mardis, Vincent Magrini. Solid-Phase Multiplexed Capture for Validation of Single-Nucleotide Variants, Insertions, Deletions and Structural Variants. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2011.
T. Wylie, V. Magrini, S. McGrath, A. Ly, J. Walker, J. Hundal, E. R. Mardis. C. elegans: 30x or Bust!. Pacific Biosciences Bioinformatics User Group Meeting (AGBT), Marco Island, Florida, 2011.
Jason Walker, Todd Wylie, Jasreet Hundal, Ryan Demeter, Josh McMichael, Daniel C. Koboldt, Vincent Magrini, Richard K. Wilson, Elaine R. Mardis. Assessment Of Efficiency In Directed Sequencing Strategies. Genome Informatics 2010, Hinxton, UK, 2010.
Daniel C. Koboldt, David E. Larson, Nathan Dees, Dong Shen, Jason Walker, Todd Wylie, Ryan Demeter, Vincent Magrini, Michael D. McLellan, Lucinda Fulton, Robert S. Fulton, Li Ding, Elaine R. Mardis, Richard K. Wilson. Somatic mutation discovery in ovarian cancer by whole genome and exome sequencing. Personal Genomes Cold Spring Harbor Laboratory (CSHL), CSHL, New York, 2010.
Sean D McGrath, Jason Walker, Devin P Locke, Todd Wylie, Lisa Cook, Eric D Tycksen, Elaine R Mardis, Richard K Wilson, Vincent Magrini. Performance analysis of low input Illumina sequencing libraries. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2010.
Todd Wylie, Jason Walker, Sean McGrath, Vincent Magrini, Josh McMichael, Xiaoqi Shi, Devin Locke, Richard K. Wilson, Elaine R. Mardis. Automated Primary Coverage/Expression Analysis of High Throughput Human RNA-seq. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2010.
Giridharan Ramsingh, Dan C Koboldt, Todd A Fehniger, Todd Wylie, Vincent Magrini, Maria Trissal, Sunita Koul, Li-Wei Chang, Rakesh Nagarajan, Timothy J. Ley, Elaine Mardis, Daniel C. Link. Comprehensive Evaluation of MicroRNA Genes and Gene Expression Using Next Generation Sequencing in a Patient with Acute Myelogenous Leukemia. 51st ASH Annual Meeting and Exposition, Orlando, Florida, 2009.
Daniel C. Koboldt, Todd Wylie, Ken Chen, David E. Larson, David Dooling, Li Ding, Elaine R. Mardis, Richard K. Wilson. Short Read Aligners: A Comparison of Tools for Next-generation Sequence Analysis. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2009.
Todd Wylie, Vincent Magrini, Todd A Fehniger, Rakesh Nagarajan, Sunita Koul, Seth D Crosby, Michael Heinz, Timothy J Ley, Richard K Wilson, Elaine R Mardis. High-throughput characterization of miRNAs using massively parallel sequencing technology. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2009.
Jarret Glasscock, Todd Wylie, Ryan Richt, Sean McGrath, Vincent Magrini, Matthew Hickenbotham, Elaine R. Mardis. New Sequencing Technologies Characterize cDNA-Based Variation. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2008.
Jarret Glasscock, Todd Wylie, Ryan Richt, Vincent Magrini, Matthew Hickenbotham, Richard K. Wilson, Elaine R. Mardis. New Sequencing Technologies: Breaking All the Tools. Cold Spring Harbor Laboratory (CSHL), Biology of Genomes Meeting, CSHL, New York, 2007.
A Siddiqui, J Bonfield, V Alekseyev, G Marth, T Bloom, A Zimmer, P Flicek, J Glassock, D Platt, N Hanson, J Knight, J Sorenson, E Thayer, C Brown, S Jones, M Attili, M Bainbridge, D Church, A Cox, L Du, W Huang, J Maguire, J Malek, J Manning, K Maisinger, D Messina, K Moulton, A Quinlan, C Stewart, M Stromberg, R Warren, T Wylie. A New Format for DNA Sequence Data. Cold Spring Harbor Laboratory (CSHL), Biology of Genomes Meeting, CSHL, New York, 2007.
Matthew Hickenbotham and Technology Development Group. Initial Validation of the Solexa 1 G Genome Analyzer. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2007.
T. Wylie, V. Magrini, J. Glasscock, D. Messina, E. Mardis, R. Wilson. APEX: Software for Sequence Alignment Data Mining and Extraction. Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics, Hinxton, UK, 2006.
Glasscock, J., Hillier, L., Wylie, T., Messina, D., Mardis, E., Wilson, R. The Chimpanzee Genome, Swinging the Other Way with Comparative Analysis. The Biology of Genomes, Cold Spring Harbor Laboratory (CSHL), CSHL, New York, 2006.
Glasscock, J., Wylie, T., Messina, D., Mardis, E., Wilson, R. Assessing and guiding primate assemblies via Human mRNAs. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2006.
James P McCarter, M Mitreva, M Wendel, T Wylie, J Parkinson, M Blaxter, R H Waterston. Codon usage patterns in Nematoda: analysis based upon 26 million codons in 32 species. 15th International Worm Meeting, University of California at Los Angeles, Los Angeles, California, 2005.
Glasscock, J., Cliften, P., Wylie, T., Messina, D., Mardis, E., Wilson, R. Quantitative assessment of genome sequence coverage. Advances in Genome Biology and Technology (AGBT), Marco Island, Florida, 2005.
Mitreva, M., D. P. Jasmer, J. Appleton, J. Martin, M. Dante, T. Wylie, S. W. Clifton, R. H. Waterston, J. P. McCarter. Discovery of Candidate Developmentally Expressed Genes in Trichinella spiralis. XIth International Conference on Trichinellosis, San Diego, California, 2004.
M. Mitreva, J. C. Martin, T. N. Wylie, M. Dante, S. W. Clifton, D. McK. Bird, R. Wilson, J. P. McCarter. Discovery of Candidate Developmentally Expressed Genes in Plant Parasitic Nematodes. European Society of Nematologists 27th International Symposium, Rome, Italy, 2004.
M. Dautova, J. P. McCarter, S. W. Clifton, C. Murphy, J. C. Martin, T. N. Wylie, M. Dante, D. Pape, R. H. Waterston. Revealing Genes Expressed in Parasitic Nematodes by Single Pass cDNA Sequencing. Plant and Animal Genome XI, San Diego, California, 2003.
D. Bird, C. Opperman, J. Thorne, R. Schaffer, J. Kieber, S. Clifton, T. Kepler., Chiapelli, B., Crane, Z., Dante, M., Huston, N., Hraber, P., Martin, J., McCarter, J., Pape, D., Rashotte, A., Scholl, E., Schaff, J., Snyder, D., Waterman, J., Waterston, R., Watkins, J., Wylie, T. Genomic Dissection of a Nematode-plant Interaction: a Tool to Study Plant Biology. National Science Foundation Plant Genome Meeting, Washington, DC, 2002.
M. Dante, J. Martin, T. Wylie, J. McCarter, S. Clifton. Clustering Parasitic Nematode ESTs Using Phrap & Consed. Midwest C. elegans Meeting, St. Louis, Missouri, 2002.
M. Dante, J. Martin, T. Wylie, J. McCarter, S. Clifton. Clustering Parasitic Nematode ESTs Using Phrap & Consed. Conference on Genome Sequencing and Biology, Cold Spring Harbor Laboratory (CSHL), CSHL, New York, 2002.
T. Wylie, J. McCarter, J. Martin, S. Clifton, R. Waterston. Nematode.net, a Tool for Navigating Sequences from Parasitic and Free-living Nematodes. 13th Biennial International C. elegans Conference, Los Angeles, California, 2001.
McCarter, J., Clifton, S., Chiapelli, B., Pape, D., Martin, J., Wylie, T., Dante, M., Waterston, R. Genes from Other Nematodes: A Progress Report on the GSC Parasitic Nematode EST Project. 13th Biennial International C. elegans Conference, Los Angeles, California, 2001.
K. Wylie, T. Wylie, GSC Mapping and EST Groups. Utilization of Expressed Sequence Tags in Generation of Radiation Hybrid and Physical Maps of Model Organisms. HUGO Human Genome Meeting, Edinburgh, Scotland, 2001.
McCarter, J., D. Bird, U. Rao, A. Kloek, S. Clifton, D. Pape, J. Martin, T. Wylie, S. Eddy, R. Waterston, and the Washington University GSC EST Team. Progress Toward High Throughput Gene Discovery in Parasitic Nematodes; Initial Findings from Meloidogyne incognita EST Sequencing. Society of Nematology Annual Meeting, Quebec City, Quebec Canada, 2000.
T. Wylie and the Washington University GSC EST Team. ESTs at Washington University Genome Sequencing Center. Tenth International Genome Sequencing and Analysis Conference, Miami Beach, Florida, 1998.

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