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

  • BS, 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. 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. 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. 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. Enhanced virome sequencing using targeted sequence capture. Genome Res. 2015. doi:10.1101/gr.191049.115  PMID:26395152 
  5. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487(7407):330-7. doi:10.1038/nature11252  PMCID:PMC3401966  PMID:22810696 
  20. A framework for human microbiome research. Nature. 2012;486(7402):215-21. doi:10.1038/nature11209  PMCID:PMC3377744  PMID:22699610 
  21. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-14. doi:10.1038/nature11234  PMCID:PMC3564958  PMID:22699609 
  22. 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. Integrated genomic analyses of ovarian carcinoma. Nature. 2011;474(7353):609-15. doi:10.1038/nature10166  PMCID:PMC3163504  PMID:21720365 
  24. 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. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010;363(25):2424-33. doi:10.1056/NEJMoa1005143  PMCID:PMC3201818  PMID:21067377 
  26. 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. 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. 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. 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. 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. 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. 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. 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. Whole-genome sequencing and variant discovery in C. elegans. Nat Methods. 2008;5(2):183-8. doi:10.1038/nmeth.1179  PMID:18204455 
  35. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222-34. doi:10.1126/science.1139247  PMID:17431167 
  36. 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. 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. 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. 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. 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. 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. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol. 2003;4(4):R26. PMCID:PMC154577  PMID:12702207 
  43. A compilation of soybean ESTs: generation and analysis. Genome. 2002;45(2):329-38. PMID:11962630 
  44. 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. 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 
  46. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921. doi:10.1038/35057062  PMID:11237011 
  47. An encyclopedia of mouse genes. Nat Genet. 1999;21(2):191-4. doi:10.1038/5976  PMID:9988271 
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