Todd N. Wylie  twylie@wustl.edu

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Assistant Professor of Pediatrics
Gastroenterology, Hepatology and Nutrition

phone: (314) 454-6173

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 (63)


  1. Longitudinal Dynamics of Skin Bacterial Communities in the Context of Staphylococcus aureus Decolonization. Microbiol Spectr. 2022. 
  2. Fecal microbiome and bile acid metabolome in adult short bowel syndrome. Am J Physiol Gastrointest Liver Physiol. 2022;322(1):G154-G168. PMCID:PMC8793869  PMID:34816756 
  3. Chronic villitis of unknown etiology: Investigations into viral pathogenesis. Placenta. 2021;107:24-30. PMCID:PMC8101289  PMID:33730616 
  4. ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data. Microbiol Resour Announc. 2021;10(9). PMCID:PMC7936641  PMID:33664143 
  5. The microbiome of the human female reproductive tract. Current Opinion in Physiology.. 2020;Volume 13:87-93. 
  6. A virome sequencing approach to feline oral squamous cell carcinoma to evaluate viral causative factors. Vet Microbiol. 2020;240:108491. PMCID:PMC7117531  PMID:31902496 
  7. Carriage of the Toxic Shock Syndrome Toxin Gene by Contemporary Community-Associated Staphylococcus aureus Isolates. Pediatric Infect Dis Soc.. 2019. PMCID:PMC6831934   PMID:30285124 
  8. Impaired Chylomicron Assembly Modifies Hepatic Metabolism Through Bile Acid-Dependent and Transmissible Microbial Adaptations. Hepatology. 2019;70(4):1168-1184. doi:10.1002/hep.30669  PMCID:PMC6783349  PMID:31004524 
  9. Genome Organization of Canada Goose Coronavirus, A Novel Species Identified in a Mass Die-off of Canada Geese. Sci Rep. 2019;9(1):5954. PMCID:PMC6459860  PMID:30976080 
  10. Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection. Front Cell Infect Microbiol. 2019;9:14. PMCID:PMC6375827  PMID:30800643 
  11. Host Gene Expression in Nose and Blood for the Diagnosis of Viral Respiratory Infection. J Infect Dis. 2018. PMID:30339221 
  12. Detection of Viruses in Clinical Samples Using Metagenomic Sequencing and Targeted Sequence Capture. J Clin Microbiol. 2018. PMID:30232133 
  13. Remnant Small Bowel Length in Pediatric Short Bowel Syndrome and the Correlation with Intestinal Dysbiosis and Linear Growth. J Am Coll Surg. 2018. PMID:30077861 
  14. The vaginal eukaryotic DNA virome and preterm birth. Am J Obstet Gynecol. 2018;219(2):189.e1-189.e12. PMCID:PMC6066425  PMID:29738749 
  15. Carriage of Cronobacter sakazakii in the Very Preterm Infant Gut. Clin Infect Dis. 2018;67(2):269-274. PMCID:PMC6030953  PMID:29394356 
  16. Genome Sequence of Enterovirus D68 from St. Louis, Missouri, USA, 2016. Genome Announc. 2017;5(9). PMCID:PMC5334578  PMID:28254971 
  17. 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 
  18. 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 
  19. 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 
  20. Enhanced virome sequencing using targeted sequence capture. Genome Res. 2015. doi:10.1101/gr.191049.115  PMID:26395152 
  21. 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 
  22. 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 
  23. 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 
  24. Enterovirus D68-associated acute respiratory distress syndrome in adult, United States, 2014. Emerg Infect Dis. 2015;21(5):914-6. PMCID:PMC4412249  PMID:25897542 
  25. 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 
  26. Genome sequence of enterovirus D68 from St. Louis, Missouri, USA. Emerg Infect Dis. 2015;21(1):184-6. PMCID:PMC4285240  PMID:25532062 
  27. 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 
  28. 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 
  29. Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis. J Clin Microbiol. 2013;51(12):3950-4. PMCID:PMC3838074  PMID:24048526 
  30. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45(10):1113-20. doi:10.1038/ng.2764  PMCID:PMC3919969  PMID:24071849 
  31. 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 
  32. Genomic impact of transient low-dose decitabine treatment on primary AML cells. Blood. 2013;121(9):1633-43. PMCID:PMC3587326  PMID:23297133 
  33. 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 
  34. 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 
  35. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487(7407):330-7. doi:10.1038/nature11252  PMCID:PMC3401966  PMID:22810696 
  36. A framework for human microbiome research. Nature. 2012;486(7402):215-21. doi:10.1038/nature11209  PMCID:PMC3377744  PMID:22699610 
  37. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-14. doi:10.1038/nature11234  PMCID:PMC3564958  PMID:22699609 
  38. 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 
  39. Integrated genomic analyses of ovarian carcinoma. Nature. 2011;474(7353):609-15. doi:10.1038/nature10166  PMCID:PMC3163504  PMID:21720365 
  40. 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 
  41. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010;363(25):2424-33. doi:10.1056/NEJMoa1005143  PMCID:PMC3201818  PMID:21067377 
  42. 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 
  43. 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 
  44. 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 
  45. 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 
  46. 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 
  47. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008;456(7218):66-72. doi:10.1038/nature07485  PMCID:PMC2603574  PMID:18987736 
  48. 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 
  49. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008;453(7192):175-83. doi:10.1038/nature06936  PMCID:PMC2803040  PMID:18464734 
  50. Whole-genome sequencing and variant discovery in C. elegans. Nat Methods. 2008;5(2):183-8. doi:10.1038/nmeth.1179  PMID:18204455 
  51. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222-34. doi:10.1126/science.1139247  PMID:17431167 
  52. Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species Genome Biol.. 2006;7(8):75. PMCID:PMC1779591  
  53. 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 
  54. 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 
  55. 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 
  56. 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 
  57. 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 
  58. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol. 2003;4(4):R26. PMCID:PMC154577  PMID:12702207 
  59. A compilation of soybean ESTs: generation and analysis. Genome. 2002;45(2):329-38. PMID:11962630 
  60. 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 
  61. 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 
  62. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921. doi:10.1038/35057062  PMID:11237011 
  63. An encyclopedia of mouse genes. Nat Genet. 1999;21(2):191-4. doi:10.1038/5976  PMID:9988271 
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