Todd Wylie  Wylie_T@kids.wustl.edu

Laboratory Medicine

phone: (314) 747-4069

Research Interests

I have over 19 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 organism genomes, including mouse, macaque, platypus, soybean, zebrafish, toxoplasma, and numerous parasitic and free-living nematode species. More recently, I contributed my experience and analytic skills 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 under Dr. Elaine R. Mardis, Co-Director of The McDonnell Genome Institute, 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 in a lab applying DNA sequencing, genome-wide analysis, bioinformatics, and other genetic methods to the study of human and microbial genomes. I have an extensive background in targeted sequence capture, transcriptomics, and the analysis of whole exome data. As Department of Pediatrics faculty, my current focus is to collaborate with clinicians and basic scientists by using genomic approaches and bioinformatics to understand problems in medical microbiology, and improve diagnosis and treatment through applied genomics. Research interests: genomics; human microbiome; bacterial and viral characterization; transcriptomics and RNA-seq; Next-generation sequencing (NGS) technologies and related analyses; applied bioinformatics solutions in large-scale research; R&D pipeline and analytical software development; exome and custom targeted sequencing platforms; early-access sequencing technology evaluation and application; data visualization, representation, and set theory approaches for big data.

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

Selected 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.
Enhanced virome sequencing using targeted sequence capture. Genome Res. 2015. doi:10.1101/gr.191049.115  PMID:26395152 
4.
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 
5.
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 
6.
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 
7.
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 
8.
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 
9.
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