Todd Wylie is an Assistant Professor in the Department of Pediatrics at Washington University School of Medicine and the McDonnell Genome Institute. He develops/utilizes bioinformatics methods and tools for the analysis of high throughput multi-omics data.

Mr. Wylie has over 20 years experience in large-scale genomics, applying biology, informatics, and analytic skills to a wide range of scientific research. He is highly experienced in the technology development and informatics operations of a large genome center. Early in his career, Mr. Wylie contributed to the International Human Genome Sequencing Consortium that sequenced and mapped the first human genome (pubmed). Subsequently, he 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. Mr. Wylie contributed to the sequencing and publication of the first human cancer genome (pubmed), a patient with acute myeloid leukemia, as well as subsequent projects involving sequence data from human cancers. Mr. Wylie 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, Mr. Wylie has extensive experience handling and analyzing high throughput sequencing data as produced by multiple next-generation sequencing platforms. Prior to joining the Department of Pediatrics, Mr. Wylie directed Dr. George Weinstock’s microbial computing group, focusing on software development and analysis for the study of human and microbial genomes. He also has an extensive background in targeted sequence capture, transcriptomics, and the analysis of whole exome data. Mr. Wylie and colleagues recently developed a comprehensive targeted sequence capture panel called ViroCap (pubmed), 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.

Mr. Wylie’s current focus is to collaborate with clinicians and basic scientists in improving medical practice through the application of high-throughput multi-omics and associated computational methods. He is involved in many collaborative efforts studying the microbiome and its association with disease.

Publications

title citation publication date
Genome Sequence of Enterovirus D68 from St. Louis, Missouri, USA, 2016 Genome Announc. 2017 Mar 2;5(9). pii: e01630-16. doi: 10.1128/genomeA.01630-16. 1970-08-22
High-throughput sequencing of cerebrospinal fluid for diagnosis of chronic Propionibacterium acnes meningitis in an allogeneic stem cell transplant recipient. Transpl Infect Dis. 2016 Feb 20. doi: 10.1111/tid.12512. [Epub ahead of print] 2016-02-20
The transcriptional profile of coronary arteritis in Kawasaki disease. BMC Genomics. 2015 Dec 18;16(1):1076. doi: 10.1186/s12864-015-2323-5. 2015-12-18
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. 2015-10-01
Enhanced virome sequencing through solution-based capture enrichment. Genome Res. 2015 Sep 22. pii: gr.191049.115. [Epub ahead of print] 2015-09-22
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. 2015-07-09
Development and Evaluation of an Enterovirus D68 Real-Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) Assay. J Clin Microbiol. 2015 Jun 10. pii: JCM.00923-15. [Epub ahead of print] 2015-06-10
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. 2015-05-01
Genome sequence of enterovirus D68 from St. Louis, Missouri, USA. Emerg Infect Dis. 2015;21(1):184-6. doi: 10.3201/eid2101.141605. 2015-01-01
RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease. Glia. 2014 Sep 24. doi: 10.1002/glia.22754. [Epub ahead of print] 2014-09-24
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. 2014-05-01
F11R Is a Novel Monocyte Prognostic Biomarker for Malignant Glioma. PLoS One. 2013 Oct 11;8(10):e77571. doi: 10.1371/journal.pone.0077571. 2013-10-11
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Sep 26;45(10):1113-20. doi: 10.1038/ng.2764. 2013-09-26
Precise Dissection of an Escherichia coli O157:H7 outbreak by Single Nucleotide Polymorphism Analysis. J Clin Microbiol. 2013 Sep 18. [Epub ahead of print] 2013-09-18
NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics. 2008 Nov 4;9:525. doi: 10.1186/1471-2164-9-525. 2008-11-04
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. 2009-01-01
Genomic impact of transient low-dose decitabine treatment on primary AML cells. Blood. 2013 Jan 7. [Epub ahead of print] 2013-01-07
Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma. Genome Res. 2012 Dec 5. [Epub ahead of print] 2012-12-05
The origin and evolution of mutations in acute myeloid leukemia. Cell. 2012 Jul 20;150(2):264-78. 2012-07-20
Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252. 2012-07-18
A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209. 2012-06-13
Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234. 2012-06-13
Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature. 2012 Feb 8 [Epub ahead of print]. 2012-02-08
Integrated genomic analyses of ovarian carcinoma Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. 2011-06-29
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. 2011-04-27
Complete characterization of the microRNAome in a patient with acute myeloid leukemia. Blood. 2010 Dec 9;116(24):5316-26. Epub 2010 Sep 28. 2010-12-09
Next-generation sequencing identifies the natural killer cell microRNA transcriptome. Genome Res. 2010 Nov;20(11):1590-604. Epub 2010 Oct 8. 2010-11-01
DNMT3A Mutations in Acute Myeloid Leukemia N Engl J Med. 2010 Nov 10. 2010-11-10
Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009 Sep 10;361(11):1058-66. Epub 2009 Aug 5. 2009-09-10
VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009 Sep 1;25(17):2283-5. Epub 2009 Jun 19. 2009-06-19
DNA sequencing of a cytogenetically normal acute myeloid leukaemia (AML) genome. Nature. 2008 Nov 6;456(7218):66-72. 2008-11-06
Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008 May 8;453(7192):175-83. 2008-05-08
Whole-genome sequencing and variant discovery in C. elegans. Nat Methods. 2008 Feb;5(2):183-8. Epub 2008 Jan 20. 2008-02-10
Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13;316(5822):222-34. 2007-04-13
Investigating hookworm genomes by comparative analysis of two Ancylostoma species. BMC Genomics. 2005 Apr 26;6(1):58. 2005-04-26
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. 2003-03-01
Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol. 2003;4(4):R26. Epub 2003 Mar 31. 2003-03-31
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. 2004-02-01
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res. 2004 Jan 1;32 Database issue:D423-6. 2004-01-01
An encyclopedia of mouse genes. Nat Genet. 1999 Feb;21(2):191-4. 1999-02-01
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. 2004-10-25
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. 2001-04-06
A compilation of soybean ESTs: generation and analysis. Genome. 2002 Apr;45(2):329-38. 2002-03-31