October 21, 2017
This is the academic website of Todd Wylie, bioinformatician and genomicist. I am an Assistant Professor at Washington University School of Medicine (St. Louis, MO). I develop/utilize bioinformatics methods and tools for the analysis of high throughput multi-omics data. You can find information about my research, publications, and scientific interests here.

Abstracts and Presentations (51)

I periodically update this page with abstracts from presentations and conferences, listed in reverse chronological order. (Underlining 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.