Photo of Kyle Ellrott, Ph.D.

Kyle Ellrott Ph.D.

    • Assistant Professor of Computational Biology Program School of Medicine
    • Biomedical Engineering Graduate Program School of Medicine
    • Program in Molecular and Cellular Biosciences School of Medicine
    • OHSU Center for Spatial Systems Biomedicine School of Medicine

My research considers the various aspects of large scale data integration in the field of computational biology specifically as related to Cancer Biology. I have also worked in protein structure prediction and metagenomics, but through these different topics I have worked to integrate multiple types of experimental data, different forms of analysis and existing knowledge to improve analysis and recognition techniques.

The goal of my current research has been to create systems that allow the integration of data from large cancer cohorts in hopes of doing synthetic lethality target detection, significant non-coding mutation detection, and pathway level mutational effect analysis. To enable this research I have spent time working on pipeline systems to automate the running of analytical tools as well as working to define the which techniques will provide the most accurate data as well as developing frameworks for large scale distributed computing.

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Areas of interest

  • Computational biology
  • Data science
  • Machine learning
  • Precision medicine
  • Cancer early detection

Education

  • B.S., University of California, Riverside California 2004
  • Ph.D., University of Tennessee, Knoxville Tennessee 2008

Publications

  • "The cancer genome atlas pan-cancer analysis project" Nature Genetics October 2013
  • "The somatic genomic landscape of glioblastoma" Cell October 10 2013
  • "Global optimization of somatic variant identification in cancer genomes with a global community challenge" Nature Genetics  2014
  • "Comprehensivemolecular characterization of clear cell renal cell carcinoma" Nature  2013
  • "Comprehensive molecular portraits of human breast tumours" Nature October 4 2012
  • "Comprehensive molecular characterization of human colon and rectal cancer" Nature July 19 2012
  • "Enabling transparent and collaborative computational analysis of 12 tumor types within the Cancer Genome Atlas" Nature Genetics October 2013
  • "Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection" Nature Methods June 30 2015
  • "Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes" Journal of Biological Chemistry September 11 2009
  • "Structure of BT-3984, a member of the SusD/RagB family of nutrient-binding molecules" Acta Crystallographica Section F:Structural Biology Communications October 2010
  • "Identifying transcription factor binding sites through Markov chain optimization" Bioinformatics  2002
  • "PROSPECT-PSPP" Nucleic Acids Research July 1 2004
  • "Expansion of the protein repertoire in newly explored environments" PLoS Computational Biology  2010
  • "A computational pipeline for protein structure prediction and analysis at genome scale"   2003
  • "A computational pipeline for protein structure prediction and analysis at genome scale" Bioinformatics October 12 2003
  • "The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation" Acta Crystallographica Section F:Structural Biology Communications October 2010
  • "Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Ã… resolution" Acta Crystallographica Section F:Structural Biology Communications October 2010
  • "The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold" Acta Crystallographica Section F:Structural Biology Communications October 2010
  • "Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-d-Glu" Acta Crystallographica Section F:Structural Biology Communications October 2010
  • "Bacterial Pleckstrin Homology Domains" Journal of Molecular Biology February 12 2010
  • "A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Ã… resolution" Acta Crystallographica Section F:Structural Biology Communications October 2010
  • "PROSPECT II" Protein Engineering, Design and Selection September 2003
  • "The UCSC cancer genomics browser" Nucleic Acids Research January 1 2013
  • "Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism" Acta Crystallographica Section F:Structural Biology Communications October 2010
  • "Improving the performance of protein threading using insertion/deletion frequency arrays" Journal of Bioinformatics and Computational Biology June 2008
  • "Restriction enzyme recognition sequence search program" BioTechniques December 1 2002
  • "Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+Î’ core domain and an auxiliary C-terminal treble-clef zinc finger" Acta Crystallographica Section F:Structural Biology Communications October 2010
  • "Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays." Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference  2007
  • "Comprehensive genomic characterization of squamous cell lung cancers" Nature September 27 2012
  • "Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron" Acta Crystallographica Section F:Structural Biology Communications October 2010

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