Jonathan M. Carlson

Researcher, eScience Research Group


Ph.D. University of Washington, 2009

carlson@microsoft.com

vita

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Projects

  • PhyloD: Statistical modeling of HIV adaptation. We've used this approach to identify sites of HLA-mediated escape and related covariation in HIV. Code available here.
  • PhyloD Viewer: Visualization tool for sequence covariation and adaptation.
  • Phylo Detective: Visualization tool for viewing traits on a large phylogeny.
  • False discovery rates for contingency tables: A computationally efficient means of calculating exact FDR for a set of 2x2 contingency tables or Fisher's exact test for a single table.
  • .NET Bio: .NET Bio is a bioinformatics library for .NET. Upcoming versions of PhyloD will be available as part of the suite of tools packaged with .NET Bio.

Selected Videos

Publications

Selected Publications

All publications (Citations)

2013
2012
2011
2010
2009
2008
2007
2006

Theses

  • Phylogenetic dependency networks: Identifying patterns of adaptation in HIV. Jonathan M. Carlson. Doctoral Dissertation, Dept. Computer Science and Engineering, University of Washington, February 2009.
    UW distinguished dissertation, Council of Graduate School's distinguished dissertation semi-finalist.
    [abstract, summary, extended summary, pdf (4MB)]
  • Creation of a Relational Database for Identifying Functional DNA Sequence Motifs in A. thaliana and Other Genomes. Jonathan M. Carlson. Undergraduate Honors thesis, Dept. Biology, Dartmouth College, June 2003.
    Dartmouth Kemeny Computing prize and Reed Biology Award
    [pdf]

Contact

Microsoft Research
1100 Glendon Ave PH-1
Los Angeles, CA 90024
Tel: (425) 704-8906
Fax: (425) 936-7329
carlson@microsoft.com

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