Anton Valouev

Ph.D.

E-mail: valouev@{usc, stanford}.edu

I received my Ph.D. inApplied Mathematics at the University of Southern California. I was very fortunate to have Michael Waterman as my mentor. Currently I am a postdoc atArend Sidow's lab at theDept. of Pathology atStanford University School of Medicine.

Research

My primary Ph.D. project concerns statistical and computational aspects of restriction mapping technology termed Optical Mapping developed by David Schwartz. Some of my work addresses  probabilistic alignment methods for optical mapping data. I also worked on the whole-genome optical map assembly method that allows reconstruction of genome-wide ordered restriction maps from single DNA molecule optical maps produced by random shearing of genomic DNA. Optical mapping is very well suited for analysis of genomic differences for which we developed a statistical method to assess the differences based on optical mapping data. The differences (also dubbed variants) come in different flavors, our method primarily addresses insertions/deletions (greater than 5Kb), sequence differences at the restriction sites, inversions and rearrangements.

Papers

  1. Anton Valouev, David C. Schwartz, Shiguo Zhou, and Michael S. Waterman
    An algorithm for assembly of ordered restriction maps from single DNA molecules
    PNAS 2006 103: 15770-15775 [pdf] [software]

  2. Anton Valouev
    Shotgun optical mapping: a comprehensive statistical and computational analysis.
    Ph.D. Thesis 2006 [pdf]

  3. Anton Valouev, Yu Zhang, David C. Schwartz, and Michael S. Waterman
    Refinement of optical map assemblies
    Bioinformatics 2006 22(10): 1217-1224 [pdf] [software]

  4. Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz,  Yi Yang, Yu Zhang, and Michael S. Waterman
    Alignment of optical maps
    RECOMB 2005; Journal of Computational Biology 2006 13(2): 442-462 [pdf] [ps] [software]

Miscellaneous

 

Last modified: 24-10-2006