Research Interests Publications CV Miscellaneous Contact Information


 
Jennifer Listgarten

I am a post-doc in the eScience group (formerly, the Machine Learning and Applied Statistics group) at Microsoft Research in Redmond, Washington.

 
 
Research Interests

My interests are in machine learning and applied statistics, especially as applied to large-scale, biologically-based problems (this area lies within the broader field of bioinformatics / computational biology). Projects which aim to reveal new fundamental biological insight, as well as those centered on more clinical applications both appeal to me.

My current biological focus, is, broadly, on the rational design of an HIV vaccine. In this domain, I have tackled the problems of: deducing HLA restrictions from Elispot assays which provide this information only indirectly; resolving ambiguity in HLA typing results in order to achieve high-resolution HLA data when this was not actually generated in the laboratory; and in silico epitope prediction. Solutions to these problems are also of broader practical importance, such as in vaccine design and infectious disease research in general, and in transplant medicine. The biological focus during my Ph.D. was a platform focus---that of Liquid Chromatography Mass Spectrometry (LCMS) proteomics for the purposes of biomarker discovery. Prior to that, I worked toward understanding genetic components of various cancers through SNP and microarray data.

Novel machine learning methodology developed throughout these projects includes: a class of generative models for alignment and comparison of time series; generalization of False Discovery Rates (FDR) to Graphical Model structure learning for pair wise entity extraction; a more accurate method for phasing genotype data tailored to the HLA domain; fast and convex multi-task learning by way of specialized features with logistic regression.
Publications
  • Statistical resolution of ambiguous HLA typing data. (abstract, paper, coverage in the magazine BioInform, press release)
    Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Phillip Goulder, David Heckerman,
    in PLoS Computational Biology, 2008, 4(2):e1000016
    For the public web server tool based on this work, (and soon, also executables to run locally), go here .

  • A statistical framework for modeling HLA-dependent T-cell response data. (abstract, paper, press release)
    Jennifer Listgarten, Nicole Frahm, Carl Kadie, Christian Brander and David Heckerman,
    PLoS Computational Biology, 2007, 3(10):e188
    Web tool, executable and source code available here, under "HLA Assignment"

  • Extensive HLA class I allele promiscuity among viral CTL epitopes. (abstract)
    N. Frahm, K. Yusim, T. Suscovich, S. Adams, J. Sidney, P. Hraber, H. Hewitt, CH. Linde, D. Kavanagh, T. Woodberry, L. Henry, K. Faircloth, J. Listgarten, C. Kadie, N. Jojic, K. Sango, N. Brown, E. Pae, M. Zaman, F. Bihl, A. Khatri, M. John, S. Mallal, F. Marincola, B. Walker, A. Sette, D. Heckerman, B. Korber, C. Brander
    European Journal of Immunology, 2007 37(9):2419-2433.
    See paper above for code/tools used in this paper.

  • Evidence that dysregulated DNA mismatch repair characterizes human non-melanoma skin cancer (abstract)
    Leah C. Young, Jennifer Listgarten, Martin J. Trotter, Susan E. Andrew, Victor A. Tron
    British Journal of Dermatology, 2008 158(1):59-69.

  • Determining the number of non-spurious arcs in a learned DAG model: Investigation of a Bayesian and a frequentist approach. (abstract, paper)
    Jennifer Listgarten and David Heckerman
    Proceedings of Twenty-Third Conference on Uncertainty in Artificial Intelligence, UAI Press, July 2007.

  • Analysis of sibling time series data: alignment and difference detection. (abstract, thesis and code)
    Jennifer Listgarten,
    Ph.D. Thesis, Department of Computer Science, University of Toronto, Dec. 2006.

  • Bayesian detection of infrequent differences in sets of time series with shared structure. (abstract, paper)
    Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Rachel Puckrin and Sean Cutler,
    Advances in Neural Information Processing Systems 19, MIT Press, Cambridge, MA, 2007 ( NIPS 2006).
    Best Student Paper, Honorable Mention.

  • Difference detection in LC-MS data for protein biomarker discovery. (abstract, paper and data set)
    Jennifer Listgarten, Radford M. Neal, Sam T. Roweis, Peter Wong and Andrew Emili,
    Bioinformatics, 2007 23:e198-e204 [by way of ECCB 2006 (European Conference on Computational Biology)]
    Best Student Paper, 3rd prize

  • Leveraging information across HLA alleles/supertypes improves epitope prediction. (abstract, paper)
    David Heckerman, Carl Kadie, Jennifer Listgarten,
    Journal of Computational Biology, 2007 14: 736-746
    (shorter version also appears Proceedings of Research in Computational Molecular Biology. Lecture Notes in Computer Science, Volume 3909, Mar 2006, 296-308.)
    (an yet an older version appears as Technical Report MSR-TR-05-127, Microsoft Research, September, 2005)
    Web tool, executable and source code available here, under "Epitope Prediction"

  • Practical proteomic biomarker discovery: taking a step back to leap forward. (abstract) (paper)
    Jennifer Listgarten and Andrew Emili,
    Drug Discovery Today, 2005 10:1697-1702.

  • Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. (abstract) (paper)
    Jennifer Listgarten and Andrew Emili,
    Molecular and Cellular Proteomics, 2005 4:419-434.

  • Multiple alignment of continuous time series. (abstract, paper, slides, and audio demo)
    Jennifer Listgarten, Radford M. Neal, Sam T. Roweis and Andrew Emili,
    Advances in Neural Information Processing Systems 17, MIT Press, Cambridge, MA, 2005 (NIPS 2004).
    The Continuous Profile Models (CPM) Matlab Toolbox is available here.

  • Predictive models for breast cancer susceptibility from multiple, single nucleotide polymorphisms. (abstract) (paper)
    Jennifer Listgarten, Sambasivarao Damaraju, Brett Poulin, Lillian Cook, Jennifer Dufour, Adrian Driga, John Mackey, David Wishart, Russ Greiner and Brent Zanke,
    Clinical Cancer Research 2004:10(8):2725-37.

  • Clinically validated benchmarking of normalization techniques for two-colour oligonucleotide spotted microarray slides. (abstract) (paper)
    Jennifer Listgarten, Kathryn Graham, Sambasivarao Damaraju, Carol Cass, John Mackey and Brent Zanke,
    Applied Bioinformatics 2003:2(4)219-228.

  • Lymphovascular invasion is associated with poor survival in gastric cancer: an application of gene-expression and tissue array techniques.
    Bryan J. Dicken, Kathryn Graham, Stewart M. Hamilton, Sam Andrews, Raymond Lai, Jennifer Listgarten, Gian S. Jhangri, L. Duncan Saunders, Sambasivarao Damaraju and Carol E. Cass,
    Annals of Surgery 2006: 243(1):64-73.

  • Exploring qualitative probabilities for image understanding. (pdf 1.2MB) (ps.gz 0.6MB)
    Jennifer Listgarten,
    M.Sc. Thesis, Department of Computer Science, University of Toronto, October 2000. (Supervisor: Allan Jepson)


CV

(pdf)

Miscellaneous
  • Code: Continuous Profile Models (CPM) Matlab Toolbox, for alignment of time series, is available here.
  • Credit/debit card fraud to watch out for and why to avoid movietickets.com (and some other on-line stores) -- "Reservation Rewards"/webloyalty.com.
  • Password protected photos.
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    Contact Information
    Physically Located:
    		   Redmond, WA
    Mailing Address:
    		   One Microsoft Way, Redmond, WA, 98052
    E-mail address:
    		   YYY @ microsoft.com (replace YYY with jennL)
     
    Links for me
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