Research Interests Publications CV Miscellaneous Contact Information


 
Jennifer Listgarten

I am a researcher in the eScience Research Group at Microsoft Research in Los Angeles.

 
 
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.
Publications


  • Learning Transcriptional Regulatory Relationships Using Sparse Graphical Models
    Xiang Zhang, Wei Cheng, Jennifer Listgarten, Carl Kadie, Shunping Huang, Wei Wang, David Heckerman
    PLoS One, 2012, doi:10.1371/journal.pone.0035762

  • Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1
    Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder and David Heckerman
    Journal of Virology, February 2012, doi:10.1128/?JVI.06728-11 (abstract,paper)

  • Personalized Medicine: From Genotype and Molecular Phenotypes Towards Computed Therapy
    Oliver Stegle, Frederick P. Roth, Quaid Morris, Jennifer Listgarten
    Proceedings of the Pacific Symposium on Biocomputing 2012

  • FaST Linear Mixed Models for Genome-Wide Association Studies
    *Christoph Lippert, *Jennifer Listgarten, Ying Liu, Carl M. Kadie, Robert I. Davidson and *David Heckerman
    (*equal contributions)
    Nature Methods, Aug. 2011, doi:10.1038/nmeth.1681 ,
    freely available author copy including SI, Source and executables available here.

  • HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703.
    P. Matthews, E. Adland, J. Listgarten, A. Leslie, N. Mkhwanazi, J. Carlson, M. Harndahl, A. Stryhn, R. Payne, A. Ogwu, K. Huang, J. Frater, P. Paioni, H. Kloverpris, P.Jooste, D. Goedhals, C. van Vuuren, D. Steyn, L. Riddell, F. Chen, G. Luzzi, T. Balachandran, T. Ndung'u, S. Buus, M. Carrington, R. Shapiro, D. Heckerman, and P. Goulder
    Journal of Immunology April 2011, doi: 10.4049

  • Correction for Hidden Confounders in the Genetic Analysis of Gene Expression
    Jennifer Listgarten, Carl Kadie, Eric Schadt, David Heckerman
    Proceedings of the National Academy of Sciences, September 1, 2010, doi: 10.1073/pnas.1002425107
    (paper, Supplementary Information, software, GenomeWeb coverage)

  • Additive contribution of HLA class I alleles in the immune control of HIV-1 infection
    Leslie A, Matthews PC, Listgarten J, Carlson JM, Kadie C, Ndung'u T, Brander C, Coovadia H, Walker BD, Heckerman D, Goulder PJ
    Journal of Virology , 2010

  • Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles
    Christine M. Rousseau, David W. Lockhart, Jennifer Listgarten, Carl Kadie, Gerald H. Learn, David C. Nickle, David E. Heckerman, Wenjie Deng, Christian Brander, Thumbi Ndung'u, Hoosen Coovadia, Philip J. R. Goulder, Bette T. Korber, Bruce D. Walker, James I. Mullins
    AIDS Research and Human Retroviruses , 2009; 25(3):297-303

  • In silico resolution of ambiguous HLA typing data (pdf)
    Jennifer Listgarten, Zabrina Brumme, Carl Kadie, Gao Xiaojiang, Bruce Walker, Mary Carrington, Phillip Goulder, David Heckerman,
    in ASHI (American Society for Histocompatibility and Immunogenetics) Quarterly, Volume 32, Number 2, 2008
    For the public web server tool based on this work, go here ; for .exe and source code (training code not included), go here.
    [Note: this is a non-technical, summary version of the original research article below: Statistical resolution of ambiguous HLA typing data].

  • 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, go here ; for .exe and source code (training code not included), go here.
    [Note: for a non-technical summary of this article, see the publication above: In Silico resolution of ambiguous HLA typing data]

  • 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.
  • Radford Neal's new blog focussing on statistics and machine learing.
  • 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.
    •  
    Contact Information
    Mailing Address:
    		   Microsoft Research, 1100 Glendon Avenue, PH 1 Los Angeles, California 90024
    E-mail address:
    		   YYY @ microsoft.com (replace YYY with jennL)
     
    Links for me
  • How to get latitude & longitude from Google Maps.
  • Prevent Windows Update from forcibly rebooting your computer
  • MSR webmail
  • DCS Webmail access
  • AppGate MindTerm DCS