Research Interests Publications CV Miscellaneous Contact Information


 
Jennifer Listgarten

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

Check out our PSB 2014 session on Personalized Medicine: from genotypes and molecular phenotypes towards therapy , to be held January 3-7, 2014 on the Big Island of Hawaii. Accepted papers will be published electronically, indexed in PubMed and receive an oral presentation. Submission deadline is July 31, 2013. Our invited speaker is Robert Gentleman.

Internship opportunities: please contact me if you are a Ph.D. student with expertise in genetics, applied statistics and/or machine learning, and interested in a 3-month internship. Relocation, including work visa, housing and transportation all are taken care of. Internships are well-paid.
 
 
Research Interests

My area of expertise is in statistical machine learning/applied statistics, with application to problems in biology. I'm interested both in methods development, as well as application of methods to enable new insight into basic biology and medicine. My current focus has been on problems in statistical genetics, and in particular on association studies (genetic and epigenetic) in the presence of unknown confounders. I have also worked on problems in immunoinformatics, liquid-chromatography proteomics, and microarray analysis.
Selected Publications
  • Epigenome-wide association studies without the need for cell-type composition
    James Zou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten
    Nature Methods,309–311 (2014) (journal link)
    Python software available from here, and R software available from here.

  • FaST-LMM-Select for addressing confounding from spatial structure and rare variants
    Jennifer Listgarten, Christoph Lippert, David Heckerman
    (equal contributions)
    Nature Genetics, 45, 470-471 (2013) doi:10.1038/ng.2620 (journal link)

  • A powerful and efficient set test for genetic markers that handles confounders
    Jennifer Listgarten, Christoph Lippert, Eun Yong Kang, Jing Xiang, Carl M. Kadie, David Heckerman
    (equal contributions)
    Bioinformatics 2013, doi: 10.1093/bioinformatics/btt177 (open access)
    Source and executables available here.

  • Patterns of methylation heritability in a genome-wide analysis of four brain regions
    Gerald Quon, Christoph Lippert, David Heckerman, Jennifer Listgarten
    Nucleic Acids Research, 2013, doi: 10.1093/nar/gks1449
    Matlab and R data files containing our narrow-sense heritability estimates, p-values, as well as BED files of our heritable sites and downloaded chromatin annotations can be found here.

  • Improved linear mixed models for genome-wide association studies
    Jennifer Listgarten, Christoph Lippert, Carl M. Kadie, Robert I. Davidson, Eleazar Eskin and David Heckerman
    (equal contributions)
    Nature Methods, 2012, doi:10.1038/nmeth.2037
    Source and executables available here.

  • 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.

  • 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)

  • 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.

  • 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).
All Publications
  • Epigenome-wide association studies without the need for cell-type composition
    James Zou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten
    Nature Methods,309–311 (2014) (journal link)
    Python software available from here, and R software available from here.

  • Personalized Medicine: from genotypes and molecular phenotypes toward therapy
    Jennifer Listgarten, Oliver Stegle, Quaid Morris, Steven Brenner, Leo Parts
    Proceedings of the Pacific Symposium on Biocomputing 2014

  • A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.
    István Bartha, Jonathan M Carlson, Chanson J Brumme, Paul J McLaren, Zabrina L Brumme, Mina John, David W Haas, Javier Martinez-Picado, Judith Dalmau, Cecilio López-Galíndez, Concepción Casado, Andri Rauch, Huldrych F Günthard, Enos Bernasconi, Pietro Vernazza, Thomas Klimkait, Sabine Yerly, Stephen J O’Brien, Jennifer Listgarten, Nico Pfeifer, Christoph Lippert, Nicolo Fusi, Zoltán Kutalik, Todd M Allen, Viktor Müller, P Richard Harrigan, David Heckerman, Amalio Telenti, Jacques Fellay
    eLife (2013) 2:e01123 (journal link)

  • The benefits of selecting phenotype-specific variants for applications of mixed models in genomics.
    Christoph Lippert, Gerald Quon, Eun Yong Kang, Carl M. Kadie, Jennifer Listgarten, David Heckerman
    (equal contributions)
    Scientific Reports 3, (2013) doi:10.1038/srep01815 (journal link)

  • FaST-LMM-Select for addressing confounding from spatial structure and rare variants
    Jennifer Listgarten, Christoph Lippert, David Heckerman
    (equal contributions)
    Nature Genetics, 45, 470-471 (2013) doi:10.1038/ng.2620 (journal link)

  • A powerful and efficient set test for genetic markers that handles confounders
    Jennifer Listgarten, Christoph Lippert, Eun Yong Kang, Jing Xiang, Carl M. Kadie, David Heckerman
    (equal contributions)
    Bioinformatics 2013, doi: 10.1093/bioinformatics/btt177 (open access)
    Source and executables available here.

  • An Exhaustive Epistatic SNP Association Analysis on Expanded Wellcome Trust Data
    Christoph Lippert, Jennifer Listgarten, Robert Davidson, Scott Baxter, Hoifung Poon, Carl M. Kadie, David Heckerman,
    (equal contributions)
    Scientific Reports, 2013, doi:10.1038/srep01099

  • Patterns of methylation heritability in a genome-wide analysis of four brain regions
    Gerald Quon, Christoph Lippert, David Heckerman, Jennifer Listgarten
    Nucleic Acids Research, 2013, doi: 10.1093/nar/gks1449
    Matlab and R data files containing our narrow-sense heritability estimates, p-values, as well as BED files of our heritable sites and downloaded chromatin annotations can be found here.

  • The future of genome-based medicine.
    Quaid Morris, Steven Brenner, Jennifer Listgarten, Oliver Stegle
    Proceedings of the Pacific Symposium on Biocomputing 2013, 16:456-458. doi:10.1142/9789814447973_0046

  • Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1
    Jonathan M. Carlson, Chanson J. Brumme, Eric Martin, Jennifer Listgarten, Mark A. Brockman, Anh Q. Le, Celia K. S. Chui, Laura A. Cotton, David J. H. F. Knapp, Sharon A. Riddler, Richard Haubrich, George Nelson, Nico Pfeifer, Charles E. DeZiel, David Heckerman, Richard Apps, Mary Carrington, Simon Mallal, P. Richard Harrigan, Mina John, Zabrina L. Brumme, and the International HIV Adaptation Collaborative
    Journal of Virology, Dec. 2012, 86(4)

  • Co-Operative Additive Effects between HLA Alleles in Control of HIV-1
    Philippa C. Matthews, Jennifer Listgarten, Jonathan M. Carlson, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Dominique Goedhals, Dewald Steyn, Cloete van Vuuren, Paolo Paioni, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Zenele Mncube, Thumbi Ndung'u, Bruce D. Walker, David Heckerman, Philip J. R. Goulder
    (equal contributions)
    PLoS One, 2012, 7(10): e47799. doi:10.1371/journal.pone.0047799

  • Improved linear mixed models for genome-wide association studies
    Jennifer Listgarten, Christoph Lippert, Carl M. Kadie, Robert I. Davidson, Eleazar Eskin and David Heckerman
    (equal contributions)
    Nature Methods, 2012, doi:10.1038/nmeth.2037
    Source and executables available here.

  • 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. ( 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

pending update

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.
  •  
    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
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