Recent work:

  • G. K. Gerber.
    Computational Discovery of Gene Modules, Regulatory Networks and Expression Programs.
    Harvard-MIT HST Ph.D. Thesis, July 2007.
    pdf

  • G. K. Gerber, R. D. Dowell, T. S. Jaakkola, D. K. Gifford
    Automated Discovery of Functional Generality of Human Gene Expression Programs.
    PLoS Computational Biology, 3:8, 2007.
    pdf

  • G. K. Gerber, R. D. Dowell, T. S. Jaakkola, D. K. Gifford
    Hierarchical Dirichlet Process-Based Models For Discovery of Cross-species Mammalian Gene Expression Programs.
    MIT-CSAIL Technical Report, MIT-CSAIL-TR-2007-037.
    dspace

  • Y. Qi*, A. Rolfe*, K. D. MacIsaac*, G. K. Gerber, D. Pokholok, J. Zeitlinger, T. Danford, R. D. Dowell, E. Fraenkel, T. S. Jaakkola, R. A. Young and D. K. Gifford.
    High-resolution computational models of genome binding events.
    Nature Biotechnology, 24:963-970, 2006.
    * Equal contributing authors.
    pdf

  • J. Schreiber, R. G. Jenner, H. L. Murray, G. K. Gerber, D. K. Gifford and R. A. Young.
    Coordinated binding of NF-kB family members in the response of human cells to lipopolysaccharide.
    Proceedings of the National Academy of Sciences (PNAS), 103(10):5899-5904, 2006.
    pdf

  • Z. Bar-Joseph*, G. K. Gerber*, T. Lee*, N. Rinaldi, J. Yoo, F. Robert, B. Gordon, E. Fraenkel, T. Jaakkola, R. Young and D. Gifford.
    Computational discovery of gene modules and regulatory networks.
    Nature Biotechnology, 21(11):1337-42, 2003.
    * Equal contributing authors.
    pdf

  • Z. Bar-Joseph, G.K. Gerber, I. Simon, D.K. Gifford, and T.S. Jaakkola
    Comparing the Continuous Representation of Time Series Gene Expression Profiles to Identify Differentially Expressed Genes.
    Proceedings of the National Academy of Sciences 2003 Sept. 2; 100(18):10146-10151.
    pdf

  • Z. Bar-Joseph, G.K. Gerber, D.K. Gifford, T.S. Jaakkola, and I. Simon
    Continuous Representations of Time-Series Gene Expression Data.
    Journal of Computational Biology 2003; 10(3-4): 341-356.
    pdf

  • G. K. Gerber.
    Do the Time-Warp: Continous Alignment of Gene Expression Time-Series Data.
    MIT Masters' thesis, February 2003.
    pdf

  • T. Lee, N. Rinaldi, F. Robert, D. Odom, Z. Bar-Joseph, G. Gerber, N. Hannett, C. Harbison, C. Thompson, I. Simon, J. Zeitlinger, E. Jennings, H. Murray, D. Gordon, B. Ren, J. Wyrick, J. Tagne, T. Volkert, E. Fraenkel, D. Gifford, and R. Young.
    Transcriptional Regulatory Networks in Saccharomyces cerevisiae.
    Science 2002 October 25; 298: 799-804.
    pdf

  • Z. Bar-Joseph, G.K. Gerber, D.K. Gifford, and T.S. Jaakkola.
    A new approach to analyzing gene expression time series data.
    In The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2002.
    pdf

  • G. K. Gerber.
    Action!: A System For Creating and Delivering Multi-participant Interactive Cinematic Dramas.
    In International Conference on Application and Development of Computer Games in the 21st Century (ADCOG21), 2001.
    pdf

    • Presentations/Lectures:

  • Lecture on clustering microarray gene expression data for BIO3120 Expression Analysis course at Northeastern University.
    Power-Point

  • Lecture on the GRAM algorithm for 7.90J Computational Functional Genomics Spring 2006 at MIT.
    Power-Point

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