Tommi S. Jaakkola, Ph.D.
Professor of Electrical Engineering and Computer Science

MIT Computer Science and Artificial Intelligence Laboratory
Stata Center, Bldg 32-G470
Cambridge, MA 02139

E-mail: tommi at csail.mit.edu

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Papers

More information about research areas is available in research descriptions. You also can view papers by partially overlapping categories

Computational biology papers

  • R. Sherwood, T. Hashimoto, C. O'Donnell, S. Lewis, A. Barkal, J.P. van Hoff, V. Karun, T. Jaakkola, and D. Gifford.
    Discovery of directional and nondirectional pioneer transcription factors by modeling dnase profile magnitude and shape.
    Nature Biotechnology, 32(2):171--178, 2014.
    [pdf]

  • T. Hashimoto, T. Jaakkola, R. Sherwood, E. Mazzoni, H. Witchterle, and D. Gifford.
    Lineage based identification of cellular states and expression programs.
    In Proceedings of the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2012.

  • Y. Guo, G. Papachristoudis, R. Altshuler, G. Gerber, T. Jaakkola, D. Gifford, and S. Mahony.
    Discovering homotypic binding events at high spatial resolution.
    Bioinformatics, 2010.
    [link to paper]

  • G. Gerber, R. Dowell, T. Jaakkola, and D. Gifford.
    Automated discovery of functional generality of human gene expression programs.
    PloS Computational biology, 2007.
    [link to paper]

  • L. Perez-Breva, L. Ortiz, C-H. Yeang, and T. Jaakkola.
    Game theoretic algorithms for protein-dna binding.
    In Advances in Neural Information Processing Systems 19, 2006.
    [pdf]

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

  • Y. Qi, P. Missiuro, A. Kapoor, C. Hunter, T. Jaakkola, D. Gifford, and H. Ge.
    Semi-supervised analysis of gene expression profiles for lineage-specific development in the caenorhabditis elegans embryo.
    Bioinformatics, 22(14):417--423, 2006.
    [pdf]

  • L. Perez-Breva, L. Ortiz, C-H. Yeang, and T. Jaakkola.
    Dna binding and games.
    MIT CSAIL Technical Report TR-2006-018, 2006.
    [pdf]

  • C-H. Yeang and T. Jaakkola.
    Modeling the combinatorial functions of multiple transcription factors.
    In The Ninth Annual International Conference on Research in Computational Molecular Biology, 2005.
    [pdf]

  • C-H. Yeang, H. Mak, S. McCuine, C. Workman, T. Jaakkola, and T. Ideker.
    Validation and refinement of gene-regulatory pathways on a network of physical interactions.
    Genome Biology, 6(7):R62, 2005.
    [pdf], [link to paper]

  • C-H. Yeang, T. Ideker, and T. Jaakkola.
    Physical network models.
    Journal of Computational Biology, 11(2-3):243--263, 2004.
    [pdf]

  • Z. Bar-Joseph, G. Gerber, I. Simon, D. Gifford, and T. Jaakkola.
    Comparing continuous representations of time series expression profiles to identify differentially expressed genes.
    Proceedings of the National Academy of Sciences, 100(18):10146--10151, 2003.
    [pdf], [link to paper]

  • Z. Bar-Joseph, G. 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--1342, 2003.
    [pdf], [link to paper]

  • Z. Bar-Joseph, G. Gerber, D. Gifford, T. Jaakkola, and I. Simon.
    Continuous representations of time series gene expression data.
    Journal of Computational Biology, 10(3-4):241--256, 2003.
    [pdf]

  • C-H. Yeang and T. Jaakkola.
    Time series analysis of gene expression and location data.
    In Proceedings of the Third IEEE Symposium on Bioinformatics and Bioengineering, pages 305--312, 2003.
    [pdf]

  • C-H. Yeang and T. Jaakkola.
    Physical network models and multi-source data integration.
    In The Seventh Annual International Conference on Research in Computational Molecular Biology, 2003.
    [pdf]

  • Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angele M. Hamel, Tommi S. Jaakkola, and Nathan Srebro.
    K-ary clustering with optimal leaf ordering for gene expression data.
    Bioinformatics (to appear), 2002.
    [pdf]

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

  • A. Hartemink, D. Gifford, T. Jaakkola, and R. Young.
    Combining location and expression data for principled discovery of genetic regulatory network models.
    In Pacific Symposium on Biocomputing, volume 7, 2002.
    [pdf]

  • Z. Bar-Joseph, D. Gifford, and T. Jaakkola.
    Fast optimal leaf ordering for hierarchical clustering.
    In Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001.
    [pdf]

  • A. Hartemink, D. Gifford, T. Jaakkola, and R. Young.
    Maximum likelihood estimation of optimal scaling factors for expression array normalization.
    In Microarrays: Optical Technologies and Informatics, Proceedings of SPIE, volume 4266, 2001.
    [postscript], [gzipped postscript]

  • A. Hartemink, D. Gifford, T. Jaakkola, and R. Young.
    Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.
    In Pacific Symposium on Biocomputing, volume 6, pages 422--433, 2001.
    [pdf]

  • T. Jaakkola, M. Diekhans, and D. Haussler.
    A discriminative framework for detecting remote protein homologies.
    Journal of Computational Biology, 7(1,2):95--114, 2000.
    [postscript], [gzipped postscript]

  • T. Jaakkola, M. Diekhans, and D. Haussler.
    Using the fisher kernel method to detect remote protein homologies.
    In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999.
    [postscript], [gzipped postscript]

  • T. Jaakkola and D. Haussler.
    Exploiting generative models in discriminative classifiers.
    In Advances in Neural Information Processing Systems 11, 1998.
    [postscript], [gzipped postscript]