Massachusetts Institute of Technology
Computer Science and Artificial Intelligence Laboratory

Computational Biology

• "Tissue-specific transcriptional regulation has diverged significantly between human and mouse." D. T. Odom, R. D. Dowell, E. S. Jacobsen, W. Gordon, T. W. Danford, K. D. MacIsaac, P. A. Rolfe, C. M. Conboy, D. K. Gifford, and E. Fraenkel. Nature Genetics 39:6, 730-732, June, 2007. pdf
  
  
• "Automated Discovery of Functional Generality of Human Gene Expression Programs". G. K. Gerber, R. D. Dowell, T. S. Jaakkola, and D. K. Gifford PLOS Computational Biology, 3:8, August 2007. pdf
  
  
• "Polycomb complexes repress developmental regulators in murine embryonic stem cells. L. A. Boyer, K. Plath, J. Zeitlinger, T. Brambrink, L. A. Medeiros, T. I Lee., S. S. Levine, M. Wernig, A. Tajonar, M. K. Ray, G. W. Bell, A. P. Otte, M. Vidal, D. K. Gifford, R. A. Young, and R. Jaenisch. Nature 441:349-353, May 2006. pdf
  
  
• "Coordinated binding of NF-kB family members in the response of human cells to lipopolysaccharide." J. Schreiber, R. G. Jenner, H. L. Murray, G. K. Gerber, D. K. Gifford and R. A. Young. Proceedings of the National Academy of Sciences (PNAS), 103(10):5899-5904, 2006. pdf
  
  
• High-resolution computational models of genome binding events. A. Qi, P.A. Rolfe, K. 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 Nature Biotechnology *24*, 963-960 (2006) [pdf]     Supplemental material      Download the software
  


• "Core Transcriptional Regulatory Circuitry in Human Hepatocytes." D.T. Odom, R.D. Dowell, E.S. Jacobsen, L. Nekludova, P.A. Rolfe, T.W. Danford, D.K. Gifford, E. Fraenkel, G.I. Bell, and R.A. Young. Nature/EMBO Molecular Systems Biology, msb4100059, 2 May 2006. [pdf] 
  
  
• "Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells." L. A. Boyer, T. I. Lee, M. F. Cole, S. E. Johnstone, S. S. Levine, J. P. Zucker, M. G. Guenther, R. M. Kuman, H. L. Murray, R. G. Jenner, D. K. Gifford, D. A. Melton , R. Jaenisch, and R. A. Young. Cell Vol. 122, 1-20, September, 2005. pdf
  
  
• "Deconvolving cell cyle expression data with complementary information. Z. Bar-Joseph, S. Farkash, D. K. Gifford, I. Simon, R. Rosenfeld. Bioinformatics Vol. 20 Suppl. 1, 2004. pp i23-i30.pdf
  
  
• "Transcriptional regulatory code of a eukaryotic genome." C. Harbison, D. B. Gordon, T. I Lee, N. J. Rinaldi, K. D. MacIsaac, T. W. Danford, N. M. Hannett, J.B. Tagne, D. B. Reynolds, J. Yoo, E. G. Jennings, J. Zeitlinger, D. K. Pokholok, M. Kellis, P. A. Rolfe, K. T. Takusagawa, E. S. Lander, D. K. Gifford, E. Fraenkel, and R. A. Young. Nature, 431:99-104, September, 2004. [pdf] 
  
  
• "Control of Pancreas and Liver Gene Expression by HNF Transcription Factors." Odom, D. T., Zizlsperger, N., Gordon, D. B., Bell, G. W., Rinaldi, N. J., Murray, H. L., Volkert, T. L., Schreiber, J., Rolfe, P. A., Gifford, D. K., Fraenkel, E., Bell, G. I., Young, R. A. Science, 303:1378-1381, February, 2004. [pdf]
  
  
• "Comparing the Continuous Representation of Time Series Gene Expression Profiles to Identify Differentially Expressed Genes." Z. Bar-Joseph, G.K. Gerber, I. Simon, D.K. Gifford, and T.S. Jaakkola. Proceedings of the National Academy of Sciences 2003 Sept. 2; 100(18):10146-10151. pdf
  


• "Negative Information for Motif Discovery." Takusagawa, K. T., Gifford, D. K., Pacific Symposium on Biocomputing, 9:360-371, 2004. [pdf]
  
  
• "Computational discovery of gene modules and regulatory networks." Bar-Joseph, Z., Gerber, G. K., Lee, T. I., Rinaldi, N. J., Yoo, J. Y., Robert, F., Gordon, D. B., Fraenkel, E., Jaakkola, T. S., Young, R. A., Gfford D. K. Nature Biotechnology, 21, pp. 1337-1342 November, 2003. [pdf]
  
  
• "Continuous Representations of Time Series Gene Expression Data." Bar-Joseph, G. Gerber, D. Gifford, T. Jaakkola and I. Simon.  Journal of Computational Biology, 10(3-4) pp. 241-156. 
  
  
• "K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data."  Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommy S. Jaakkola and Nathan Srebro. Bioinformatics, Vol. 19, No. 9, 2003. [pdf]   [ps]
  
  
• "Transcriptional Regulatory Networks In Saccharomyces cerevisiae."  T.I. Lee, N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber, ... D. K Gifford and R. A. Young.    Science, 298:799-804 (2002) [pdf]
  
  
• "K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data."  Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi S. Jaakkola and Nathan Srebro. To appear in Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI 2002), Rome, Italy, September 17-11. [pdf]   [ps]
  
  
• "Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models." Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, and Richard A. Young.  Pacific Symposium on Biocomputing 2002, Kauai, January 2002. [pdf]   [ps]
  
  
• "Bayesian Methods for Elucidating Genetic Regulatory Networks." Hartemink, A. J., Gifford, D. K., Jaakkola, T. S., Young, R. A“” IEEE Intelligent Systems in Biology, Vol. 17, No. 2, March, 2002, pp. 37-43. [pdf]   [ps]
  
  
• Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle." Simon, I., Barnett, J., Hannett, N., Harbison, C. T., Rinaldi, N. J., Volkert, T. L. Wyrick, J. J., Zeitlinger, J., Gifford., D. K., Jaakkola, T. S., Young, R. A.,  Cell, 106, Sept., 2001, p. 667-708. [pdf]   [ps]
  
  
• "A new approach to analyzing gene expression time series data."  Z. Bar-Joseph, G. Gerber, D. Gifford, T. Jaakkola and I. Simon.  In Proceedings of The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2002, pp 39-48.  [pdf]   [ps]
  
  
• "Blazing pathways through genetic mountains."  Gifford, D. K.   Science 2001 Sep 14;293(5537):2049-51. [pdf]    [ps]
  
  
• "Fast optimal leaf ordering for hierarchical clustering." Z. Bar-Joseph, D. Gifford, and T. Jaakkola.   Bioinformatics (Proceedings of ISMB 2001),, 17(S1), 2001, pp 22-19 . [pdf] [ps]
  
  
• "Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks."  Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, and Richard A. Young Pacific Symposium on Biocomputing 2001, Hawaii, January 2001. [pdf]   [ps]
  
  
• "Maximum Likelihood Estimation of Optimal Scaling Factors for Expression Array Normalization."  Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, and Richard A. Young SPIE BiOS 2001, San Jose, California, January 2001.  [pdf]   [ps]