Massachusetts Institute of Technology
Computer Science and Artificial Intelligence Laboratory

Education:
Massachusetts Institute of TechnologyCambridge, MA
B.S. Computer Science, 1976

Stanford University, Stanford, CA
M.S. Computer Science, 1978

Stanford UniversityStanford, CA
Ph.D. Computer Science, 1981

Cold Spring Harbor Laboratory
Molecular Cloning, 1989

Professional Experience:

Massachusetts Institute of Technology Professor, Tenured 1995 - Present
Massachusetts Institute of Technology Associate Professor, Tenured 1989 - 1995
Karl Van Tassel Professor 1989 - 1989
Massachusetts Institute of Technology Associate Professor 1987 - 1989
Massachusetts Institute of Technology KDD Career Development Professor
of Communication & Technology 1986 - 1988
Massachusetts Institute of Technology ITT Career Development Professor in
Computer Technology 1984 - 1986
Massachusetts Institute of Technology Assistant Professor 1982 - 1987
Xerox Corporation Research Intern 1977 - 1981
Xerox Corporation Member Research Staff 1981 - 1982
Ford Motor Company Systems Programmer 1971 - 1976

Appointments:

1999 Program Chair, 5th International Meeting on DNA-Based Computers
1998 - Present Member JASON Advisory Board to U.S. Government
1996 - 1997 Program Committee, ACM Symposium on Operating System Principles
1987 Program Committee, ACM Symposium on Operating System Principles
1985 Program Committee, ACM Symposium on Operating System Principles

Selected Publications:

• "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]
  
• "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. 241-256. 
  
• "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 17-21. [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, 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 22-29 . [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]

Biological Computation

• "Simulating Biological Reactions: A Modular Approach."  Alexander J. Hartemink, Tarjei S. Mikkelsen, and David K. Gifford 5th Annual DIMACS Workshop on DNA-Based Computers, Boston, Massachusetts, June 1999. [pdf]  [ps]
  
• "Automated Constraint-Based Nucleotide Sequence Selection for DNA Computation."  Alexander J. Hartemink, David K. Gifford, and Julia Khodor 4th Annual DIMACS Workshop on DNA-Based Computers, Philadelphia, Pennsylvania, June 1998. [pdf]  [ps]
  
• "Design & Implementation of Computational Systems Based on Programmed Mutagenesis." Khodor, J. and Gifford, D. K. DIMACS Workshop on Nucleic Acid Selection and Computing, Princeton University, March, 1998.
  
• "Thermodynamic Simulation of Deoxyoligonucleotide Hybridization for DNA Computation."  Alexander J. Hartemink and David K. Gifford 3rd Annual DIMACS Workshop on DNA-Based Computers, Philadelphia, Pennsylvania, June 1997.  [pdf] [ps]
  
• "The Efficiency of Sequence-Specific Separation of DNA Mixtures for Biological Computing." Julia Khodor and David K. Gifford 3rd Annual DIMACS Workshop on DNA-Based Computers, Philadelphia, Pennsylvania, June 1997.  [pdf]  [ps]