David Gifford

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

CDP Education Program

7.90 / 6.874 Computational Functional Genomics
D. Gifford, T. Jaakkola, R. Young
URL: web.mit.edu/7.90/www/

With the support of the CDP Center, in Spring 2006 we offered a very successful interdisciplinary class on computational and systems biology that brought together 20 graduate students in Computer Science, Mathematics, Health Sciences and Technology, CSBi, and Biology. The class included both lectures and a laboratory component. In the laboratory component students were organized into interdisciplinary laboratory teams and given four different laboratories assignments that they cooperatively completed.

In addition to proscribed laboratory projects, each student team chose their own interdisciplinary project, completed research on the project, and presented the results to the class. Short summaries of the projects follow:

Malaria – Finding Elusive Mitochondrial Motifs

The promoters for 114 mitochondrial genes were searched for a motif that could explain disparate expression in samples from clinically ill patients, gametocytes, and an overall life cycle series. A potentially explanatory motif was found and explored.

Marray – A Microarray Search Tool

A tree based search structure for expression data sets was explored that permits the rapid retrieval of expression data sets that are similar to a query dataset. Extensions to permit queries on subsets of GO terms were presented.

Pleiotropy Analysis in Yeast with Phenotypic and Interactome Data.

Clusters of pleiotropic genes with the same phenotypes are interconnected in an interactome network using novel methods. Five clusters of forty have shorter distances between members of their members and higher mutual clustering coefficients, and include functions such as pH homeostasis and membrane biosynthesis.

Motif Discovery, Algorithm and Application

Motif discovery was performed on Nanog, and genes containing the discovered Nanog motif were used in a gene set analysis to see if there are other gene sets relevant to other biological phenotypes, such as cancer

Transciptome Annotation Using Sequence Tags

The position sensitivity of novel sequence tags were examined for their utility for transcriptome annotation. A novel gene database was constructed form selected fungi to look at the utility of sequence tags, and tags in the middle of ORFs were found to have the highest information density.