David Haussler

David Haussler
David Haussler. Photo by Ron Jones.
Nationality	United States
Fields	Bioinformatics, Genomics, AI
Institutions	University of California, Santa Cruz
Alma mater	Connecticut College, University of Colorado at Boulder
Doctoral advisor	Andrzej Ehrenfeucht
Doctoral students	Yoav Freund, Kimmen Sjölander, Adam Siepel
Known for	hidden Markov models, Human Genome Project
Notable awards	2011 Weldon Memorial Prize, 2009 Curt Stern Award, 2008 ISCB Accomplishment by a Senior Scientist Award, 2005 Dickson Prize, 2003 ACM/AAAI Allen Newell Award in Artificial Intelligence

David Haussler is a Howard Hughes Medical Institute Investigator. He is also Professor of Biomolecular Engineering and Director of the Center for Biomolecular Science and Engineering at the University of California, Santa Cruz; director of the California Institute for Quantitative Biosciences (QB3) on the UC Santa Cruz campus; and a consulting professor at Stanford University School of Medicine and UC San Francisco Biopharmaceutical Sciences Department.

David Haussler’s research combines mathematics, computer science, and molecular biology. He develops new statistical and algorithmic methods to explore the molecular function and evolution of the human genome, integrating cross-species comparative and high-throughput genomics data to study gene structure, function, and regulation. He is credited with pioneering the use of hidden Markov models (HMMs), stochastic context-free grammars, and the discriminative kernel method for analyzing DNA, RNA, and protein sequences. He was the first to apply the latter methods to the genome-wide search for gene expression biomarkers in cancer, now a major effort of his laboratory.

As a collaborator on the international Human Genome Project, his team posted the first publicly available computational assembly of the human genome sequence on the Internet on July 7, 2000. Following this, his team developed the UCSC Genome Browser, a web-based tool that is used extensively in biomedical research and serves as the platform for several large-scale genomics projects, including NHGRI’s ENCODE project to use omics methods to explore the function of every base in the human genome (for which UCSC serves as the Data Coordination Center), NIH’s Mammalian Gene Collection, NHGRI’s 1000 genomes project to explore human genetic variation, and NCI’s Cancer Genome Atlas project to explore the genomic changes in cancer.

His group’s informatics work on cancer genomics, including the UCSC Cancer Genomics Browser, provides a complete analysis pipeline from raw DNA reads through the detection and interpretation of mutations and altered gene expression in tumor samples. His group collaborates with researchers at medical centers nationally, including members of the Stand Up To Cancer “Dream Teams” and the Cancer Genome Atlas, to discover molecular causes of cancer and develop a new personalized, genomics-based approach to cancer treatment.

He co-founded the Genome 10K Project to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species—to capture genetic diversity as a resource for the life sciences and for worldwide conservation efforts.

Through wet-lab experiments, Haussler explores and validates predictions generated from computational genomic research about the evolution and function of human genes. For instance, his lab uses embryonic and induced pluripotent stem cells to investigate neurodevelopment from a functional and evolutionary perspective. Research project areas include genome evolution, comparative genomics, alternative splicing, and functional genomics.

Haussler received his PhD in computer science from the University of Colorado at Boulder. He is a member of the National Academy of Sciences and the American Academy of Arts and Sciences and a fellow of AAAS and AAAI. His awards include the 2011 Weldon Memorial Prize from University of Oxford, the 2009 ASHG Curt Stern Award in Human Genetics, the 2008 Senior Scientist Accomplishment Award from the International Society for Computational Biology, the 2005 Dickson Prize for Science from Carnegie Mellon University, and the 2003 ACM/AAAI Allen Newell Award in Artificial Intelligence.

Early research interests

Haussler studied art and then psychotherapy before settling on mathematics as a college major. During summers, he worked for his brother, Mark, a biochemist at the University of Arizona studying vitamin D metabolism. Haussler became interested in the mathematical analysis of DNA while pursuing a doctorate at the University of Colorado in the early 1980s, as the field of bioinformatics was emerging. Haussler's current research stems from his early work in machine learning, statistical decision theory, pattern recognition, neural networks, algorithms, and complexity.

External links

• David Haussler on the Genome 10K Project - Interview on the 7th Avenue Project radio show.
• David Haussler biography, Howard Hughes Medical Institute
• Computer scientists may have what it takes to help cure cancer David Patterson, New York Times, Dec 5, 2011.
• Don't throw it out: 'Junk DNA' essential in evolution, radio interview by Joe Palca, NPR, Aug 19, 2011.