David Haussler develops new statistical and algorithmic methods to explore the molecular evolution of the human genome, integrating cross-species comparative and high-throughput genomics data to study gene structure, function, and regulation. He focuses on computational analysis and classification of DNA, RNA, and protein sequences.
He leads the
Genome Bioinformatics Group, which participates
in the public consortium efforts to produce, assemble,
and annotate the first mammalian genomes. His group designed
and built the program that assembled the first working
draft of the human genome sequence from information produced
by sequencing centers worldwide and participated in the
informatics associated with the finishing effort.
Recent findings from the Haussler laboratory include the existence of "ultraconserved" elements in the human genome that have remained essentially unchanged across millions of years of evolution Science, May 6, 2004, suggesting important function. The Haussler group has also identified genome segments that have undergone unusually rapid change in one species, such as a gene linked to brain development that has changed dramatically between chimpanzees and humans Nature, Aug 16, 2006.
UCSC Genome Browser
The UCSC Genome Browser provides interactive
exploration of metazoan genome sequences. The browser fuses
multiple
kinds of genome-wide annotation in a web-based "genome
microscope."
The genomes are annotated based on high-throughput experimental
projects, bioinformatics, and large human-curated data sets.
These projects receive funding from the Howard Hughes Medical Institute (HHMI), the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the California Institute for Quantitative Biosciences (QB3).
ENCODE
The
ENCODE project is a scientific reconnaissance mission aimed
at discovering all parts of the human genome that are crucial
to biological function. It focuses the efforts of a diverse
set of investigators on about 50 selected regions (1%) of
the human genome that appear to have functional significance.
The project aims to discover and fully annotate all the functional
elements in these regions. The UCSC group is providing bioinformatics
analysis via extensions of the human genome browser. The
NHGRI sponsors this project.
NISC comparative genomes
Comparative genomics projects at
the NIH Intramural Sequencing Center (NISC) are sequencing
orthologs of the 50 regions
studied by the ENCODE project in other vertebrate species.
The UCSC group uses this data to make improved mathematical
models of vertebrate molecular evolution then applies these
models to reconstruct the evolutionary history of each
base in the human genome. This work aims to discover both
coding and non-coding functional elements. The NHGRI sponsors
this project.
Mammalian
Gene Collection
A critical next step in the development of the human genome
as a foundation for biomedical research is the completion
of a high quality set of full-length mRNAs with identified
coding regions. With this goal in mind, the UCSC group
works with NIH to develop the Mammalian Gene Collection.
The NCI funds this project.
Translational research to
validate computational predictions
Research by the
Genome Bioinformatics Group generates
an increasing number of very specific
hypotheses about the evolution and function
of human genes. Through wet-lab experiments,
we explore and validate predictions generated
from computational genomic research. Research
project areas include genome evolution,
comparative genomics, alternative splicing,
protein structure, and functional genomics.
The HHMI funds this work.
Early research
interests
His current research
stems from his early work in machine learning,
statistical decision theory, pattern recognition,
neural networks, algorithms, and complexity. |
