Bernard Moret, 277-5699
Contact: David Bader, 277-6724
Michael Padilla, 277-1816
October 11, 2001
UNM Engineering Professors receive $1.1 million in NSF Grants
University of New Mexico School of Engineering Professors Bernard Moret, Computer
Science, and David Bader, Electrical and Computer Engineering, have received more
than $1.1 million in grants this fall from the National Science Foundation (NSF) to
pursue research in reconstructing evolutionary trees (known as “phylogenies”).
This research program is being conducted in collaboration with the University of Texas
at Austin. The UT-UNM group received two other awards from the NSF, made directly
to the University of Texas, bringing the total group funding for the next five years to
more than $7 million. This makes the joint UT-UNM research group the largest and
most active group in the world in the area of computational phylogenetics.
A phylogeny, or evolutionary tree, is a reconstruction of the evolutionary history of a
collection of present-day organisms from unknown ancestral organisms through the
process of bifurcation, in which an ancestral species gives rise to two new species. Such
reconstructions are based on molecular data such as DNA sequences collected from
present-day species and on a hypothesized model of evolution.
Moret said the project will create tools for biologists to conduct research on evolution.
He said that phylogenetic analyses are used in biological, medical and pharmaceutical
research.
“For instance, public health researchers use phylogenies to track the spread of various
strains of the HIV virus (the cause of AIDS). Pharmaceutical companies use them to
identify likely drug targets. A notable success was the herbicide Roundup,” he said,
adding that agricultural laboratories use them to produce better strains of basic foods
such as rice or wheat.
Moret said that the UNM team focuses on the development, implementation and testing
of computer algorithms to reconstruct phylogenies, with particular emphasis on
efficiency and high-performance computing—because many of the algorithms in use
today can require years of computation even on problems of modest size.
Bader said that high-performance computers, which are now used for time-sensitive
applications such as weather forecasting, financial investment decision-making, or
tracking and guidance systems, will be used for these computational biology problems.
“The shortened turnaround time will speed up the pace of research, leading to more and
less expensive new drugs, for instance, and also improve its quality by enabling
researchers to test more alternatives and thus gain a better understanding of the
problems,” Bader said.
The $1.1 million is broken up into three separate grants, which deal with different
aspects of the project. Two of the grants were awarded under the competitive
Information Technology Research (ITR) programs.
A three-year grant for $162,000 titled, “Computing Optimal Phylogenetic Trees under
Genome Rearrangement Metrics,” was one in 1,295 proposals received by NSF in its
ITR category—only 10 percent of these proposals were funded. Under this and the
matching UT grant, Moret, with Robert Jansen, UT biology professor, and Tandy
Warnow, UT computer science professor, will design, implement and evaluate new
algorithms to reconstruct phylogenies from a new type of molecular data, the complete
ordering of genes along the chromosomes.
A five-year grant for $793,000 titled, “Reconstructing Complex Evolutionary
Histories,” was one in 661 pre-proposals in its ITR category received by NSF; again
only 10 percent of these pre-proposals were eventually selected for funding. Under this
and the matching UT grant, Moret and Bader will collaborate with Warnow and several
UT-Austin biologists to tackle complex and more realistic models of evolution and
develop algorithms that can reconstruct phylogenies under these models for very large
problems.
A five-year grant for $193,000 is part of a larger grant titled, “Comparative Chloroplast
Genomics: Integrating Computational Methods, Molecular Evolution, and Phylogeny,”
awarded to UT- Austin under an NSF program on Biocomplexity in the Environment.
The UNM team led by Moret will help the biologists at UT Austin and other institutions
in analyzing new genomic data collected from a sampling of land plants and refined into
complete gene orderings at the Department of Energy’s Joing Genome Institute in
California.
Moret said that funding from NSF is the “gold standard” in the scientific community.
All proposals undergo rigorous peer evaluation and fierce competition, as indicated by
the funding rate of 10 percent. “Receiving five separate awards in the same year from
the NSF for work in the same area is nearly unheard of and a tribute to the success of
the UT-UNM collaboration of computer scientists and biologists,” Moret said.
At UNM, these grants will enhance the profile of the research laboratory run by Moret
and Bader, which is already funded by four other NSF awards. This includes a
three-year ITR award to Moret and Bader granted last year, a five-year CAREER
Award to Bader, a three-year biology award in which Bader is a co-PI, and part of a
research infrastructure award to the Department of Computer Science.
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