CBCB Seminar Series
Spring 2005
12:30 p.m. Tuesday Feburary 1, 2005
Title: organizational meeting
Speaker: Stephen M. Mount, Ph.D.
Venue: Biomolecular Science
Building Room 3118
Abstract: To discuss the schedule
in Spring 2005.
12:30 p.m. Tuesday March 8, 2005
Title: Defining motifs for low
complexity domains
Speaker: Stephen M. Mount, Ph.D.
Venue: Biomolecular Science
Building Room 3118
12:30 p.m. Tuesday March 29, 2005
Title: ESTmapper
Speaker: Xue Wu
Venue: Biomolecular Science
Building Room 3118
Abstract:
With continuing improvements in both the speed and cost of automatic DNA
sequencers, scientists are able to sequence the genomic DNA (genome) of an
increasing number of organisms. One way biologists can take advantage of
this genomic data is to use it in conjunction with expressed sequence tag
(EST) information to find genes and their splice sites. We describe how
ESTmapper uses an eager write-only top-down (WOTD) suffix tree to
efficiently align DNA sequences against known genomes, and compare its
precision and performance against popular techniques for DNA alignment
(BLAT, sim4, Spidey, BLAST, megaBLAST) and EST clustering (TGICL and
PaCE). Experimental results show that ESTmapper is 3 to 1000 times faster
than current techniques for aligning and clustering DNA sequences, and
produces alignments of comparable or better quality.
12:30 p.m. Tuesday April 5, 2005
Title: Infusing mathematics into
the biology curriculum
Speaker: Leslie Ries, Ph.D.
Venue: Biomolecular Science
Building Room 3118
12:30 p.m. Tuesday April 12, 2005
Title: Learning from mutation and
protein robustness
Speaker: Zhen Shi
Venue: Biomolecular Science
Building Room 3118
12:30 p.m. Tuesday April 19, 2005
Title: Towards the 1000 genome
microbial species
Speaker: Tim Read, Ph.D. (Naval
Medical Research Center)
Venue: Biomolecular Science
Building Room 3118
12:30 p.m. Tuesday April 26, 2005
Title: A Homotopy Optimization
Method for Finding Low Energy Conformations of Small Polypeptides
Speaker: Daniel M. Dunlavy
Venue: Biomolecular Science
Building Room 3118
Abstract:
A new optimization method is presented that minimizes the potential energy
of polypeptides. A polypeptide is modeled as a chain of beads, with each
bead corresponding to a hydrophobic, hydrophilic, or neutral residue. The
method uses the lowest energy conformation of one polypeptide to predict
that of another by following the path determined by a homotopy between the
potential energy functions for the two polypeptides. Results comparing the
new method with simulated annealing are presented for small chains with
hairpin structure.
12:30 p.m. Tuesday May 3, 2005
Title: Inference of demographic
history of African human populations from genome wide genetic markers
Speaker: Floyd Reed, Ph.D.
Venue: Biomolecular Science
Building Room 3118
Abstract:
I will present some of our initial work with a large multilocus human
dataset. This data consists of 1,275 microsatellite and indel markers
genotyped in 3,020 individuals from 120 ethnic populations around the
world, with heavy representation of African populations. The size and
samples included in this dataset offer an opportunity to discover details
about the history of modern humans that thus far have not been possible.
This should be much less formal than the last few presentations and have a
bit of an anthropology focus to explain some of the background questions
related to human genetic variation in Africa. We received the full dataset
only a few weeks ago so we currently have only preliminary results and a
lot of the work thus far has been in learning how to manage this much data
and in ways to quickly summarize and visualize the distribution of genetic
variation. Still, we have already made some unexpected discoveries
relating to the origins and connections between various populations both
within and outside of Africa.
12:30 p.m. Tuesday March 8, 2005
Title: Analyzing the Structure of
Repetitive DNA
Speaker: Suzanne Sindi
Venue: Biomolecular Science
Building Room 3118
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