Spring 2000
Mathematical Biology Seminar
Seminars at UH meet from 1:30 to 2:30 in room 646,
Phillip Guthrie Hoffman Building.
Seminars at Rice meet from 1:30 to 2:30 in Duncan Hall 1044.
Exceptions are noted in schedule below.
Parking at UH is available in the paid parking garage underneath
University Hilton Hotel and Hotel School, Entrance 1 off Calhoun.
Parking tokens will be provided by the Math Department.
Parking at Rice is available in visitor spots in Lot C (Abercrombie lot), Entrance 16 from Rice Blvd.
- Note time and room change: 11:00
a.m. DH 2014
23 February at Rice
Alex Schaffer, National Instisute of Health
Using Comparative Genomic Hybridization Data to
Infer Tree Models of Oncogenesis
ABSTRACT: Comparative genome hybridization (CGH) is a laboratory method to
measure gains and losses of chromosomal regions in tumor cells. It is
believed that DNA gains and losses in tumor cells do not occur
entirely at random, but partly through some flow of causality. Models
that relate tumor progression to the occurrence of DNA gains and
losses could be very useful in hunting cancer genes and in cancer
diagnosis. We lay some mathematical foundations for inferring a model
of tumor progression from a CGH data set. We consider a class of tree
models that are more general than a path model that has been developed
for colorectal cancer. We derive two tree model inference algorithms
based on the ideas of (1) maximum-weight branching in a graph
and (2) fitting a matrix of distances to a phylogenetic tree. We
prove that under plausible assumptions our algorithms infer
good trees. We have implemented our methods in software, and we
illustrate
with a CGH data set for renal cancer. Our tree models confirm
the known role of losses on 3p, and suggest an important role for losses on 4q in renal cell carcinoma. Our methods and software can also
be used to make tree models from cytogenetic breakpoint data.
- Note time and room change: 10:00
a.m. DH 1049
18 May at Rice
Elise Eller, Anthropology Department, University of Utah
Population extinction and recolonization in human
demographic history
Abstract:
A primary objection, from a population genetics perspective, to the
multiregional model of modern human origins is that the multiregional model
posits a large census size while the genetic data suggest a small effective
population size of approximately 10,000. The relationship between census
size and effective size is complex, but it has been argued that 10,000
breeding individuals could not have occupied Africa, southern Eurasia, east
Asia and Australasia for much of the Pleistocene and remained a cohesive
species via gene flow.
However, this argument does not consider the effects of local
population extinction and recolonization on effective population size.
Population extinction and recolonization increases the genetic variance
among demes and reduces effective population size. By applying
metapopulation models, I show that a large census size is consistent with
an effective population size of 10,000 if the extinction rate is relatively
high, interdemic migration rates are low, and the colonization process
incorporates a small number of colonists or kin-structured colonization.
Therefore, in spite of earlier arguments to the contrary, a small effective
population size is consistent with the multiregional model if population
extinction and recolonization is incorporated. However, better parameter
estimates from ethnographic studies are necessary in order to obtain a
narrower range of possible census sizes.
-
26 May at Rice
Note time and room change: 12pm
DH 1044
Uma Nagaswamy, University of Houston
A Database for Non-Canonical base pairing in RNA
secondary structures
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