Combi Seminars

Co-sponsored by the Department of Genomes Sciences and the Computational Molecular Biology (CMB) Program, the Combi Seminars focus specifically on developments in molecular and computational biology-related research and often feature UW faculty and researchers from regionally affiliated centers and institutes.

All Combi Seminars take place on Wednesdays from 1:30 - 2:30 in Foege Auditorium unless otherwise noted.
compbio-seminars [ a t ] -- Biology seminar announcements from all around campus.  Subscribe or unsubscribe at

Please follow this link for a listing of past seminars.


Autumn 2015

December 2 - Siva Kasinathan
graduate student, Henikoff Lab
Fred Hutchinson Cancer Research Center
“Insights into evolution of primate centromeres from single molecule sequencing”

December 9 - Dr. Christian Landry
"Speciation driven by hybridization and chromosomal plasticity in a wild yeast"
Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfill all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the misconception that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.

Winter 2016

January 6 - Dr. Ted Weinert
University of Arizona
"Three Puzzles of Chromosome Instability in Budding Yeast: Time, Replication into Telomeres, & Chromosome-Wide (!) Silencing"

January 13 - Dr. Brendan MacLean
MacCoss Lab, University of Washington

January 20 - Dr. William Noble
University of Washington

January 27 - Dr. Trevor Bedford
Fred Hutchinson Cancer Research Center

February 3 - Dr. Tandy Warnow
University of Illinois
"Grand Challenges in Phylogenomics"

Estimating the Tree of Life will likely involve a two-step procedure, where in the first step trees are estimated on many genes, and then the gene trees are combined into a tree on all the taxa. However, the true gene trees may not agree with with the species tree due to biological processes such as deep coalescence, gene duplication and loss, and horizontal gene transfer. Statistically consistent methods based on the multi-species coalescent model have been developed to estimate species trees in the presence of incomplete lineage sorting; however, the relative accuracy of these methods compared to the usual "concatenation" approach is a matter of substantial debate within the research community.

I will present results showing that coalescent-based estimation methods are impacted by gene tree estimation error, so that they can be less accurate than concatenation in many cases. I will also present two new methods (ASTRAL and statistical binning) for estimating species trees in the presence of gene tree conflict due to ILS. Statistical binning and weighted statistical binning are used to improve gene tree estimation, while ASTRAL is a coalescent-based method that is provably statistically consistent that can construct species trees with 1000 species. Key to these methods is addressing gene tree estimation error more effectively. Finally, I present theoretical results investigating whether statistically consistent accurate species tree estimation is possible when gene trees have estimation error.

relevant papers: 
ASTRAL (Mirarab et al., Bioinformatics 2014) 
ASTRAL-2 (Mirarab and Warnow, Bioinformatics 2015) 
Statistical Binning (Mirarab et al., Science 2014) 
Weighted Statistical Binning (Bayzid et al., PLOS One 2015) 
Comment by Liu and Edwards (Science 2015) 
Response to Comment by Mirarab et al. (Science 2015) 
Theory given bounded number of sites (Roch and Warnow, Systematic Biology 2015) 
Thousand Plant Transcriptome Project (Wickett, Mirarab et al., PNAS 2014), 
Avian Phylogenomics Project (Jarvis, Mirarab, et al., Science 2014).


February 10 - Dr. Evandro Ferrada
Fowler Lab
University of Washington

February 17 - Dr. Arvind Subramaniam
Fred Hutchinson Cancer Research Center

February 24 - Dr. Jeff Vierstra
Stamatoyannopoulos Lab, University of Washington

March 2 - Dr. Elhanan Borenstein
University of Washington

March 9 - Dr. Erick Matsen
Fred Hutchinson Cancer Research Center


Spring 2016

March 30 - reserved for postdoctoral research talks

April 6 - reserved for GS event

April 13 - reserved for postdoctoral research talks

April 20 - reserved for postdoctoral research talks

April 27 - reserved for postdoctoral research talks

May 4 - Matt Rich

May 11 - reserved for postdoctoral research talks

May 18 - reserved for postdoctoral research talks

May 25 - reserved for postdoctoral research talks

June 1 - reserved for postdoctoral research talks