Research Reports
Fridays from 3:15 - 4:20 in Foege Auditorium (S 060) unless otherwise noted
Our program will include reports on research progress and proposed work by graduate students. Talks are planned for 25 minutes each. If you are unable to speak at the appointed time, please arrange to change dates with someone else. Please email Brian Giebel (bgiebel [ a t ] uw.edu) with any changes.
Follow this link for a listing of past Research Reports topics.
Follow this link for Research Reports presentation guidelines.
NEW: All talks (except for rotation talks) should be no longer than 25 minutes, including time for questions.
Spring 2020
5/15 -
Tuesday, 5/19, 12:30 - Dr. C.J. Battey
Dr. C.J. Battey
University of Oregon
“Space is the Place: Simulation and Inference for Population Genetics in Continuous Space”
I’ll be talking about why space matters, how we can simulate it, and showing results from two new methods we’ve developed to predict spatial locations and visualize population structure in human genomes.
5/22 - Anna Minkina
Tuesday, 5/26, 12:30 -
5/29 -
Tuesday, 6/2, 12:30 -
6/5 - Jolie Carlisle
Jolie Carlisle
"The Rise and Fall of Fertilization Proteins"
presentation video
Tuesday, 6/9, 12:30 - Dr. Jeffrey Spence
Dr. Jeffrey Spence
Stanford University
"Exchangeability in biology: from populations to cells"
presentation video
Abstract:
Exchangeability--the notion that no information is encoded in the ordering of data--is a pervasive phenomenon in biology: order does not matter for reads coming off a sequencer, for performing biological replicates, or for sampling individuals from a population. I will present a series of examples across biology where exchangeability can be leveraged to extract biological insight. I will mainly focus on three case studies.
1. An exact statistical test for detecting heterogeneity in binary datasets with applications to population genetics as well as single-cell omics data.
2. A neural network architecture that respects exchangeability by enforcing permutation equivariance.
3. Using exchangeable neural networks for imputing the results of unperformed epigenetic assays and disentangling cis- and trans-effects on gene expression.
This is joint work with Alan Aw, Sanjit Batra, Jeffrey Chan, Jonathan Fischer, Paul Jenkins, Sara Mathieson, Valerio Perrone, and Yun Song.
6/19 - Michael Goldberg
remote presentation link available at https://depts.washington.edu/gsrestrc/remote.htm
6/26 - Dr. Jeannette Tenthorey
Fred Hutchinson Cancer Research Center
"How the host fights back: the evolutionary landscape of host-virus arms races"
Abstract: Viruses and their hosts are locked in evolutionary arms races, in which viruses mutate to evade host defenses and hosts mutate to counter viral escape mutants. However, the mutational landscapes that dictate how antiviral proteins participate in these arms races remain undefined. In particular, it is unclear how likely random mutations within critical virus-binding interfaces are to improve or ablate viral restriction. We define the first comprehensive mutational landscape for an antiviral protein, TRIM5α. TRIM5α has undergone rapid mutational evolution within a flexible loop that binds HIV-1, and mutations within this loop dramatically alter its ability to restrict HIV-1. We employ a deep mutational scanning strategy to evaluate the effect of all individual point mutations in this loop on HIV-1 restriction. Surprisingly, we find that half of all single mutations significantly improve the ability of human TRIM5α to restrict HIV-1. Similarly, rhesus macaque TRIM5α, a potent restrictor of HIV-1, tolerates half of all single mutations with no loss in restriction. This unexpected mutational resilience suggests that TRIM5α can sample a wide variety of mutations, with low cost and high potential for gain, to maximize the chances of success in its evolutionary arms race with lentiviruses.
Tuesday, 6/30, 12:30 - Dr. Tyler Starr
Fred Hutchinson Cancer Research Center
"Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding"
Tuesday, 7/14, 12:30 - Dr. Olivia Dong
Duke University
remote presentation link available at https://depts.washington.edu/gsrestrc/remote.htm
"Cost-effectiveness of Genomic Profiling in Patients with Metastatic Lung Adenocarcinoma"
Abstract: Tumor profiling identifies patients who are eligible for targeted anticancer therapies. Common tumor profiling approaches include targeted gene panel testing (TGPT), which tests for common mutations in select genes, and multigene panel sequencing (MGPS), which tests for a broad range of mutations in a comprehensive set of genes. The lifetime cost-effectiveness of MGPS and TGPT compared to no tumor profiling for Veterans with metastatic lung adenocarcinoma from the Veterans Health Administration’s (VHA) perspective will be discussed.
Tuesday, 7/21, 12:30 - Dr. Peter Louis
Vanderbilt University
remote presentation link available at https://depts.washington.edu/gsrestrc/remote.htm
Tuesday, 7/28, 12:30 - Dr. Marie Mooney
Duke University
remote presentation link available at https://depts.washington.edu/gsrestrc/remote.htm
1/8, 12:30, K-069. Foege Auditorium to be used by Medical Genetics at 3:30.