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|Course Info||CSE 590C is a weekly seminar on Readings and Research in Computational Biology, open to all
graduate students in computational, biological, and mathematical sciences.|
|Theme||Traditionally, we reserve Spring quarter for "homegrown" research --- highlights of work by researchers in the Seattle area. Our tentative Spring schedule is:|
|Papers, etc.|| |
Note on Electronic Access to JournalsThe UW Library is generally a paid subscriber to non-open-access journals we cite. You can freely access these articles from on-campus computers. For off-campus access, follow the "[offcampus]" links below or look at the library "proxy server" instructions. You will be prompted for your UW net ID and password.
03/26: -- ---- Organizational Meeting ----
Abstract: Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone. We trained our model (APARENT, APA REgression NeT) on isoform expression data from over three million APA reporters, built by inserting random sequence into twelve distinct 3' UTR contexts. Predictions are highly accurate across both synthetic and genomic contexts; when tasked with inferring APA in human 3' UTRs, APARENT outperforms a model trained exclusively on endogenous data. Visualizing features learned across all network layers reveals that APARENT recognizes sequence motifs known to recruit APA regulators, discovers previously unknown sequence determinants of cleavage site selection, and integrates these features into a comprehensive, interpretable cis-regulatory code.
For background reading, Johannes recommends:
04/23: -- No Meeting
04/30: Hypoxemia + DeepProfile -- Alex + Ayse
05/07: Two Short Talks on Single-Cell RNA-seq -- Erin + Yue
05/21: Biocellion: high-performance software for modeling,
simulation and visualization of many-cell systems -- Dr. Simon Kahan, Biocellion/Dr. Ilya Shmulevich, ISB
Abstract: For decades, 3d models have been reducing cost, accelerating progress and improving results in the automotive, aerospace, and architecture and petroleum industries. Despite the continued failure of in vitro and animal testing to reliably demonstrate efficacy and establish safety of drug and consumer care products, the life science industries are only just beginning to embrace whole-system 3d modeling and simulation as an alternative.
Why? Because modeling complex living systems is hard; simulating these models at sufficient scale and duration demands purpose-built high-performance software; and interactive visualization of the highly dynamic simulation results poses new challenges for graphics engines.
We present Biocellion and Biovision software solutions. Biocellion is a platform that supports development of living system models at cell-resolution, integrating biological, chemical and mechanical rules of interaction. Biocellion simulates these models as they grow to tens of billions of cells. Biovision provides interactive exploration of the simulation results over time.
We illustrate results from the application of Biocellion at P&G to skin growth and response to toxic materials. We also show images from Pacific Northwest National Laboratory comparing simulations of intestinal response to a low- versus high-fiber diet.
Though only recently developed, our models are able already to recapitulate many aspects of tissue growth, homeostasis and response to some interventions. Using Biocellion, they can be incrementally extended and improved to become increasingly predictive under an ever broadening spectrum of interventions.
05/28: -- Holiday
|Other Seminars||Past quarters of CSE 590C|
COMBI & Genome Sciences Seminars
Microbiology Department Seminars
|Resources||Molecular Biology for Computer Scientists, a primer by Lawrence Hunter (46 pages)|
A Quick Introduction to Elements of Biology, a primer by Alvis Brazma et al.
A comprehensive FAQ at bioinformatics.org, including annotated links to online tutorials and lectures.
CSE 527: Computational Biology
CSEP 590A: Computational Biology (Professional Masters Program)
Genome 540/541: Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis
Computer Science & Engineering|
University of Washington
Seattle, WA 98195-2350
(206) 543-1695 voice, (206) 543-2969 FAX