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The Next Talk Fa'18 Talks General Info Speaking Req't

Learning Gene Networks Underlying Clinical Phenotypes Using SNP Perturbations

Friday, November 2nd, 2018 from 12-1 pm in GHC 6501.

Calvin McCarter, MLD

Recent technologies are generating an abundance of genome sequence data and molecular and clinical phenotype data, providing an opportunity to understand the genetic architecture and molecular mechanisms underlying diseases. Previous approaches have largely focused on the co-localization of single-nucleotide polymorphisms (SNPs) associated with clinical and expression traits, each identified from genome-wide association studies and expression quantitative trait locus (eQTL) mapping, and thus have provided only limited capabilities for uncovering the molecular mechanisms behind the SNPs influencing clinical phenotypes. Here we aim to extract rich information on the functional role of trait-perturbing SNPs that goes far beyond this simple co-localization. We introduce a computational framework called Perturb-Net for learning the gene network that modulates the influence of SNPs on phenotypes, using SNPs as naturally occurring perturbation of a biological system. Perturb-Net uses a probabilistic graphical model to directly model both the cascade of perturbation from SNPs to the gene network to the phenotype network and the network at each layer of molecular and clinical phenotypes. Perturb-Net learns the entire model by solving a single optimization problem with an extremely fast algorithm that can analyze human genome-wide data within a few hours. In our analysis of asthma data, for a locus that was previously implicated in asthma susceptibility but for which little is known about the molecular mechanism underlying the association, Perturb-Net revealed the gene network modules that mediate the influence of the SNP on asthma phenotypes. Many genes in this network module were well supported in the literature as asthma-related.

Fall 2018 Schedule
Mon, Aug 27 GHC 6501 Expired
Fri, Aug 31 GHC 8102 Hongyang Zhang New Paradigms and Global Optimality in Non-Convex Optimization
Mon, Sep 3 GHC 6501 Labor Day Holiday UNAVAILABLE
Fri, Sep 7 GHC 6501 Expired
Mon, Sep 10 GHC 7101 Expired
Fri, Sep 14 GHC 8115 Expired
Mon, Sep 17 GHC 6501 Expired
Fri, Sep 21 GHC 6501 Expired
Mon, Sep 24 GHC 6501 Expired
Fri, Sep 28 GHC 6501 Expired
Mon, Oct 1 GHC 8102 Expired
Fri, Oct 5 GHC 8115 Expired
Mon, Oct 8 GHC 6501 Expired
Fri, Oct 12 GHC 6501 Expired
Mon, Oct 15 GHC 8115 Expired
Fri, Oct 19 GHC 6501 Expired
Mon, Oct 22 GHC 6501 Expired
Fri, Oct 26 GHC 8102 AVAILABLE
Mon, Oct 29 GHC 6501 AVAILABLE
Fri, Nov 2 GHC 6501 Calvin McCarter Learning Gene Networks Underlying Clinical Phenotypes Using SNP Perturbations
Mon, Nov 5 GHC 6501 AVAILABLE
Fri, Nov 9 NSH 3002 Evan Shimizu Exploratory Stage Lighting Design using Visual Objectives
Mon, Nov 12 GHC 6501 Steven Osman How AI Has Learned to Play Atari Games
Fri, Nov 16 GHC 8102 Conglong Li Workload Analysis and Caching Strategies for Search Advertising Systems
Mon, Nov 19 GHC 6501 AVAILABLE
Fri, Nov 23 GHC 6501 AVAILABLE
Mon, Nov 26 GHC 6501 AVAILABLE
Fri, Nov 30 GHC 6501 AVAILABLE
Mon, Dec 3 GHC 6501 AVAILABLE
Fri, Dec 7 GHC 6501 AVAILABLE
Mon, Dec 10 GHC 6501 AVAILABLE
Fri, Dec 14 GHC 6501 AVAILABLE
Mon, Dec 17 GHC 6501 AVAILABLE

General Info

The Student Seminar Series is an informal research seminar by and for SCS graduate students from noon to 1 pm on Mondays and Fridays. Lunch is provided by the Computer Science Department (personal thanks to Debbie Cavlovich!). At each meeting, a different student speaker will give an informal, 40-minute talk about his/her research, followed by questions/suggestions/brainstorming. We try to attract people with a diverse set of interests, and encourage speakers to present at a very general, accessible level.

So why are we doing this and why take part? In the best case scenario, this will lead to some interesting cross-disciplinary work among people in different fields and people may get some new ideas about their research. In the worst case scenario, a few people will practice their public speaking and the rest get together for a free lunch.

Guideline & Speaking Requirement Need-to-Know

Note: Step #1 below are applicable to all SSS speakers. You can schedule AT MOST THREE talks per semester.

SSS is an ideal forum for SCS students to give presentations that count toward fulfilling their speaking requirements. The specifics, though, vary with each department. For instance, students in CSD will need to be familiar with the notes in Section 8 of the Ph.D. document and follow the instructions outlined on the Speakers Club homepage. Roughly speaking, these are the steps:

  1. Schedule a talk with SSS by sending your talk title, abstract, additional info (like "Joint work with..." or "In Partial Fulfillment of the Speaking Requirement"), and a link to your home page to sss@cs at least TWO WEEKS before your scheduled talk.
  2. After you are confirmed with your SSS slot, go to the Speakers Club Calendar and schedule your talk at least THREE WEEKS in advance of the talk date.
  3. On the day of your talk, make sure you print Speakers Club evaluation forms for your evaluators to use.
Students outside of CSD will need to check with their respective departments regarding the procedure. As another example, ISRI students fulfill their speaking requirements by attending a semesterly Software Research Seminar and giving X number of presentations per school year. If you have experience with your department that might help others in your department, please feel free to contribute your knowledge by emailing us. Thank you!

SSS Coordinators

Qing Zheng, CSD


Web contact: sss+www@cs