[Sdcsb-l] Guest lecture by Dr. Emek Demir from OHSU - 9/26/16 @ 11am

Beaudette, Jennifer jbeaudette@ucsd.edu
Tue Sep 20 10:32:12 PDT 2016


Guest lecture by Dr. Emek Demir, Oregon Health and Science University
Monday, September 26 from 11 am – 12 pm
BRF2, room 1104

Abstract: Advances in molecular technologies have led to rapid generation of data and information about cellular processes at an increasing rate. Current means of knowledge representation and scientific communication in biology cannot adequately deal with the complexity and volume of this information - a serious bottleneck for developing a causal, predictive understanding of the cell.

Through standardization and knowledge integration/aggregation we have built the largest collection of human cell maps: detailed system scale models of cellular processes (PathwayCommons.org<http://pathwaycommons.org>). In this talk I will describe three cancer biology applications of cell maps we developed to (i) find causal explanations to correlations in phosphoproteomic data, (ii) improve network inference algorithms, (iv) finding mutually altered pathway fragments. I will then discuss two new directions we are focusing now : A common gene expression analysis framework for cancer called PRECEPTS and mapping them to single cell RNAseq and imaging data.

Bio: I am a computational biologist who works on formal representation of biological networks and their analysis. My primary goal is to catalyze the construction of cell maps—formal, cell-scale, biochemical models  of cellular processes—and use them to develop personalized medicine solutions. Cell maps cover  and link a broad spectrum of cellular processes, including metabolism, signaling, and gene regulation,  enabling computational reasoning over hundreds or even thousands of processes. Building cell maps is  a multifaceted challenge that requires large-scale collaboration, computational tools as well as advancements in knowledge representation, visualization, and data integration. I am heavily involved in BioPAX<https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.biopax.org%2f&data=01%7c01%7choifung%40microsoft.com%7ccb87e8c781774ac5c37c08d33ccea5fc%7c72f988bf86f141af91ab2d7cd011db47%7c1&sdata=CTKmSM7cxDNCUaECPDu0AEt2b9NutSqGP4JZY8uTyQQ%3d> <https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.biopax.org%2f&data=01%7c01%7choifung%40microsoft.com%7ccb87e8c781774ac5c37c08d33ccea5fc%7c72f988bf86f141af91ab2d7cd011db47%7c1&sdata=CTKmSM7cxDNCUaECPDu0AEt2b9NutSqGP4JZY8uTyQQ%3d> and SBGN<https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.sbgn.org%2f&data=01%7c01%7choifung%40microsoft.com%7ccb87e8c781774ac5c37c08d33ccea5fc%7c72f988bf86f141af91ab2d7cd011db47%7c1&sdata=NgM8pO2rNWWSAwxAEXKrFEspDSG6i0W%2brBGWv6EmDV4%3d> standard languages, PATIKA<https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.patika.org%2f&data=01%7c01%7choifung%40microsoft.com%7ccb87e8c781774ac5c37c08d33ccea5fc%7c72f988bf86f141af91ab2d7cd011db47%7c1&sdata=3P6ua1lUwg5V2QqiT4xIV5I0Bu3MYZ5PR%2f%2b6KFauUbA%3d> and Pathway Commons<https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.pathwaycommons.org%2f&data=01%7c01%7choifung%40microsoft.com%7ccb87e8c781774ac5c37c08d33ccea5fc%7c72f988bf86f141af91ab2d7cd011db47%7c1&sdata=skk0Sf45eT%2f1BYAYgUntTxQU%2b6MToZSKW%2frGul3vFdA%3d> projects.

Light refreshments will be provided.

Best wishes,

Jennifer Beaudette
Information Specialist
Center for Computational Biology & Bioinformatics MC 0681
www.compbio.ucsd.edu<http://www.compbio.ucsd.edu/> // www.ccbb.bio<http://www.ccbb.bio/>
JBeaudette@ucsd.edu<mailto:JBeaudette@ucsd.edu> // 858-822-6258











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