Dr. Smith: Using Database and Sematic Web Tools to Link Genes to Complex Behaviors, Dr. Arsuaga: Using Computational Persistent Homolgy for clustering Breast cancer CGH-datas, Dr. Levine: Open Source Project Development Opportunities

Wednesday, February 27, 2008 - 17:30
TH 331
5:30 Chris Smith, San Francisco State University, 5:50 Javier Arsuaga, San Francisco State University, 6:10 Barry Levine, San Francisco State University

Dr. Smith: In his lab at SFSU, Dr. Smith uses comparative genomics approaches and ~20 insect genomes to study conserved genes, regulatory elements,and repeated sequences. Using datamining and bioinformatics techniques he is currently working on a catalog of genes and gene networks involved in complex social behaviors including cooperation and group aggression. He will talk about projects that students can contribute to that employ the design of web site interfaces to simplifying making complex database queries, using natural language processing to more efficiently extract behavior information from Medline abstracts and PDFs articles, and creating new visualization tools to better understand the relationships between gene networks and behavior.

Dr. Arsuaga: I am interested in mathematical and computational modeling of chromosomes. In this talk I will mainly focus on our computational efforts to understand chromosome aberrations in cancer. It has been estimated than 1 in 3 people will developed cancer during their life time. One key problem is to identify patients at an early stage of cancer development and with aggressive tumors. I will present how one can use computational methods to interrogate chromosomes to infer properties of the tumor and will discuss how this can be used for personalized treatments. However these methods are in their infancy and there is an enormous need for new computational tools (data base management, data mining, imaging, etc...) to analyze the data.

Dr. Levine will describe several ongoing projects being developed as open source projects. There is an ongoing need to attract students to contribute to these projects, which are gaining recognition in the international arena.


Chris Smith did his PhD work at UCSF probing the molecular structure of chromosome ends (telemores) and was a post-doctoral fellow and staff scientist at UC Berkeley and Lawrence Berkeley National Lab, focusing on large scale computational analysis of the fruitfly genome.

Javier Arsuaga earned his PhD from Florida State University. His topic of research was chromosome organization in viruses. During this time he was a fellow of the Program in Mathematics and Molecular Biology (PMMB). After graduating he spent 3 years at UCB as a postdoctoral fellow in the Department of Mathematics and in the Department of Molecular and Cell Biology.During these years he investigated chromosome organization in Bacteria and the effects of radiation in chromosomes. After his postdoc and before joining SFSU he was a researcher at the UCSF Comprehensive Cancer center. His current research interests include chromosome organization across organisms and how aberrant organizations are related to disease.

Dr. Levine: Concurrently with his position at SFSU, Dr. Levine is Professor and Director of the Computer & Information Science Program at American University of Armenia (affiliate with the University of California). He initiated the CIS program at AUA in 2001. He has consulted for various organizations, including the World Bank, USAID, the U.S. Government and private industry. His interests include programming language design, compiler construction, functional programming, object-oriented programming and asynchronous distance learning. He has traveled and lectured worldwide in countries including Kenya, China, Jordan and Armenia. He is currently leading projects in collaboration with Sun (Armenian Virtual Science Library project, developed from the Iraqi Virtual Science Library project - https://www.ivsl.org/), Stanford (re-design of "Turing World" software), the Oakland Solar Energy initiative and Sakai http://sakaiproject.org/).