Vineet Bafna, UC San Diego
Hunting for the Huntington disease gene

Bio: Vineet Bafna is an Associate Professor in the Computer Science and Engineering Department at UC San Diego's Jacobs School of Engineering. Prior to joining UCSD in 2003, he spent seven years in the bio-science industry, ultimately as Director of Informatics Research, at Celera Genomics. At Celera, he participated in the human genome project, designing novel tools for gene discovery, and leading the analysis of mass spectrometry data for identifying cancer bio-markers. His current research focus is on computational problems arising is mass spectrometric data analysis, population genetics, non-coding genes, and cancer genomics. He is an Associate Editor for JBCB, IEEE TCBB, and Biology Direct, and has served on the program committees of ISMB, RECOMB, and other conferences. He has co-authored over seventy research articles in refereed journals and conference proceedings. Dr. Bafna is the Director of the Undergraduate Bioinformatics Program at UCSD.
http://www-cse.ucsd.edu/~vbafna/

Gill Bejerano, Stanford University
All your base are belong to us": Thinking non-conservatively about genome conservation.

Bio: Gill Bejerano holds a BSc, summa cum laude, in Mathematics, Physics, and Computer Science, and a PhD in Computer Science from the Hebrew University of Jerusalem, Israel. Twice recipient of the RECOMB best paper by a young scientist award, and a former Eshkol pre-doctoral Scholar and HHMI postdoc with David Haussler at UC Santa Cruz. Gill is currently an Assistant Professor in the Department of Developmental Biology and the Department of Computer Science at Stanford university. As co-discoverer of ultraconserved elements, his research focuses on deciphering the function and evolution of the non-coding regions of the Human Genome.

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Michael Eisen, UC Berkeley

Bio: Dr. Eisen is an Howard Hughes Investigator and Associate Professor of Genetics, Genomics and Development at University of California Berkeley. He received his Ph.D. in biophysics in 1996 from Harvard. His doctoral research with Don Wiley focused on the structure and evolution of influenza virus proteins. After a brief stint as the play-by-play voice of the Columbia Mules, a minor league baseball team in Tennessee, he moved to Stanford Medical School where he was a postdoctoral fellow with Pat Brown and David Botstein. He joined the Brown and Botstein labs right as DNA microarrays was being developed, and developed the methods for analyzing microarray data that transformed this technology into an invaluable tool for exploring biology. His seminal 1998 paper on cluster analysis that demonstrated the close relationship between expression patterns and gene function has been cited over 5,000 times and is the foundation for extensive subsequent research in computational analysis of genomic data. In 2000, he established his own research group that has focused on understanding the function and evolution of regulatory sequences. For his research accomplishments, he was named a Pew Scholar in the Biomedical Sciences in 2001 and received the 2004 Presidential Early Career Award for Scientists and Engineers.

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Terry Gaasterland, UCSD
Deciphering variant splice forms in proteins that control transcription

Dr. Terry Gaasterland is a computer scientist turned molecular biologist. Her work seeks to understand the program of the cell encoded in the genome. She earned her undergraduate degree in Computer Science and Russian with a minor in Chemistry from Duke University as an A.B. Duke Scholar, and her Ph.D. in Computer Science from University of Maryland. As an Enrico Fermi Fellow at the Department of Energy's Argonne National Laboratory and then as an Assistant Professor of Computer Science at the University of Chicago, she applied techniques from her work in "cooperative answering", natural language processing, and deductive database research to the interpretation of the first three DOE-funded microbial genomes and a fourth Canadian-funded archaeal genome. During seven years as a Head of Lab at Rockefeller University, Dr. Gaasterland focused on the integration of gene expression data and genome sequence data analysis in human and model eukaryotic organisms. Recently, Dr. Gaasterland moved her Laboratory of Computational Genomics to UCSD to establish the Scripps Genome Center, a UCSD resource based at the Scripps Institution of Oceanography in the Marine Biology Division, with bioinformatics hardware and software housed at the San Diego Supercomputing Center. At UCSD, she is now a Professor of Computational Biology and Genomics at SIO and an Adjunct Professor in the Molecular Biology Department of the Biology Division.

In her current research, Dr. Gaasterland designs and uses computational tools to decipher and interrogate cell systems through integrated analysis of genomic and proteomic data. Her work aims to address the general question: How does regulation of transcription and translation modulate and affect cell state changes? Her laboratory focuses on two specific areas of investigation: how tissue-specific and developmental-stage-specific alternative splicing impacts the function of transcription factors and RNA-binding proteins; and evolution of microRNA::mRNA binding in plants and animals, with particular focus on the impact of mRNA alternative splicing, alternative promotion, and alternative termination on microRNA binding sites. The Gaasterland Lab maintains a database of alternatively spliced introns and exons in the human, mouse, rat, drosophila, and C.elegans genomes. This resource is a building block for the lab's alternative splicing research allows interrogation of variant exons and introns in the context of gene structure, proximal promoters and UTRs. The laboratory developed and now uses medium-throughput RT-qPCR strategies to validate predictions about effects of alternative splicing and microRNA activity on the transcriptome. It uses a combination of high-throughput sequencing and computational analysis to identify non-coding RNAs and their functions in pre-vertebrate and eukaryotic microbial organisms, including sea squirt (Ciona sp.), sea urchin, diatoms and dinoflagellates.

Sridhar Hannenhalli, Penn Center of Bioinformatics
Survival of the fittest - detecting adaptive evolution

Dr. Hannenhalli is an assistant professor in the department of Genetics at the university of Pennsylvania and also has a secondary appointment in the Computer and Information Science department at Penn. He received his PhD in 1996 in Computer Sc. from the Penn St. University where he worked on genome rearrangement problems and developed the first polynomial time algorithm for the so-called "sorting by signed reversal" problem. After a postdoctoral fellowship at the University of Southern California, he spent 6 years in the industry, first at Glaxo Smithkline and then at Celera Genomics. His current research focus is on comparative genomics, transcriptional regulation and evolution.

[website]

Alex Kondrashov, University of Michigan
Detecting selection from sequence data

Alexey Kondrashov is a Professor in the Department of Ecology and Evolutionary Biology at University of Michigan. Dr. Kondrashov came to the United States from Russia in 1990 as a Visiting Scientist in the Department of Genetics at the University of Wisconsin - Madison. In 1993, Dr. Kondrashov became Assistant Professor of Ecology & Systematics at Cornell University, and moved up to an Associate Professorship in 1996. In 1999, Dr. Kondrashov moved to Bethesda, Maryland as senior investigator for the National Center for Biotechnology Information at the National Institutes of Health. He moved to University of Michigan in 2006. Dr. Kondrashov is best known for the deterministic mutation hypothesis explaining the maintenance of sexual reproduction and his work on evaluating mutation rates.

[website]

Christopher Lee, UCLA
How can we fight the scourge of AIDS drug resistance?

Bio: Dr. Lee is Professor of Chemistry & Biochemistry at UCLA, and director of the UCLA Bioinformatics Ph.D. program. His research includes bioinformatics analysis of alternative splicing, genome evolution, and selection pressure network models of HIV drug resistance evolution. He also works on bioinformatics algorithms and software, including highly scalable indexing and query tools for comparative genomics data (Pygr, the Python Graph Database framework for bioinformatics) and truly transparent scientific data sharing (pygr.Data). In the past, Dr. Lee has worked on topics including protein structure and stability, partial order sequence alignment, large-scale detection of coding region sequence polymorphism, and bioinformatics data mining and visualization tools. He has served on the Board of Scientific Counselors of NCBI, was a co-founder of Molecular Applications Group with Michael Levitt in 1993, and has received the MIT Technology Review TR100 award.

[website]

Pavel Pevzner, CASB and UC San Diego
DNA sequencing: a million piece jigsaw puzzle

Bio: Dr. Pevzner is the Ronald R. Taylor Chair Professor of Computer Science and Director of the Center for Algorithmic and Systems Biology at University of California, San Diego. He holds a Ph.D. (1988) from Moscow Institute of Physics and Technology, Russia. Dr. Pevzner is author of the graduate textbook "Computational Molecular Biology: An Algorithmic Approach" in 2000 and the undergraduate textbook "Introduction to Bioinformatics Algorithms" in 2004 (jointly with Neal Jones). He was named Howard Hughes Medical Institute Professor in 2006. Dr. Pevzner is the director of the Interdisciplinary Bioinformatics Program at UCSD.

[website]

Natasa Przulj, UCI
From Network Topology to Biological Function and Disease.

Natasa Przulj is an Assistant Professor in the Department of Computer Science at the University of California, Irvine. She obtained her Ph.D. from the Department of Computer Science at the University of Toronto in 2005. Her research involves applications of graph theory to solving large-scale problems in computational and systems biology focusing on the development of new techniques for analysis and modeling of protein-protein interaction and other biological networks.

Amos Tanay, Weizman Institute of Sciences
Evolution: An omnipotent optimizer or a sloppy problem solver? or both?

Amos Tanay is a Senior Scientist in the Department of Computer Science and Applied Mathematics at the Weizmann Institute. Amos joined Weizmann after spending two years as a fellow in the center for Physics and Biology at the Rockefeller University. He received his PhD from Tel-Aviv University on 2005, where he studied mathematics and computational biology with Ron Shamir. Prior to that, Amos spent 6 years working in the software and resource optimization industry.

Amos's research focuses on finding ways to understand genome organization and regulation through a new breed of evolutionary models. In particular, Amos's group uses both model organisms and cancer models to study epigenetic mechanisms and how they co-evolve with the underlying genomic sequence.

[website]