Speakers


Computer Science and Engineering

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/



Computer Science
Serafim Batzoglou, Stanford University
Read Clouds for DNA Sequencing

Bio: Dr. Batzoglou is an associate professor in the Computer Science Department at Stanford University. He received his Ph.D. from MIT in June 2000, with a thesis on computational genomics. Professor Batzoglou is a recipient of a Sloan Research Fellowship and Career Award in Computer Science from the National Science Foundation. He earned the Best Paper Award at ISMB 2004. Serafim's research has focused on the development of algorithms and systems for genomics. Some of the topics he is working on include sequence alignment algorithms; hidden Markov models; whole-genome comparison; annotation of biological features in genomes; microarray analysis; gene regulation; and DNA sequencing.

[website]

Developmental Biology

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.

[website]


Department of Genetics, Genomics, and Development

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.

[website]

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.

Mikhail Gelfand, Russian Academy of Sciences and Moscow State University
From computer to a lab bench and back. How comparative genomics leads to the discovery of bacterial transporters with a new mode of action.


Bio: Dr. Gelfand received his Ph.D. in mathematics in 1993 from the Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, in Pushchino, and his D.Sc. in biology in 1998 from the Research Institute for the Genetics and Selection of Industrial Microorganisms in Moscow. Currently he is the Vice-Director for Science and the head of the Research and Training Center on Bioinformatics at the A.A.Kharkevich Institute for Information Transmission Problems, RAS, and a Professor at the Department of Bioengineering and Bioinformatics of the M.V.Lomonosov Moscow State University. His Howard Hughes Medical Institute-funded project focuses on "Comparative Genomics, Metabolic Reconstruction, and Analysis of Regulation in Bacterial Genomes." Gelfand's primary research areas include comparative genomics, metabolic reconstruction, analysis of regulation in bacterial genomes, and evolution of alternative splicing.

[website]

The Department of Genetics at U Penn

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]


Department of Bioengineering
Trey Ideker, UC San Diego
Facebook for Proteins - Mapping Protein Networks in the Cell

Bio: Trey Ideker, Ph. D. is Associate Professor of Bioengineering at UC San Diego, Adjunct Professor of Computer Science, and Member of the Moores UCSD Cancer Center. He received predoctoral degrees from MIT in Electrical Engineering and Computer Science and his Ph.D. from the University of Washington in Molecular Biology under the supervision of Dr. Leroy Hood. Ideker is a pioneer in using genome-scale measurements to construct network models of cellular processes and disease. His recent research activities include development of software and algorithms for protein network analysis, network-level comparison of pathogens, and genome-scale models of the response to DNA-damaging agents. His work has been featured recently in the Scientist, Technology Review, the San Diego Union Tribune, and Forbes magazine.

[website]

Department of Electrical Engineering and Computer Science
Richard Karp, UC Berkeley
Haplotypes, Genotypes and Phenotypes

Bio: Dr. Karp attended Harvard University, receiving the Ph.D. in 1959. From 1959 to 1968 he was a member of the Mathematical Sciences Department at IBM Research. From 1968 to 1994 and from 1999 to the present he has been a Professor at the University of California, Berkeley, where he held the Class of 1939 Chair and is currently a University Professor. From 1988 to 1995 and 1999 to the present he has been a Research Scientist at the International Computer Science Institute in Berkeley. From 1995 to 1999 he was a Professor at the University of Washington. During the 1985-86 academic year he was the co-organizer of a Computational Complexity Year at the Mathematical sciences research Institute in Berkeley. During the 1999-2000 academic year he was the Hewlett-Packard Visiting Professor at the Mathematical Sciences Research Institute. The unifying theme in Karp's work has been the study of combinatorial algorithms. His current activities center around algorithmic methods in genomics and computer networking. Karp's awards include: U.S. National Medal of Science, Turing Award, Fulkerson Prize, Harvey Prize (Technion), Centennial Medal (Harvard), Lanchester Prize, and the Von Neumann Theory Prize, among many others.

[website]

Department of Computer Science at Massachusetts Institute of Technology and Broad Institute
Manolis Kellis, Massachusetts Institute of Technology
Understanding genomes from their evolutionary signatures

Bio: Dr. Kellis is an Assistant Professor of Computer Science at MIT, a member of the Computer Science and Artificial Intelligence Laboratory, and of the Broad Institute of MIT and Harvard. His research is in the area of computational biology, and in particular comparative genomics, genome interpretation, gene regulation, cellular networks, and genome evolution. He holds the Distinguished Alumnus (1964) Career Development Professorship, and is one of three young scientists recognized as the next generation in biotechnology by the Museum of Science. He obtained his Ph.D. from MIT, where he received the Sprowls award for the best doctoral thesis in computer science, and the first Paris Kanellakis graduate fellowship. Prior to computational biology, Manolis worked on artificial intelligence, sketch and image recognition, robotics, and computational geometry, at MIT and at the Xerox Palo Alto Research Center. Kellis lived in Greece and France before moving to the US. He was recently selected by Technology Review magazine as one of 35 top young innovators.

[website]

Department of Ecology and Evolutionary Biology at University of Michigan

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]


Department of Chemistry and Biochemistry

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]


Mathematics and Molecular & Cell Biology
Lior Pachter, UC Berkeley
What is epigenomics?

Bio: Dr. Pachter is an Associate Professor of Mathematics and Molecular & Cellular Biology at UC Berkeley, with a joint appointment in Computer Science. Pachter received his Ph.D. in mathematics from the Massachusetts Institute of Technology in 1999. He then moved to the mathematics department at UC Berkeley where he was a postdoctoral researcher for two years, before being hired as an assistant professor. He has been awarded an NSF Career award, and has received the Sloan Fellowship for his work on molecular biology and evolution. Pachter is the co-editor of "Algebraic Statistics for Computational Biology" (with B. Sturfels), and is working on the fundamental problem of comparative genomics: the determination of the origins and evolutionary history of the nucleotides in all extant genomes. His work incorporates various aspects of genomics, including the reconstruction of ancestral genomes (paleogenomics), the modeling of genome dynamics (phylogenomics and systems biology) and the assignment of function to genome elements (functional genomics).

[website]

Computer Science and Engineering

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.


Mathematics and Statistics
David Sankoff, University of Ottawa
Whole genome duplication and its consequences for genome organization

Bio: Dr. Sankoff is a Professor of Mathematics and Statistics at the University of Ottawa, where he also holds a Canada Research Chair in Mathematical Genomics. From 1984 to 2002, he was a Professor of Mathematics and Statistics at l'Université de Montréal, and he continues to be a member of the university's Centre de recherches mathématiques. Dr. Sankoff holds a B. Sc. (1963), M. Sc. (1965) and Ph. D (1969) all from McGill University. The focus of Sankoff's research is to model the processes of long-term genomic evolution, to devise algorithms and statistical analyses capable of reconstructing evolutionary history and to characterize it quantitatively making use of comparative genomic data.
[website]

Computer Science
Ron Shamir, Tel Aviv University
From DNA chips to disease diagnostics

Bio: Dr. Shamir is professor of computer science and holds the Raymond and Beverly Sackler Chair in Bioinformatics at Tel Aviv University (TAU). He has a BSc in mathematics and physics from Hebrew University and a Ph.D. in operations research from UC Berkeley. Dr. Shamir founded the bioinformatics undergraduate degree program at TAU. He specializes in design and analysis of algorithms, and since 1990 has focused on computational biology, specifically focusing on using computation to advance biology. Specific areas of study include gene expression analysis, comparative genomics, gene regulation, systems biology and medical genetics. He is on the editorial board of ten leading journals and series in theoretical computer science and computational biology, and was on the steering committee of RECOMB for 13 years. Dr. Shamir has published over 190 scientific publications. He heads the Edmond J. Safra Bioinformatics Program at Tel Aviv University.

[Website]

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]

Martin Vingron, Max Planck Institute and Free University of Berlin
Sorting gene expression matrices (linear algebra can be good for something!)

Bio: Dr. Vingron studied mathematics in Vienna and did his PhD at the EMBL Biocomputing Programme. After postdoctoral work first at the University of Southern California and then at the German National Research Center for Computer Science he became Head of the Theoretical Bioinformatics Division at the German Cancer Research Center in Heidelberg. In 2000 Vingron moved to Berlin to take the position of Director at the Max Planck Institute for Molcular Genetics, heading the Computational Molecular Biology Departement there. He holds a Honorary Professorship at Berlin Free University. His main research interests lie in sequence analysis and comparison, in the analysis of gene expression data, and in the study of patterns involved in transcriptional regulation.

[website]