St. Petersburg, Russia | August 27-29, 2012
Invited Speakers
Max AlekseyevUniversity of South Carolina |
Vineet BafnaUniversity of California, San Diego |
Mikhail GelfandRussian Academy of Sciences and Moscow State University |
Sorin IstrailBrown University |
Richard KarpUniversity of California, Berkeley |
Bernard MoretÉcole Polytechnique Fédérale de Lausanne |
Steve O'BrienSaint Petersburg University |
Pavel PevznerUniversity of California, San Diego |
Marie-France SagotINRIA, Université Lyon 1 |
Cenk SahinalpSimon Fraser University |
Ron ShamirTel Aviv University |
Glenn TeslerUniversity of California, San Diego |
Tandy WarnowThe University of Texas at Austin |
Mike WatermanUniversity of Southern California |
Max Alekseyev
University of South Carolina
Homepage: http://www.cse.sc.edu/~maxal/
Dr. Max Alekseyev received a Ph.D. in computer science in 2007 from the University of California, San Diego. Currently he is an Assistant Professor in the Computer Science and Engineering department at University of South Carolina. In 2011, he served as a Scientific Director for Algorithmic Biology Lab at St. Petersburg Academic University, Russia. Dr. Alekseyev's research interests range from discrete mathematics (including combinatorics and graph theory) to bioinformatics (including comparative genomics and phylogenomics). His research is focused on the development and application of new methods of discrete mathematics to solve old and recently emerged open biological problems. Dr. Alekseyev is an Associate Editor of the Frontiers in Bioinformatics and Computational Biology journal and an Editor-in-Chief of the On-Line Encyclopedia of Integer Sequences. He has served on the program committees for CPM 2011 and ACM SE 2012 conferences.
Vineet Bafna
University of California, San Diego
Homepage:http://www-cse.ucsd.edu/~vbafna/
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.
Mikhail Gelfand
Russian Academy of Sciences and Moscow State University
Homepage: http://www.rtcb.iitp.ru/mg_e.htm
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.
Sorin Istrail
Brown University
Homepage: http://www.cs.brown.edu/~sorin/
Sorin Istrail is the Julie Nguyen Brown Professor of Computational and Mathematical Sciences and former Director of the Center for Computational Molecular Biology at Brown University. Before joining Brown, he was the Senior Director and then Head of Informatics Research at Celera Genomics, where his group played a central role in the construction of the Sequence of the Human Genome; they co-authored the 2001 Science paper “The Sequence of the Human Genome,” which, with over 9500 citations to date, is one of the most cited scientific paper. His group at Celera also built a powerful suite of genome-wide algorithms that was used for the comparison of all human genome assemblies to date. In 2002 his Celera group in collaboration with the company ClearForrest won the ACM KDD Cup – the top international data mining/machine learning competition – for automatic annotation of the Drosophila genome. In 2003 he joined the ranks of Applied Biosystems Science Fellows, one of just six Science Fellows in a company of 800 scientists. Before Celera, Professor Istrail founded and led the Computational Biology Project at Sandia National Laboratories (1992-2000). In 2000, he obtained the negative solution (computational intractability) of a 50 years old unresolved problem in statistical mechanics, the Three-Dimensional Ising Model Problem. This work was included in the Top 100 Most Important Discoveries of the U.S. Department of Energy’s first 25 years, and as the 7th top achievement in Scientific Computing. Professor Istrail's research focuses on computational molecular biology, human genetics and genome-wide associations studies, medical bioinformatics of multiple sclerosis, autism, HIV, preterm labor and viral immunology, statistical physics, algorithms and computational complexity. He is co-editor-in-chief with Mike Waterman of the Journal of Computational Biology, and together with Pavel Pevzner and Mike Waterman, he is co-founder with of the RECOMB Conference series, and co-editor-in-chief of the MIT Press Computational Molecular Biology series and the Springer-Verlag Lecture Notes in Bioinformatics series. He is Professor Honoris Causa of the “Alexandru Ioan Cuza” University, Iasi, Romania.
Richard Karp
University of California, Berkeley
Homepage: http://www.cs.berkeley.edu/~karp/
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.
Bernard Moret
École Polytechnique Fédérale de Lausanne
Homepage: http://people.epfl.ch/bernard.moret
Dr. Moret is Professor of Computer Science, holding the chair of Bioinformatics at the Swiss Federal Institute of Technology (EPFL) in Lausanne, Switzerland. He received his Ph.D. in 1980 from the University of Tennessee and was on the faculty of the Department of Computer Science at the University of New Mexico until 2006, serving as chair from 1991 to 1993. His research interests are in the area of algorithms and applications, particularly in computational molecular biology. He founded the ACM Journal of Experimental Algorithmics in 1995, serving as its editor-in-chief for seven years. Since 2000, he has focused on the development of models and algorithms for evolutionary genomics, publishing around 80 peer-reviewed articles in the area and founding, in 2001, the annual Workshop on Algorithms in Bioinformatics (WABI).
Steve O'Brien
Saint Petersburg University
Homepage: http://dobzhanskycenter.bio.spbu.ru/?page_id=73&lang=en
Stephen J. O’Brien served as Chief of the Laboratory of Genomic Diversity at the National Cancer Institute (NCI), National Institutes of Health (NIH) from 1986-2011. In December 2011, he joined the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University as Chief Scientific Officer. His research interests and expertise span human and comparative genomics, genetic epidemiology, HIV/AIDS, retro-virology, bioinformatics biodiversity and species conservation. Dr. O’Brien served as editor of six editions of Genetic Maps: Locus Maps of Complex Genomes (1980-1993) (Cold Spring Harbor Laboratory Publications; editor of Editor of Journal of Heredity (American Genetics Association) from 1987-2007; editor of “Atlas of Mammalian Chromosomes”, (John Wiley Inc. NYC, 2006) and author or “Tears of the Cheetah And Other Tales From The Genetic Frontier” (St. Martin’s Press NYC, 2004).
Dr. O’Brien received his B.S. in Biology in 1966 from St. Francis College, which presented him with a Distinguished Alumni Award in 1994. In 1971 he earned a Ph.D. in Genetics from Cornell University which honored him as “Andrew Dixon White Endowed Professor at Large” in 1998.
Dr. O’Brien has a strong dedication to education, evidenced by his appointments as adjunct professor at twelve universities. He has mentored more than fifteen Ph.D. students and multiple postdoctoral fellows. Since 1996 he has directed an internationally heralded short course sponsored by Smithsonian and American Genetics Association, entitled “Recent Advances in Conservation Genetics”, the most recent (2012) edition at The Smithsonian Tropical Research Institute , Panama.
Pavel Pevzner
University of California, San Diego
Academic University, St. Petersburg
Homepage: http://cseweb.ucsd.edu/~ppevzner/
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 the Moscow Institute of Physics and Technology, Russia. He is the author of the graduate textbook Computational Molecular Biology: An Algorithmic Approach, 2000 and the undergraduate textbook (with Neil Jones) Introduction to Bioinformatics Algorithms, 2004. He was named Howard Hughes Medical Institute Professor in 2006. Dr. Pevzner is the director of the Interdisciplinary Bioinformatics Program at UCSD.
Marie-France Sagot
INRIA, Université Lyon 1
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