Computational Gene Finding in the Human Genome: How Many Genes Do We Have? – Steven Salzberg (University of Maryland)
Scientists have been trying to count the number of genes in the human genome since the 1960s, but despite dramatic advances in technology, the quest continues. In this talk, I will describe the decades-long search for human genes, and the changing technology that has been used to identify these genes. I will focus on recent computational gene finding methods, including those based on hidden Markov models and on DNA sequence alignments to closely related species. Finally I will discuss evolutionary analyses that use other mammals to distinguish genes from functionally meaningless sequences that were previously identified as genes.
Dr. Steven Salzberg is the Director of the Center for Bioinformatics and Computational Biology (CBCB) and the Horvitz Professor of Computer Science at the University of Maryland, College Park. From 1997 to 2005 he was at The Institute for Genomic Research (TIGR) in Rockville, Maryland, where he was the Senior Director of Bioinformatics, in charge of TIGR’s bioinformatics research as well as its production operations. During that time he was also a Research Professor of Computer Science and Biology at Johns Hopkins University in Baltimore. Dr. Salzberg received his B.A. degree in English and M.S. and M.Phil. degrees in Computer Science from Yale University, and his Ph.D. in Computer Science from Harvard University. Following his Ph.D. studies, he joined the Computer Science Department at Johns Hopkins as an Assistant Professor in 1989. He was promoted to Associate Professor in 1996, and become a Research Professor in 1999, after joining TIGR. Before switching to bioinformatics and genomics, Dr. Salzberg’s research focused on machine learning and its applications to fields ranging from astronomy to molecular biology. His interest in the human genome project motivated him to develop one of the first computational gene-finding systems for the human genome in the early 1990s. His initial collaborations with TIGR at that time led to the development of a gene-finding program (GLIMMER) that was subsequently used in the analysis of the bacterial genomes of Borrelia burgdorferi (the Lyme disease bacterium), Treponema pallidum (the syphilis bacterium), Mycobacterium tuberculosis, Vibrio cholerae, Bacillus anthracis (anthrax), and hundreds more bacterial and viral organisms that have been sequenced since then. Dr. Salzberg and his research team developed a eukaryotic gene finder, first used for Plasmodium falciparum, the malaria parasite, and later adapted for the human genome, the model plant Arabidopsis thaliana, rice, Cryptococcus neoformans, Brugia malayi, and other species. His group has also developed systems for large-scale genome sequence alignment and genome assembly, including the open-source genome assembler, AMOS. Their open-source systems have been distributed to thousands of scientific laboratories around the globe. In addition to his software systems, Salzberg has contributed analyses to many genome sequencing projects, using computational methods to analyze genome duplications, rearrangements, and other evolutionary phenomena in a wide range of organisms. His current genomics projects include the Influenza Genome Sequencing Project, the first large-scale genomics study of the human and avian influenza A viruses. Dr. Salzberg has authored or co-authored two books and over 150 publications in leading scientific journals. He is a Fellow of the American Association for the Advancement of Science (AAAS) and a member of the Board of Scientific Counselors of the National Center for Biotechnology Information at NIH. He currently serves on the Editorial Boards of the journals BMC Biology, Journal of Computational Biology, PLoS ONE, BMC Genomics, BMC Bioinformatics, Applied Bioinformatics, and Evolutionary Bioinformatics Online. He co-chaired the Third (1999) through the Eighth (2005) Conferences on Computational Genomics. Personal information: Dr. Salzberg is married to Claudia Salzberg (nee Pasche) with two daughters. His hobbies include tennis, golf, and the history of polar exploration.