CBDS Distinguished Speaker Seminar Series: "The Human Genome and Our Genes: How Much Are We Missing?"
How many genes do we have? The Human Genome Project was launched with the promise of revealing all of our genes, the “code” that would help explain our biology. The publication of the genome in 2001 provided only a very rough answer to the question of how many genes we have, and a highly-fragmented draft genome sequence. For more than a decade following, the number of protein-coding genes steadily shrank, but the invention of RNA sequencing revealed a vast new world of splice variants and RNA genes.
In this talk, I will review where we’ve been and where we are today, and I will describe our use of an unprecedentedly large RNA sequencing resource to create a comprehensive new human gene database, containing thousands of novel genes and gene variants. I will describe how we created new, more efficient algorithms to assemble 10,000 human RNA-seq experiments containing nearly 900 billion reads, and then to create a comprehensive new human gene catalog, called CHESS, that contains thousands of novel genes and gene variants. I will also discuss recent breakthroughs that have finally allowed the human genome itself to be completed, and how that effort has revealed hundreds of new genes that were previously hidden in the gaps.
Steven Salzberg is the Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics and the Director of the Center for Computational Biology at Johns Hopkins University. From 2005-2011, he was 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 1997-2005 he was Senior Director of Bioinformatics at The Institute for Genomic Research (TIGR) in Rockville, Maryland, one of the world's leading DNA sequencing centers at the time. Prior to that, from 1989-97 he was an Assistant and Associate Professor of Computer Science at Johns Hopkins.
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.
Early in his career, Dr. Salzberg's 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 work at TIGR in the 1990s led to the development of the bacterial gene finder called Glimmer, which was used in the analysis of thousands of bacterial, archaeal, and viral genomes, including Borrelia burgdorferi (the Lyme disease bacterium), Treponema pallidum (the syphilis bacterium), Mycobacterium tuberculosis, Vibrio cholerae, Bacillus anthracis (anthrax), and many others. He and his lab developed eukaryotic gene finders the human genome, for plants including rice and the model plant Arabidopsis thaliana, and for pathogens including Plasmodium falciparum, the malaria parasite.
Also while at TIGR, Salzberg co-founded the Influenza Genome Sequencing Project, the first large-scale genomics study of human influenza viruses. In 2001 and 2002, he led the computational team that analyzed the genome of the anthrax bacteria used in the 2001 anthrax attacks.
In recent years, Salzberg's lab has focused on next-generation sequence alignment and large-scale genome assembly. They have assembled hundreds of genomes, large and small, and developed several widely-used assembly algorithms. Beginning in 2009, Salzberg and his students introduced several pioneering, highly efficient systems for analysis of next-generation sequencing reads, including the Bowtie, Tophat, and Cufflinks systems, which are now used by thousands of labs around the world. All of the group's software is free and open source, and their systems have been downloaded hundreds of thousands of times.
Dr. Salzberg has authored or co-authored over 300 scientific publications that have garnered over 250,000 citations, and his h-index is 152. He is a member of the American Academy of Arts and Sciences, a Fellow of the American Association for the Advancement of Science (AAAS), and a Fellow of the International Society for Computational Biology (ISCB). He was the 2013 winner of the Benjamin Franklin Award for Open Access in the Life Sciences. In 2001 and each year from 2014 through 2021, he was selected by Thomson Reuters/Clarivate Analytics as a Highly Cited Researcher, a compilation of the 1% most-cited researchers in the world. He also writes a widely-read column at Forbes that focuses on science and pseudoscience.
Steven L. Salzberg, Ph.D.
Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics
Director, Center for Computational Biology
Johns Hopkins University http://salzberg-lab.org
Forbes blog: http://www.forbes.com/sites/stevensalzberg
Johns Hopkins University School of MedicineSteven Salzberg, PhDBloomberg Distinguished Professor, Professor of Biomedical Engineering