[[{"fid":"802","view_mode":"embedded_left","fields":{"format":"embedded_left","field_file_image_alt_text[und][0][value]":"Lior Pachter","field_file_image_title_text[und][0][value]":"","field_file_caption_credit[und][0][value]":"","field_file_caption_credit[und][0][format]":"full_html"},"type":"media","link_text":null,"attributes":{"alt":"Lior Pachter","height":293,"width":250,"class":"media-element file-embedded-left"}}]]I will survey a number of recently developed sequencing based assays for functional genomics, and discuss a number of fundamental statistical and computational ideas that make allow for extracting genomic information from sequencing reads.
Examples will be drawn from assays such as RNA-Seq, DMS/SHAPE-Seq, PseudoSeq and iCLIP. I will be discussing work that is joint with Sharon Aviran, Nicolas Bray, Shannon Hateley, Bo Li, Shannon McCurdy, Páll Melsted, Vasilis Ntranos, Harold Pimentel, Akshay Tambe and Lynn Yi.
I was born in Ramat Gan, Israel, and grew up in Pretoria, South Africa where I attended Pretoria Boys High School. After receiving a B.S. in Mathematics from Caltech in 1994, I left for MIT where I was awarded a PhD in applied mathematics in 1999. I then moved to the University of California at Berkeley where I was a postdoctoral researcher (1999-2001), assistant professor (2001-2005), associate professor (2005-2009), and am currently the Raymond and Beverly Sackler professor of computational biology at UC Berkeley and professor of mathematics and molecular and cellular biology with a joint appointment in computer science.
My research interests span the mathematical and biological sciences, and I have authored over 100 research articles in the areas of algorithms, combinatorics, comparative genomics, algebraic statistics, molecular biology and evolution. I've been awarded a National Science Foundation CAREER award, a Sloan Research Fellowship, the Miller Professorship, and a Federal Laboratory Consortium award for the successful technology transfer of widely used sequence alignment software developed in my group.