Oct - Lior Pachter¶
Speaker: Lior Pachter
Talk Title: “What do we mean by differential expression?”
Thursday, Oct. 12, 2017 6:00pm
Affiliation: Professor of Computational Biology and Computing and Mathematical Sciences, Caltech
Web-site: Lior Pachter
Lior Pachter received a B.S. in Mathematics from Caltech in 1994, then went to MIT where he was awarded a PhD in applied mathematics in 1999. He then moved to the University of California at Berkeley where he was a postdoctoral researcher (1999-2001), assistant professor (2001-2005), associate professor (2005-2009), and until 2017 the Raymond and Beverly Sackler professor of computational biology and professor of mathematics and molecular and cellular biology with a joint appointment in computer science. Since January 2017 he has been the Bren professor of computational biology at Caltech.
His research interests span the mathematical and biological sciences, and he has authored over 100 research articles in the areas of algorithms, combinatorics, comparative genomics, algebraic statistics, molecular biology and evolution. He has taught a wide range of courses in mathematics, computational biology and genomics. He has also 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 his group.
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 5:00-5:45pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC
- Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L. Pseudoalignment for metagenomic read assignment. Bioinformatics. 2017 Jul 15;33(14):2082-2088 https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx106
- Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nat Methods. 2017 Jul;14(7):687-690https://www.nature.com/nmeth/journal/v14/n7/full/nmeth.4324.html
- Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016 May;34(5):525-7 https://www.nature.com/nbt/journal/v34/n5/full/nbt.3519.html
- Li B, Tambe A, Aviran S, Pachter L. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Syst. 2017 May 24;4(5):568-574.http://www.sciencedirect.com/science/article/pii/S2405471217301394
Introductory Speaker: Shaun Jackman (PhD Candidate, BC Cancer Agency Genome Sciences Centre, Inanc Birol’s Lab)
Title: “Assembling genomes using 10x Genomics linked reads”
(This technology is brought to you by Compute Canada and WestGrid with support from PHSA Telehealth)