Spring 2016

Algorithmic Challenges in Genomics

Jan. 11May 13, 2016

Computational biology has developed dramatically over the last two decades and is now an established discipline with numerous undergraduate and graduate programs available around the world and many conferences, books, and scientific journals. Starting from strong roots in theoretical computer science, over the last decade there has been a dramatic expansion of the bioinformatics community that has drawn in many practitioners with backgrounds in such fields as biology, mathematics, physics, biochemistry, and bioengineering. As a result, a significant part of the bioinformatics community is immersed in data-driven methods, with more emphasis on analysis and less on theory. Consequently, a significant number of bioinformatics researchers today are not very familiar with the theoretically sound developments that originally defined the field of computational biology. This semester-long program aimed to balance the data-driven and theoretical developments in bioinformatics by bringing together leaders and young scientists with strong interests in the algorithmic, methodological, and theoretical aspects of computational biology. Such concentrated activity can be of great benefit both to theoretical computer science, via the exposure to — and infusion of — new problems, and to computational biologists, who get exposed to state-of-the-art theoretical developments and interaction with theorists.

This program focused on three areas, each of which has a natural pull toward algorithmic developments: computational cancer biology, regulatory genomics and epigenomics, and network biology. These areas, each of which was highlighted by a workshop, address problems that are likely to be at the heart of biomedical research in the coming years. The three topics are strongly connected: network biology modeling and analysis techniques are often used in gene regulation studies; considerations of epigenetic and genetic regulation are key in understanding dysregulation of the cancer cell; and pathway- and network-level analysis of the cancer process are becoming more prominent. Hence, a strong synergistic effect emerged among these themes.


Ron Shamir (Tel Aviv University; chair), Ming Li (University of Waterloo), Lior Pachter (UC Berkeley), Pavel Pevzner (UC San Diego)

Long-Term Participants (including Organizers):

Nadav Ahituv (UCSF), Serafim Batzoglou (Stanford University), Niko Beerenwinkel (ETH Zürich), Gill Bejerano (Stanford University), Colin Collins (Vancouver Prostate Center), Thomas Courtade (UC Berkeley), Funda Ergun (Indiana University), Dan Gusfield (UC Davis), Carl Kingsford (Carnegie Mellon University), Martin Kupiec (Tel Aviv University), Florian Markowetz (University of Cambridge), Uwe Ohler (MDC Berlin), Lior Pachter (UC Berkeley), Pavel Pevzner (UC San Diego), Katie Pollard (UCSF), Teresa Przytycka (National Center for Biotechnology Information), Ben Raphael (Brown University), Cenk Sahinalp (Simon Fraser University and University of Indiana, Bloomington), Ron Shamir (Tel Aviv University; chair), Roded Sharan (Tel Aviv University), Donna Slonim (Tufts University), Stephen Smale (City University of Hong Kong), David Tse (Stanford University), Erik van Nimwegen (Universität Basel), Jean-Philippe Vert (MINES ParisTech), Martin Vingron (Max Planck Institute for Molecular Genetics), Michael Waterman (University of Southern California), Zhiping Weng (University of Massachusetts Medical School), Limsoon Wong (National University of Singapore), Jinbo Xu (Toyota Technological Institute at Chicago), Nir Yosef (UC Berkeley)

Research Fellows:

David Amar (Tel Aviv University), Hu Ding (Michigan State University), Iman Hajirasouliha (Stanford University), Hayan Lee (Lawrence Berkeley National Laboratory), Yaron Orenstein (Massachusetts Institute of Technology), Thomas Sakoparnig (University of Basel), Fabio Vandin (University of Padova), Meirav Zehavi (Technion Israel Institute of Technology), Xiuwei Zhang (EMBL-European Bioinformatics Institute)

Visiting Graduate Students and Postdocs:

Judith Abecassis (MINES ParisTech), Simona Cristea (ETH Zürich), David Dynerman (UC Berkeley), Monica Golumbeanu (ETH Zürich), Govinda Kamath (Stanford University), Beyrem Khalfaoui (MINES ParisTech), Marine Le Morvan (MINES ParisTech), Xiaolei Lu (Institute of Statistical Mathematics), Jasmine Nirody (UC Berkeley), Victoria Popic (Stanford University), Manuel Sabin (UC Berkeley)


Tuesday, Jan. 19Friday, Jan. 22, 2016


Ron Shamir (Tel Aviv University)
Monday, Feb. 1Friday, Feb. 5, 2016


Ben Raphael (Brown University; co-chair), Cenk Sahinalp (Simon Fraser University and University of Indiana, Bloomington; co-chair), David Haussler (UC Santa Cruz), Teresa Przytycka (National Center for Biotechnology Information), Daniel Rokhsar (UC Berkeley), Ron Shamir (Tel Aviv University)
Monday, Mar. 7Thursday, Mar. 10, 2016


Martin Vingron (Max Planck Institute for Molecular Genetics; chair), Serafim Batzoglou (Stanford University), Martha Bulyk (Harvard Medical School), Erik van Nimwegen (Universität Basel)
Monday, Apr. 11Friday, Apr. 15, 2016


Mona Singh (Princeton University; chair), Roded Sharan (Tel Aviv University), Donna Slonim (Tufts University)
Tuesday, Jun. 27Friday, Jun. 30, 2017


Ron Shamir (Tel Aviv University; chair), Teresa Przytycka (National Center for Biotechnology Information), Roded Sharan (Tel Aviv University), Martin Vingron (Max Planck Institute for Molecular Genetics)

Program image credits: Ron Shamir and the National Human Genome Research Institute.

Past Internal Program Activities

Wednesday, May 11th, 4:00 pm5:30 pm
Tuesday, May 10th, 2:30 pm3:30 pm
Pavel Pevzner, UC San Diego
Wednesday, May 4th, 4:00 pm5:30 pm
Wednesday, April 27th, 4:00 pm5:30 pm
Meisam Razaviyayn (Stanford)
Tuesday, April 26th, 2:30 pm3:30 pm
Tuesday, April 19th, 2:30 pm3:30 pm
Beyrem Khalfaoui (MINES Paris Tech)
Wednesday, April 6th, 4:00 pm5:30 pm
Hannes Röst (Stanford University)
Tuesday, April 5th, 2:30 pm3:30 pm
Stephen Smale (UC Berkeley)
Wednesday, March 30th, 4:00 pm5:30 pm
Noah Spies (Stanford University)
Thursday, March 24th, 2:00 pm3:30 pm
Piotr Indyk (Massachusetts Institute of Technology)
Wednesday, March 23rd, 4:00 pm5:30 pm
Wednesday, March 16th, 4:00 pm5:30 pm
Steven Brenner (UC Berkeley)
Tuesday, March 15th, 2:30 pm3:30 pm
Sean Simmons (Massachusetts Institute of Technology)
Wednesday, March 2nd, 8:45 am8:00 pm
Thursday, February 25th, 4:00 pm5:30 pm
Anil Raj (Stanford University)
Wednesday, February 17th, 4:00 pm5:30 pm
Rebekah L. Rogers (UC Berkeley)
Tuesday, February 16th, 2:30 pm3:30 pm
Iman Hajirasouliha (Stanford University)
Thursday, February 11th, 4:00 pm5:30 pm
Gregory Valiant (Stanford University)
Tuesday, February 9th, 2:30 pm3:30 pm
Yaron Orenstein (Massachusetts Institute of Technology)
Friday, January 29th, 1:30 pm3:00 pm
David Woodruff (IBM Almaden)
Thursday, January 28th, 4:00 pm5:30 pm
Suyash Satyendra Shringarpure (Stanford University)
Tuesday, January 26th, 2:30 pm3:30 pm
Fabio Vandin (University of Southern Denmark)