Mathematical and Computational Approaches in High-Throughput Genomics

September 12 - December 16, 2011

Organizing Committee | Activities | Scientific Overview

Participation | Application | Contact Us

Organizing Committee

Eleazar Eskin (University of California, Los Angeles (UCLA), Computer Science)
Phil Green (University of Washington)
Stanley Nelson (University of California, Los Angeles (UCLA))
Lior Pachter (University of California, Berkeley (UC Berkeley))
Matteo Pellegrini (University of California, Los Angeles (UCLA), Molecular, Cell, and Developmental Biology)
Sebastien Roch (University of California, Los Angeles (UCLA), Mathematics)
Eric Schadt (Pacific Biosciences)
Elizabeth Thompson (University of Washington)
Wing Wong (Stanford University)

Activities

Orientation Day (by invitation only). September 12, 2011.
High-Throughput Genomics Tutorials. September 13 - 16, 2011.
Workshop I: Next-generation Sequencing Technology and Algorithms for Primary Data Analysis. October 3 - 6, 2011.
Workshop II: Transcriptomics and Epigenomics. October 25 - 28, 2011.
Mini-Workshop: Cancer Genomics. October 31 - November 1, 2011.
Workshop III: Evolutionary Genomics. November 15 - 18, 2011.
Workshop IV: Coancestry, Association, and Population Genomics. November 29 - December 2, 2011.
Culminating Workshop at Lake Arrowhead (by invitation only). December 11 - 16, 2011.

There will be an active program of research activities, seminars and workshops throughout the September 12 - December 16, 2011 period and core participants will be in residence at IPAM continuously for these fourteen weeks. The program will open with tutorials, and will be punctuated by four major workshops and a culminating workshop at UCLA’s Lake Arrowhead Conference Center. Several distinguished senior researchers will be in residence for the entire period. Between the workshops there will be a program of activities involving the long-term and short-term participants, as well as visitors.

Scientific Overview

Biological sciences have been transformed over the past two decades by the development of technologies capable of performing large-scale measurements of cellular states. In particular, DNA sequencing instruments have undergone an extraordinary increase in efficiency during the past few years that has reduced the time and cost required to sequence billions of bases by several orders of magnitude. This is revolutionizing the scale and potential applications of genomic studies, and creating an enormous need to develop mathematical and computational infrastructures to meet emerging data analysis challenges. To name just a few examples, applications requiring the development of novel mathematical and statistical frameworks include the reconstruction of RNA transcript populations, identifying sequence variations (both single-nucleotide and segmental) and exploring their disease associations, locating the sites of protein-DNA interactions, elucidating population histories, and reconstructing microbial communities that colonize particular hosts or environmental niches. The goal of this long program is to bring together mathematical and computational scientists, sequencing technology developers in both industry and academia, and the biologists who use the instruments for particular research applications. This presents a unique opportunity to foster interactions between these three communities over an extended period of time and advance the mathematical foundations of this exciting field.

Participation

This long-term program will involve a community of senior and junior researchers. The intent is for participants to learn about new mathematical and computational challenges in genome-scale biology, to meet a diverse group of people, and have ample opportunities to form new collaborations. In addition to these activities, there will be opening tutorials, four workshops, and a culminating workshop at Lake Arrowhead.

Full and partial support for long-term participants is available, and those interested are encouraged to fill out an online application at the bottom of this page. Support for individual workshops will also be available, and may be applied for through the online application for each workshop. We are especially interested in applicants who are interested in becoming core participants and participating in the entire program (September 12 - December 16, 2011), but give consideration to applications for shorter periods. Funding for participants is available at all academic levels, though recent PhD's, graduate students, and researchers in the early stages of their career are especially encouraged to apply.

Encouraging the careers of women and minority mathematicians and scientists is an important component of IPAM's mission and we welcome their applications.

Confirmed Participants

Orly Alter, University of Utah
Yael Baran, Tel Aviv University
Franz Baumdicker, Albert-Ludwigs-Universität Freiburg
Hadassa Brunschwig, The Hebrew University of Jerusalem
Chaochao Cai, University of California, Los Angeles (UCLA)
Dustin Cartwright, Yale University
Peter Chi, University of Washington
Charleston Chiang, University of California, Los Angeles (UCLA)
Francesca Chiaromonte, Pennsylvania State University
Chao Dai, University of Southern California (USC)
Samia Elfékih, Imperial College
Eleazar Eskin, University of California, Los Angeles (UCLA)
Susana Eyheramendy, Pontificia Universidad Catolica de Chile
Simon Foucart, Drexel University
Adam Freedman, University of California, Los Angeles (UCLA)
Nicholas Furlotte, University of California, Los Angeles (UCLA)
Nicolo Fusi, University of Sheffield
Christopher Glazner, University of Washington
David Golan, Tel Aviv University
Catherine Grasso, Oregon Health & Science University
Eran Halperin, Tel Aviv University
Eunjung Han, University of California, Los Angeles (UCLA)
Jo Hardin, Pomona College
Marc Harper, University of California, Los Angeles (UCLA)
Dan He, University of California, Los Angeles (UCLA)
David Heckerman, Microsoft Research
Farhad Hormozdiari, University of California, Los Angeles (UCLA)
Valerie Hower, University of Miami
Warin Isvilanonda, University of California, Los Angeles (UCLA)
Monica Jackson, American University
Marc Jung, City Of Hope
Eun Yong Kang, University of California, Los Angeles (UCLA)
Darren Kessner, University of California, Los Angeles (UCLA)
Aaron Kleinman, University of California, Berkeley (UC Berkeley)
Carolin Kosiol, University of Veterinary Medicine Vienna (Vetmeduni Vienna)
David Koslicki, Oregon State University
Emrah Kostem, University of California, Los Angeles (UCLA)
Martin Kreidl, Universität Duisburg-Essen
Jingyi Li, University of California, Berkeley (UC Berkeley)
David Liberles, University of Wyoming
Jennifer Listgarten, Microsoft Research
Diana Low, BioInformatics Institute
Rui Luo, University of California, Los Angeles (UCLA)
Serghei Mangul, Georgia State University
Tobias Marschall, CWI (Center for Mathematics and Computer Science)
Camila Mazzoni, Berlin Center for Genomics in Biodiversity Research (BeGenDiv)
Paul Medvedev, University of California, San Diego (UCSD)
Jianmin Meng, University of Massachusetts Medical School
Vladimir Minin, University of Washington
Anand Murugan, Princeton University
Nishanth Nair, École Polytechnique Fédérale de Lausanne (EPFL)
Gro Nilsen, University of Oslo
John Novembre, University of Chicago
Vicente Ortega Del Vecchyo, University of California, Los Angeles (UCLA)
Julia Palacios Roman, University of Washington
Juw Won Park, University of Iowa
Nathaniel Parrish, University of California, Los Angeles (UCLA)
Matteo Pellegrini, University of California, Los Angeles (UCLA)
Emiliano Pereira, University of the Republic
Zhaohui Qin, Emory University School of Public Health
Aliz Rao, University of California, Los Angeles (UCLA)
Ben Raphael, Brown University
Hugues Richard, Université de Paris VI (Pierre et Marie Curie)
Sebastien Roch, University of Wisconsin-Madison
Gregory Ryslik, Yale University
Alexander Schoenhuth, CWI (Center for Mathematics and Computer Science)
Shihao Shen, University of California, Los Angeles (UCLA)
Myung Shin Sim, John Wayne Cancer Institute at Saint John's Health Center
Meromit Singer, University of California, Berkeley (UC Berkeley)
Sagi Snir, Haifa University
Marc Suchard, University of California, Los Angeles (UCLA)
Jae Hoon Sul, University of California, Los Angeles (UCLA)
Fengzhu Sun, University of Southern California (USC)
Glenn Tesler, University of California, San Diego (UCSD)
Elizabeth Thompson, University of Washington
Yuan Tian, University of California, Los Angeles (UCLA)
Bridgett vonHoldt, University of California, Irvine (UCI)
Jinkai Wang, University of Iowa
Zhanyong Wang, University of California, Los Angeles (UCLA)
Tandy Warnow, University of Texas at Austin
Daniel Wegmann, University of California, Los Angeles (UCLA)
Yi Xing, University of California, Los Angeles (UCLA)
Wen-Yun Yang, University of California, Los Angeles (UCLA)
Zhiyuan Zhai, Shandong University
Shihua Zhang, Academy of Mathematics and Systems Science, Chinese Academy of Sciences
Xianghong Zhou, University of Southern California (USC)
Piotr Zwiernik, Mittag-Leffler Institute

Contact Us:

Institute for Pure and Applied Mathematics (IPAM)
Attn: GEN2011
460 Portola Plaza
Los Angeles CA 90095-7121
Phone: 310 825-4755
Fax: 310 825-4756
Email: ipam@ucla.edu
Website: http://www.ipam.ucla.edu/programs/gen2011/