Over the past few decades, technological developments resulted in the accumulation of large genomic data even within a single experiment. The analysis of these data led to many novel discoveries and medical applications. For this reason, the majority of the biotechnology and pharmaceutical companies today, as well as many labs in academia, include experts in such biological data analysis that is emerging from these technologies. These experts have domain expertise in subfields of genomics such as cancer genomics, statistical genetics, protein structure prediction, computational medicine, metagenomics, and others.

The analysis of these datasets requires the development of methods that are domain-specific. For this reason, over the years, many communities that are dedicated for specific subfields of genomics have emerged. Unfortunately, this resulted in smaller overlap between the different sub-domains, hence for example the statistical genomics community may have a very minimal overlap with the metagenomics community. CGSI was formed in order to bridge this gap; it is a methods-oriented program, where our goal is to create interactions between the different fields of research in computational genomics in a relatively informal setting.

In order to achieve this goal, we structure CGSI in a very non-typical way, resulting in its own unique culture. Specifically, CGSI is a fusion of a summer school and a regular conference. It has the characteristics of a conference since it brings together hundreds of researchers and trainees over a period of a month, and the researchers showcase their latest research. On the other hand, it has the characteristics of a summer school since it is a month long program that involves a combination of tutorial (broader talks that include overview of the field) and research talks, and the talks are long enough to allow for in-depth discussion. Importantly, in CGSI we particularly emphasize the need for interaction between the different individuals; we include social activities that result in ‘ice-breakers’, including a retreat in the mountains of Los Angeles, picnic at the beach, and sport activities that involve both the faculty and the trainees. It is a very informal setting with long coffee breaks that allow for ample discussions.

We are very proud of the faculty in the CGSI community; it is clear that everyone that joins these meetings view them as an opportunity to be part of a larger community. The vast majority of the faculty that join CGSI take an active part in the social events, they spend at least a week at CGSI, and they make an effort to interact with other faculty and trainees from other fields in computational genomics in order to create a sense of a larger methods-based community. We welcome to our community both new and established researchers who are interested in methods development for genomics and medical applications, and who would like to become part of a larger, friendly and intellectually intriguing community.

The institute has its roots in a program called “Mathematical and Computational Approaches in High-Throughput Genomics” which was held in the Institute for Pure and Applied Mathematics (IPAM) that was led by Russ Caflisch at the time. Many of the current CGSI faculty were involved in this program. CGSI was then founded in 2015, when Eleazar Eskin (UCLA), Eran Halperin (UCLA), John Novembre (The University of Chicago), and Ben Raphael (Princeton University) joined forces with the IPAM, with the objective of developing an annual flexible program for improving education and enhancing collaboration in genomics and related fields.

CGSI Program Directors

Eleazar Eskin


Computer Science & Human Genetics | Head of Computational Medicine Department | UCLA

Eran Halperin


Computer Science & Anesthesiology | UCLA

CGSI Organizing Committee 2019

Jessica (Jingyi) Li

Assistant Professor

Statistics, Human Genetics & Biomathematics | UCLA

Sriram Sankararaman

Assistant Professor

Computer Science, Computational Medicine & Human Genetics | UCLA

David Koslicki

Assistant Professor

Mathematics | Penn State University

CGSI Steering Committee

John Novembre


Human Genetics, Ecology & Evolution | University of Chicago

Ben Raphael


Computer Science | Princeton University

Dima Shlyakhtenko


Director of Institute for Pure & Applied Mathematics | UCLA

CGSI Faculty 2019

Can Alkan, Bilkent University David Anastasiu, San Jose State University Sharon Aviran, UC Davis Vineet Bafna, UCSD Lisa Bastarache, Vanderbilt University Gillian Belbin, Icahn School of Medicine at Mount Sinai Dan Benjamin, USC Paul Boutros, UCLA Na Cai, EBI Shai Carmi, Hebrew University of Jerusalem Rayan Chikhi, Institut Pasteur Karen Conneely, Emory University Nancy Cox, Vanderbilt University Jason Ernst, UCLA Eleazar Eskin, UCLA Jonathan Flint, UCLA Michael Gandal, UCLA Nandita Garud, UCLA Simon Gravel, McGill University Casey Greene, University of Pennsylvania Eran Halperin, UCLA Jo Hardin, Pomona College Fereydoun Hormozdiari, UC Davis Haky (Hae Kyung) Im, University of Chicago Iuliana Ionita, Columbia University Hyun Min Kang, University of Michigan Eimear Kenny, Icahn School of Medicine at Mount Sinai David Knowles, Columbia University David Koslicki, Penn State University Smita Krishnaswamy, Yale University Su-In Lee, University of Washington  Jessica (Jingyi) Li, UCLA Wei Li, Baylor College of Medicine Jian Ma, CMU Anna Sapfo Malaspina, SIB & UNIL Nick Mancuso, UCLA Serghei Mangul, USC Jonathan Marchini, Regeneron Genetics Center Siavash Mirarab, UCSD Pejman Mohammadi, Scripps Research Quaid Morris, University of Toronto Magnus Nordborg, GMI, Austria John Novembre, University of Chicago Layla Oesper, Carleton College Bogdan Pasaniuc, UCLA Dana Pe’er, Sloan Kettering Institute Itsik Pe’er, Columbia University Yanjun Qi, University of Virginia Ben Raphael, Princeton University Saharon Rosset, Tel Aviv University Sushmita Roy, WID Cenk Sahinalp, Indiana University Bloomington Sriram Sankararaman, UCLA Michael Schatz, Johns Hopkins University Alexander Schönhuth, CWI, Amsterdam Sagiv Shifman, The Hebrew University of Jerusalem Sagi Snir, University of Haifa Jae-Hoon Sul, UCLA Fabio Vandin, University of Padova Peter Visscher, University of Queensland, Australia Naomi Wray, University of Queensland, Australia Yi Xing, UCLA Noah Zaitlen, UCLA Alex Zelikovsky, Georgia State University James Zou, Stanford University Or Zuk, Hebrew University of Jerusalem

CGSI Staff 2019

Stacey Beggs

Program Director

Stephania Kay

Executive Assistant

Robert Smith

Program Manager

Leticia Ortiz

Communications Manager

CGSI Volunteers 2019