UCLA Launches CGSI with Inaugural Summer Programs

In 2015, Profs. Eleazar Eskin (UCLA), Eran Halperin (UCLA), John Novembre (The University of Chicago), and Ben Raphael (Brown University) created the Computational Genomics Summer Institute (CGSI). A collaboration with the Institute for Pure and Applied Mathematics (IPAM) led by Russ Caflisch, CGSI aims to develop a flexible program for improving education and enhancing collaboration in Bioinformatics research. In summer 2016, the inaugural program included a five-day short course (July 18-22) followed by a three-week long course (July 22 to August 12).

Over the past two decades, technological developments have substantially changed research in Bioinformatics. New methods in DNA sequencing technologies are capable of performing large-scale measurements of cellular states with a lower cost and higher efficiency of computing time. These improvements have revolutionized the potential application of genomic studies toward clinical research and development of novel diagnostic tools and treatments for human disease.

Modern genomic data collection creates an enormous need for mathematical and computational infrastructures capable of analyzing datasets that are increasingly larger in scale and resolution. This poses several unique challenges to researchers in Bioinformatics, an interdisciplinary field that cuts across traditional academic fields of math, statistics, computer science, and biology—and includes private-industry sequence technology developers. Innovation depends on seamless collaboration among scientists with different skill sets, communication styles, and institution-driven career goals. Therefore, impactful Bioinformatics research requires an original framework for doing science that bridges traditional discipline-based academic structures.

The summer 2016 courses combined formal research talks and tutorials with informal interaction and mentorship in order to facilitate exchange among international researchers. Participants in the short program attended five full days packed with lectures, tutorials, and journal clubs covering a variety of cutting-edge techniques. Senior trainees, including advanced graduate students and post-docs, underwent additional training through the long program’s residence program. The extended program enabled these scientists to interact with leading researchers through a mix of structured training programs and flexible time for collaboration with fellow participants and other program faculty.

Collaboration on a wide variety of problem types and research themes facilitated cross-disciplinary communication and networking. During both courses, CGSI participants shared technical skills in coding and data analysis relevant to genetic and epigenetic imputation, fine-mapping of complex traits, linear mixed models, and Bayesian statistics in human, canine, mouse, and bacteria datasets. Scholars at different stages of their careers explored application of these methods, among others, to emerging themes such as cancer, neuropsychiatric disorders, evolutionary adaptation, early human origins, and data privacy.

CGSI instructors and participants established mentor-mentee relationships in computational genomics labs at UCLA, including the ZarLab and Bogdan Lab, while tackling practical problems and laying groundwork for future publications. In addition, participants developed comradery and professional connections while enjoying a full schedule of social activities, including dinners at classic Los Angeles area restaurants, volleyball tournaments in Santa Monica, bike rides along the beach, morning runs around UCLA campus, and even an excursion to see a live production of “West Side Story” at the Hollywood Bowl.

CGSI organizers thank the National Institutes of Health grant GM112625, UCLA Clinical and Translational Science Institute grant UL1TR000124, and IPAM for making this unique program possible. We look forward to fostering more collaboration between mathematicians, computer scientists, biologists, and sequencing technology developers in both industry and academia with future CGSI programs.

Visit the CGSI website for an up-to-date archive of program videos, slides, papers, and more:

Enrollment in 2017 CGSI programs opens this fall with a registration deadline of February 1.

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UCLA Computational Genomics Summer Institute

ipam-logoDear Colleagues,

I am happy to announce the UCLA Computational Genomics Summer Institute, which is a new National Institutes of Health funded program at UCLA jointly hosted with the Institute of Pure and Applied Mathematics (IPAM). The program will take place each summer for one month. The dates for 2016 are July 18th – August 12th.

The program focuses on providing training in methodology development for genomics. We hope that it will be of interest to researchers at all levels. Our program builds upon a successful program hosted by IPAM in 2011 on “Mathematical and Computational Approaches in High Throughput Biology.” IPAM is a national math institute funded by the National Science Foundation.

The program consists of two parts. The first part (July 18th – July 22nd) is the Short Program which is in the format of a short course consisting of lectures from leading researchers in computational genomics. The short program is appropriate for researchers at all levels including both researchers actively involved in methodology development as well as other researchers who want to incorporate a methodology development aspect to their research program.

The second part (July 21st – August 12th) is the Long Program which is a continuation of the Short Program. The program is in the style of a typical long program hosted at IPAM where participants have opportunity to interact and collaborate with each other as well as the leading researchers who will serve as program faculty. The program is targeted toward senior trainees such as senior students or post-docs through established researchers.

Researchers at all levels — students, post-docs, staff researchers, as well as junior and senior faculty — are encouraged to participate in the program. Funding is available to support faculty and participant costs during the program. Because space is limited in the program, we are requiring interested participants and potential program faculty to apply as soon as possible.

Application materials are available on the program website (http://computationalgenomics.bioinformatics.ucla.edu). For questions about the program, interested individuals should email uclacgsi@gmail.com.

The UCLA CGSI Organizing Committee
Eleazar Eskin, UCLA, CGSI Director
Russel Caflisch, UCLA. IPAM Director
Eran Halperin, Tel Aviv University
John Novembre, University of Chicago
Ben Raphael, Brown University

US-Israel Binational Science Foundation and Gilbert Foundation Renew Support

We are very happy to announce the US-Israel Binational Science Foundation (BSF) in partnership with the Gilbert Foundation are renewing support of our collaboration with Eran Halperin’s group in Tel Aviv University. This is our labs oldest active collaboration which began in 2001 when Professor Eskin met Eran Halperin at the RECOMB conference.

Our first joint project in genetics was a collaboration with Eran Halperin in 2003 (who was in Berkeley, CA at the time) on a problem called haplotype phasing and led to the software HAP ((14988101)). That led us to become involved in the first whole-genome map of human variation, which was published on the cover of Science in 2005 ((15718463)). We have continued to work closely and publish together because we have very complementary backgrounds. We came from machine learning and Eran come from theory. We have many joint projects, regular conference calls and visits, and collaborations between our students. One of my Ph.D. students was a post doc in Professor Halperin’s group and one of his post docs was recruited to UCLA as a faculty member.

Many of our most important research contributions have been jointly authored papers. This includes our work on characterizing genetic diversity using spatial ancestry analysis (SPA-(22610118)) and genotyping common and rare variants in very large population studies using overlapping pool sequencing, which can be used for the detection of cancer fusion genes from RNA sequences ((21989232)).

Thanks to the additional funding from BSF, we are expanding our current goals to address the problem of analysis of genetic data in conjunction with other data types such as epigenetic data (changes to the DNA along one’s lifetime) and RNA expression. There is strong evidence that these additional signals can provide more insights to the mechanisms of the disease, for example, epigenetic changes have been shown to be strongly related to certain diseases and environmental effects.

Further, the project enables an exchange of ideas and collaborations between not only myself and Eran but also between our students. Everyone involved benefits from this collaboration of Israeli and American scientists. This is our first BSF project and we are very grateful for the support of our collaboration.

To read the full article on our collaboration and the BSF, please click here.