ZarLab goes to Hong Kong 2017 RECOMB Meetings

Last week many members of our group traveled to Hong Kong, China, for the 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017). This year’s meeting, which took place May 3-7, 2017, featured over 300 talks, workshops, and poster presentations on topics from all areas of computational molecular biology.

This year, our group contributed 7 poster presentations, 2 research talks, and 1 research highlight (see below for a complete list). In addition to science, ZarLab members enjoyed traveling about Hong Kong and taking in the food, sights, and bicycle paths.

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Our Papers:

Yue (Ariel) Wu, Farhad Hormozdiari, Jong Wha J Joo and Eleazar Eskin.
Improving imputation accuracy by inferring causal variants in genetic studies
https://link.springer.com/chapter/10.1007/978-3-319-56970-3_19

Elior Rahmani, Regev Schweiger, Liat Shenhav, Eleazar Eskin and Eran Halperin.
A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference
https://link.springer.com/chapter/10.1007/978-3-319-56970-3_13

 

Our Highlights:

Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh, Esteban Burchard, Eleazar Eskin, James Zou and Eran Halperin
Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies

 

Our Posters:

Yue (Ariel) Wu, Eleazar Eskin and Sriram Sankararaman
Improving imputation by maximizing power

Lisa Gai, Dat Duong and Eleazar Eskin
Finding associated variants in genome-wide associations studies on multiple traits

Harry Taegyun Yang, Serghei Mangul, Noah Zaitlen, Sagiv Shifman and Eleazar Eskin
Repeat Elements Profile Across Different Tissues in GTEx Samples

Dat Duong, Lisa Gai, Sagi Snir, Eun Yong Kang, Buhm Han, Jae Hoon Sul and Eleazar Eskin
Applying meta-analysis to Genotype-Tissue Expression data from multiple tissues to identify eQTLs and increase the number of eGenes

Jennifer Zou, Farhad Hormozdiari, Jason Ernst, Jae-Hoon Sul and Eleazar Eskin
Leveraging allele-specific expression to improve fine-mapping for eQTL studies

Serghei Mangul, Igor Mandric, Alex Zelikovsky and Eleazar Eskin
Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing

Robert Brown, Eleazar Eskin and Bogdan Pasaniuc
Haplotype-based eQTL Mapping Increases Power to Identify eGenes

Advice to Scientists and Writing Tips

We have published numerous blog posts on managing scientific labs, writing papers, and strategizing a graduate career. Articles presenting our advice on these subjects have become the top-viewed posts on our website. Moving forward, we will be organizing the ZarLab website to feature this content. We believe that the practices and strategies described in these posts have greatly improved our productivity and advanced our careers. While our posts are written with Bioinformatics in mind, the concepts can be applied broadly to careers across STEM fields.

Here we present a summary of the posts that provide advice to scientists.

Writing Tips

Advice for Scientists

Bioinformatics Training 

ZarLab Thesis Defenses

Review Articles

Register Now for UCLA Computational Genomics Summer Institute 2017

CGSI brings together mathematical and computational scientists, sequencing technology developers in both industry and academia, and the biologists who use the instruments for particular research applications. Research talks, workshops, journal clubs, and social events provide 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.

SHORT PROGRAM: July 10 – 14, 2017
LONG PROGRAM: July 6 – 26, 2017
@ UCLA Campus, Los Angeles

Visit our website to learn more:
http://computationalgenomics.bioinformatics.ucla.edu/

REGISTRATION IS OPEN

Register now for this upcoming summer’s Short and Long Courses:
http://bit.ly/2017CGSIapplication
The deadline to register for the 2017 programs is February 1, 2017.

Overview

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.

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.

Organizers

Eleazar Eskin
University of California, Los Angeles
CGSI Director

Eran Halperin
University of California, Los Angeles
CGSI Director

Russ Caflisch
University of California, Los Angeles
IPAM Director

John Novembre
University of Chicago

Ben Raphael
Brown University

Francesca Chiaromonte
Penn State University

2017 Faculty

Note: This is a list of confirmed faculty for the 2017 programs, as of Jan. 20. We will expand this list in coming weeks.

Kin Fai Au, University of Iowa domain-tiniest
Brian Browning, University of Washington domain-tiniest
Jason Ernst, UCLA domain-tiniest
Eleazar Eskin, UCLA domain-tiniest
Jonathan Flint, UCLA domain-tiniest
Ilan Gronau, Herzliya Interdisciplinary Center domain-tiniest
Eran Halperin, UCLA domain-tiniest
Jo Hardin, Pomona College domain-tiniest
Fereydoun Hormozdiari, University of California, Davis domain-tiniest
David Koslicki, Oregon State University domain-tiniest
Jessica (Jingyi) Li, UCLA + IPAM domain-tiniest
Jennifer Listgarten, Microsoft Research domain-tiniest
Kirk Lohmueller, UCLA domain-tiniest
John Novembre, University of Chicago domain-tiniest
Lior Pachter, University of California, Berkeley domain-tiniest
Bogdan Pasaniuc, UCLA domain-tiniest
Ben Raphael, Princeton University domain-tiniest
Gunnar Rätsch, Eidgenössische Technische Hochschule Zürich domain-tiniest
Saharon Rosset, Tel Aviv University domain-tiniest
Cenk Sahinalp, Simon Fraser University domain-tiniest
Sriram Sankararaman, UCLA domain-tiniest
Alexander Schönhuth, Centrum Wiskunde & Informatica, Amsterdam and UCLA IPAM domain-tiniest
Sagi Snir, University of Haifa domain-tiniest
Jae-Hoon Sul, UCLA domain-tiniest
Fabio Vandin, University of Padova domain-tiniest
Daniel Wegmann, Université de Fribourg domain-tiniest
William (Xiaoquan) Wen, University of Michigan domain-tiniest
Noah Zaitlen, University of California San Francisco domain-tiniest
Alex Zelikovsky, Georgia State University domain-tiniest
Or Zuk, Hebrew University of Jerusalem domain-tiniest

CGSI is made possible by National Institutes of Health grant GM112625.

Read more about CGSI’s 2016 programs at the ZarLab blog: http://www.zarlab.xyz/ucla-launches-cgsi-with-inaugural-summer-programs/.