ZarLab goes to Catalina Island: 2017 UCLA Bioinformatics IDP Retreat

Several members of our lab recently traveled to Catalina Island for the 2017 UCLA Bioinformatics Interdepartmental Program retreat. Every year, graduate students in the Bioinformatics IDP organize a retreat in southern California for faculty and graduate students to develop research ideas and get to know each other.

This year, Bioinformatics IDP PhD students Kikuye Koyano and Artur Jaroszewicz organized the retreat at the University of Southern California’s Wrigley Marine Science Center in Two Harbors, 20 miles offshore from Los Angeles. The Wrigley Center maintains houses, dormitories, laboratories, waterfront, and conference facilities for environmental scientists and other ventures that support the center’s mission. Situated in Big Fisherman’s Cove, a nearby marine life refuge established in 1989 offers soft clean sediment, kelp forests and a wide diversity of marine life.

During the 3-day retreat, Bioinformatics IDP graduate students presented research papers and held forums on applying for fellowships, writing letters of intent, managing graduate school funding packages, and using campus mental health resources. In addition to science, faculty and students enjoyed hiking the chaparral hills, kayaking in the bay, snorkeling in the kelp forest, and enjoying dinner overlooking the beach in Two Harbors.

Eleazar Eskin joined the retreat as a faculty advisor, along with Jason Ernst, Peipei Ping, Sriram Sankararaman, and Roy Wollman. Rob Brown, a senior graduate student in our lab, helped faculty judge best abstracts and best presentations. Harry Yang, a first-year graduate student in our lab, presented work from one of his first year lab rotations in Kathrin Plath’s lab. Harry’s work addressed developing methods for identifying transcription factors that induce the maturation of neurons. Specifically, his work focused on refining single-cell RNA sequencing methods in a reproducible way and applying the method to neuron-differentiated stem cells and fetal brain samples.

Many thanks to Kikuye and Artur for organizing a very successful and enjoyable retreat!

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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