Dr. Bo Li Brings PROBer to Japan and Beyond

Dr. Bo Li, one of our Center’s expert computational biologists in Dr. Lior Pachter’s lab – Center Grant Core 3, continued to spread the word about PROBer to our members as well as internationally, by attending the 21st Annual Meeting of the RNA Society in Japan, June 28-July 2, 2016, in his presentation titled, “PROBer: a general toolkit for analyzing sequencing-based toeprinting assays.”

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RNA Power: Experts Visit the Center in 2016-2017

This year’s outreach and education planning and activities focus on bringing experts to collaborate and share thinking with our own Center experts. Visitors hail from UC San Diego, Australia National University, The Broad Institute of MIT – Harvard, Stanford, University of Toronto, and Cornell.

Kicking off our NIGMS Grant Year 5, and UC Berkeley academic year, CRSB Post Doc, Dr. Mitch O’Connell of Jennifer Doudna’s lab – Center Grant Project 3, brings the Australia National University stateside with Professor Dr. Thomas Preiss, of Sydney, AU.

Dr. Preiss is an expert in translation complex profile sequencing (TCP-seq) to understand the dynamics of ribosome scanning. Seminar titled, “Translation cycle dynamics and compendia of RNA-protein interactions,” Thursday, September 22nd, 2016.

Professor and CRSB Faculty, Dr. Don Rio brings renowned computational biologist, Dr. Gene Yeo of UC San Diego. Dr. Yeo is an entrepreneur, inventor and expert in the area of RNA, genomics and neurological diseases. Seminar titled, “Insights Into Development and Disease from Protein-RNA Interactions”, Friday, September 23rd, 2016.

Special Symposium with International experts invited to speak in October, including –

Keynote, Dr. Aviv Regev from the Broad Institute of MIT & Harvard, “Quantitative dissection of the RNA life cycle in dynamic immune responses”,

Stanford Team of Professors Howard Y. Chang, “Genome regulation by long noncoding RNAs,” and William Greenleaf, “Building rules for RNA building: the hunt for RNA tertiary structure modules.”

This day’s activities were then followed by a collaboration-building celebratory reception, sponsored by Amgen, Inc.

In December, Center Director, Professor Jamie Cate welcomed Dr. Alex Palazzo, University of Toronto, Professor, Biochemistry presenting, “A tale of two sites: translation in the cytosol and on the endoplasmic reticulum.”

Then,  January 23, 2017, Assistant Professor Ming Hammond hosts Dr. Samie R. Jaffrey, M.D., Ph.D. from Weill Medical College, Cornell University – Department of Pharmacology presenting,  “Imaging RNA and RNA biology with RNA mimics of green fluorescent protein.”


Diversity of High Quality Research: Graduate and Post Doctoral Presentations in RNA Systems Biology 2016

CRSB’s Annual meeting in October, and December Quarterly, included the following exciting presentations and poster titles.

Bo Li, Pachter Lab, PROBer: a general toolkit for analyzing sequencing-based toeprinting assays
James Lloyd, Brenner Lab, Illuminating NMD by polysome fractionation
Dan Santos, Weissman Lab, Synchronous culture reveals translational regulation in budding yeast
Mitchell O’Connell, Doudna Lab, Programmable RNA targeting by CRISPR enzymes
Yeon Lee, Rio Lab, Analysis of the role of RNA chaperone proteins and RNA structure in alternative pre-mRNA splicing decisions
Amy Eisenberg, Brar Lab, Identifying alternate protein isoforms using modified ribosome profiling
Anna Desai, Brenner Lab, Splicing factors form a dense network governed by alternative splicing coupled with nonsense mediated mRNA decay
Courtney French, Brenner Lab, Thousands of targets of nonsense-mediated mRNA decay revealed by transcriptome analysis offer clues to the mechanism in multiple species
Ina Hollerer, Brar Lab, Redefining the meiotic translatome using start site profiling
Jeffrey Hussman, Weissman Lab, Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast
James Lloyd, Brenner Lab, Illuminating nonsense-mediated mRNA decay by polysome fractionation
Qingqing Wang, Rio Lab, The Junction Usage Model (JUM): A method for thorough differential analysis of global alternative pre-mRNA splicing patterns
Alexandra Seletsky, Doudna Lab, Two Distinct RNase Activities of CRISPR-C2c2 Enable Guide RNA Processing and RNA Detection
Robert Tunney, Lareau Lab, Regression modeling and optimization of translation elongation rates
Marina Volegova, Cate Lab, Cancer-associated mRNAs regulated by the HLH motif in human eIF3a
Jongchan Yeo, Hammond Lab, Imaging Single-Cell Dynamics of Cyclic di-GMP in E. coli
Yichi Su, Hammond Lab, Sensing and synthesizing cyclic dinucleotide analogs with potent immunostimulatory activities in human cells
Alex Padron, Ingolia Lab, Finding RNA neighbors in a crowded space: toward proximity sequencing

2015 Fall Seminar Series: CRSB Faculty, Ming Hammond & Visiting Professor, Robert Batey

CRSB Faculty, Professor Ming Hammond kicked off the Fall 2015 Organic/ChemBio Seminar series  on Tuesday, September 15th presenting, “Exploiting riboswitches to study and manipulate bacterial signaling.”

Keep an eye out for Professor Robert Batey, Tuesday, October 13th presenting, “Structure and mechanism of riboswitches and their application to synthetic biology” from University of Colorado-Boulder.

Time & Location: 11 am – Noon, 120 Latimer Hall

3rd Annual Re-Writing Genomes Symposium

August 24th, 2015
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All Hands on Deck! CRSB 3rd Annual Meeting

September 4th, 2015

Coming soon!  Save-the-Date!

We have now set the date for our 3rdAnnual CRSB Meeting where we request that all members and invited guests come and be part of the RNA systems biology conversation.

Time & Location:  

Friday, September 4th, 177 Stanley Hall

8:30 am – 12:30 pm, Light Fare Followed by Presentations

12:30-1:30 pm, Lunch & Poster Session

1:30-2:30, Faculty & Advisory Team Meeting

We are calling for posters and speakers representing each project and core of the program, as well as suggestions for guest presenters.

Please contact CRSB Coordinator, Brigid Acuña at bacuna@berkeley.edu for more information about presenting your latest research, presentation or poster.