Gene Editing Will Transform Cancer Treatment

Learn more about how RNA systems biology will transform cancer treatment.


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

CRSB Seminar, Spring 2016, Jesper Maag: Uncovering the Secrets of Barretts Esophagus and Esophageal Adenocarcinoma

On March 1st, 2016, CRSB and Dr. Mitch O’Connell of Professor Jennifer Doudna’s lab – had the special opportunity to host Jesper Maag, 3rd year doctoral student, visiting us from Garvan Institute/Kinghorn Center in Australia, to present his work titled, “Novel aberrations in Barretts esophagus and esophageal adenocarcinoma.”

Jesper completed this M.S. in pharmaceutical sciences at Uppsala University in Sweden, during this time he had his first sojourn ‘downunder’ working for Dr. Scott Smid at the University of Adelaide studying the role of microglia and the endocannabiniod system in Alzheimer’s disease using a range of cell and molecular biology and biophysical techniques.

After falling in love with Australia, Jesper switched gears and spent a year interning with Marcel Dinger at Garvan Institute/Kinghorn center for clinical genomics. Marcel is a pioneer of using RNA sequencing sometimes coupled with RNA-capture approaches to uncover a plethora of novel ncRNAs and also understanding the dynamic of lncRNA expression during cancer and neurological diseases. Here, Jesper learnt bioinformatics and RNA sequencing and after deciding to stay with Marcel for a PhD, which he is in his 3rd year, he has now become quite the expert.

Jesper spoke eloquently about his recent work on using whole transcriptome sequencing coupled with machine learning and network analysis techniques to uncover novel aberrations in Barretts esophagus and esophageal adenocarcinoma.

Thank you Jesper for sharing this thoughtful research with our team.

Jesper Maag with group 312016Jesper

Sponsorship & Partnerships: What You Can Do to Support CRSB Research

The Center for RNA Systems Biology (CRSB) is comprised of an award winning assembly of UC Berkeley and UC San Francisco faculty, working together to research important systems biology questions.

Innovations discovered by faculty in our Center are recognized for changing the face of genetic research, including CRISPR Cas9, with Drs. Jennifer Doudna and Jonathan Weissman, and research identifying disease related RNA targets with Drs. Ming Hammond, Don Rio, Lior Pachter, Jamie Cate, Steve Brenner, Nicholas Ingolia, Gloria Brar, and Liana Lareau.

Over the course of our center, CRSB has played a role in supporting both small and large grants and seed money to allied programs, projects and initiatives including:  Student Led Computational Seminars, the Center for Computational Biology, both the UC Berkeley RNA and Bay Area RNA Clubs (BARC), funds for the K-12 website out of Dr. Ming Hammond’s lab, SynBerc Diversity conferences, iGEM Undergrad conferences, AMGEN- CRSB Fellowships, Seed Money for Young and Upcoming Faculty, including Drs. Brar, Ingolia and Lareau, as well as funds to support special Post Doctoral Fellowships.  We also provide project and core funds for Drs. Rio, Hammond, Weissman, Arkin, Doudna, Cate, and Brenner.  We fund CRSB Quarterly and Annual Scientific Meetings, as well as travel reimbursement for attendance to high priority conferences.  We also promote training events and share Community Updates through our CRSB Updates e-mail blasts and other collaborative efforts, as well as support for UC Berkeley’s Chancelor’s Advisory Committee on Biology (CACB). 

To bridge the gap and as we fundraise for continued work, we are now putting the call out to our favorite vendors and other interested funders, to help us keep the work going.

How You Can Help

We are interested in pin-point sponsorships to support –

  • CRSB Quarterly/Annual Scientific Meetings
  • Workshop/Symposiums
  • Undergraduate support
  • Post-doc fellowships
  • Seed money for Young Outstanding Affiliated Faculty
  • Team Awards at a Scientific Project Level

Benefits to Sponsors

In exchange, sponsors are invited to Quarterly meetings, Workshops or Symposia; branding and credit on all electronic and written materials linked to the sponsorship – as well as table time at our events. Your sponsorship can help you get the word out about the scientific products that you make that support a worthy mission.

If you have contact information or ideas about who best to solicit sponsorship from in supporting CRSB Research, please contact Brigid by e-mail –