Abstract

. The Computational Core will enable the Center to extract RNA cis-regulatory element information in pre-mRNAs and mRNAs, as detected by DMS chemical probing data (Core 1) and protein binding signatures. The combination of RNA structure, phylogenetics, and protein-RNA interactions will make these new computafional tools of great use, both in the Center, and in the wider Systems Biology community.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Specialized Center (P50)
Project #
5P50GM102706-02
Application #
8539509
Study Section
Special Emphasis Panel (ZGM1-CBCB-3)
Project Start
Project End
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
2
Fiscal Year
2013
Total Cost
$196,019
Indirect Cost
$57,777

  Institution

Name
University of California Berkeley
Department
Type
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704

  Publications

Lee, Yeon J; Wang, Qingqing; Rio, Donald C (2018) Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5. Genes Dev 32:1060-1074
Costa, Elizabeth A; Subramanian, Kelly; Nunnari, Jodi et al. (2018) Defining the physiological role of SRP in protein-targeting efficiency and specificity. Science 359:689-692
Jost, Marco; Weissman, Jonathan S (2018) CRISPR Approaches to Small Molecule Target Identification. ACS Chem Biol 13:366-375
Horlbeck, Max A; Xu, Albert; Wang, Min et al. (2018) Mapping the Genetic Landscape of Human Cells. Cell 174:953-967.e22
Friedman, Jonathan R; Kannan, Muthukumar; Toulmay, Alexandre et al. (2018) Lipid Homeostasis Is Maintained by Dual Targeting of the Mitochondrial PE Biosynthesis Enzyme to the ER. Dev Cell 44:261-270.e6
Zhang, Yan; Burkhardt, David H; Rouskin, Silvi et al. (2018) A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation. Mol Cell 70:274-286.e7
Wang, Qingqing; Rio, Donald C (2018) JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns. Proc Natl Acad Sci U S A 115:E8181-E8190
Tambe, Akshay; East-Seletsky, Alexandra; Knott, Gavin J et al. (2018) RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a. Cell Rep 24:1025-1036
Li, Bo; Tambe, Akshay; Aviran, Sharon et al. (2017) PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Syst 4:568-574.e7
Iwasaki, Shintaro; Ingolia, Nicholas T (2017) The Growing Toolbox for Protein Synthesis Studies. Trends Biochem Sci 42:612-624

Showing the most recent 10 out of 53 publications