S
Steven M. Blue
Researcher at University of California, San Diego
Publications - 29
Citations - 2473
Steven M. Blue is an academic researcher from University of California, San Diego. The author has contributed to research in topics: RNA & RNA-binding protein. The author has an hindex of 10, co-authored 23 publications receiving 1549 citations. Previous affiliations of Steven M. Blue include University of California, Berkeley.
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Journal ArticleDOI
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
Eric L. Van Nostrand,Gabriel A. Pratt,Alexander A. Shishkin,Chelsea Gelboin-Burkhart,Mark Y. Fang,Balaji Sundararaman,Steven M. Blue,Thai B. Nguyen,Christine Surka,Keri Elkins,Rebecca Stanton,Frank Rigo,Mitchell Guttman,Gene W. Yeo +13 more
TL;DR: An enhanced CLIP (eCLIP) protocol is developed that decreases requisite amplification by ∼1,000-fold, decreasing discarded PCR duplicate reads by ∼60% while maintaining single-nucleotide binding resolution, and improves specificity in the discovery of authentic binding sites.
Journal ArticleDOI
A large-scale binding and functional map of human RNA-binding proteins
Eric L. Van Nostrand,Peter Freese,Gabriel A. Pratt,Xiaofeng Wang,Xintao Wei,Rui Xiao,Rui Xiao,Steven M. Blue,Jia-Yu Chen,Neal A.L. Cody,Daniel Dominguez,Sara Olson,Balaji Sundararaman,Lijun Zhan,Cassandra Bazile,Louis Philip Benoit Bouvrette,Julie Bergalet,Michael O. Duff,Keri E. Garcia,Chelsea Gelboin-Burkhart,Myles Hochman,Nicole J. Lambert,Hairi Li,Michael P. McGurk,Thai B. Nguyen,Tsultrim Palden,Ines Rabano,Shashank Sathe,Rebecca Stanton,Amanda Su,Ruth Wang,Brian A. Yee,Bing Zhou,Ashley L. Louie,Stefan Aigner,Xiang-Dong Fu,Eric Lécuyer,Eric Lécuyer,Christopher B. Burge,Brenton R. Graveley,Gene W. Yeo +40 more
TL;DR: The spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization are described.
Journal ArticleDOI
Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9
Ranjan Batra,David A. Nelles,Elaine Pirie,Steven M. Blue,Ryan J. Marina,Harrison Wang,Isaac A. Chaim,James D. Thomas,Nigel Zhang,Vu T. Nguyen,Stefan Aigner,Sebastian Markmiller,Guangbin Xia,Kevin D. Corbett,Kevin D. Corbett,Maurice S. Swanson,Gene W. Yeo +16 more
TL;DR: RNA-targeting Cas9 (RCas9) reverses hallmark features of disease including elimination of RNA foci among all conditions studied, reduction of polyglutamine protein products, relocalization of repeat-bound proteins to resemble healthy controls, and efficient reversal of DM1-associated splicing abnormalities in patient myotubes.
Posted ContentDOI
A Large-Scale Binding and Functional Map of Human RNA Binding Proteins
Eric L. Van Nostrand,Peter Freese,Gabriel A. Pratt,Xiaofeng Wang,Xintao Wei,Steven M. Blue,Daniel Dominguez,Neal A.L. Cody,Sara H. Olson,Balaji Sundararaman,Rui Xiao,Lijun Zhan,Cassandra Bazile,Louis Philip Benoit Bouvrette,Jia-Yu Chen,Michael O. Duff,Keri E. Garcia,Chelsea Gelboin-Burkhart,Abigail Hochman,Nicole J. Lambert,Hairi Li,Thai B. Nguyen,Tsultrim Palden,Ines Rabano,Shashank Sathe,Rebecca Stanton,Ashley L. Louie,Stefan Aigner,Julie Bergalet,Bing Zhou,Amanda Su,Ruth Wang,Brian A. Yee,Xiang-Dong Fu,Eric Lécuyer,Christopher B. Burge,Brenton R. Graveley,Gene W. Yeo +37 more
TL;DR: The mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells are described, expanding the catalog of functional elements encoded in the human genome by addition of a large set of elements that function at the RNA level through interaction with RBPs.
Journal ArticleDOI
Resources for the Comprehensive Discovery of Functional RNA Elements
Balaji Sundararaman,Lijun Zhan,Steven M. Blue,Rebecca Stanton,Keri Elkins,Sara Olson,Xintao Wei,Eric L. Van Nostrand,Gabriel A. Pratt,Stephanie C. Huelga,Brendan M. Smalec,Xiaofeng Wang,Eurie L. Hong,Jean M. Davidson,Eric Lécuyer,Brenton R. Graveley,Gene W. Yeo +16 more
TL;DR: A validated repository of 438 commercially available antibodies that interrogate 365 unique RBPs are developed that can characterize subcellular RBP localization and are invaluable to the broad scientific community.