Publications by authors named "Eric L Van Nostrand"

33Publications

AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation.

Genes Dev 2020 Oct 10;34(19-20):1330-1344. Epub 2020 Sep 10.

Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1101/gad.339895.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7528705PMC
October 2020

RBP-Maps enables robust generation of splicing regulatory maps.

RNA 2019 02 9;25(2):193-204. Epub 2018 Nov 9.

Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA.

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http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.069237.11
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http://dx.doi.org/10.1261/rna.069237.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348990PMC
February 2019

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins.

Mol Cell 2018 06 7;70(5):854-867.e9. Epub 2018 Jun 7.

Department of Biology, MIT, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062212PMC
June 2018

Isolation versus Enrichment: dCLIP Enables Stringent Profiling of RNA-Binding Sites.

Cell Syst 2017 10;5(4):312-314

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.10.007DOI Listing
October 2017

Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism.

Nucleic Acids Res 2017 Dec;45(21):12509-12528

Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada.

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http://dx.doi.org/10.1093/nar/gkx963DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716212PMC
December 2017

Advances and challenges in the detection of transcriptome-wide protein-RNA interactions.

Wiley Interdiscip Rev RNA 2018 01 29;9(1). Epub 2017 Aug 29.

Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1002/wrna.1436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739989PMC
January 2018

Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions.

Methods 2017 08 5;126:29-37. Epub 2017 Aug 5.

Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Molecular Engineering Laboratory, A*STAR, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2017.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582984PMC
August 2017

CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins.

Methods 2017 04 18;118-119:50-59. Epub 2016 Dec 18.

Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Molecular Engineering Laboratory, A*STAR, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411315PMC
April 2017

Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

Neuron 2016 Nov 20;92(4):780-795. Epub 2016 Oct 20.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Molecular Engineering Laboratory, A(∗)STAR, Singapore 138673, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2016.09.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123850PMC
November 2016

SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

Mol Cell 2016 10 6;64(2):282-293. Epub 2016 Oct 6.

Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Singapore; Molecular Engineering Laboratory, A(∗)STAR, 138673 Singapore, Singapore. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5074894PMC
http://dx.doi.org/10.1016/j.molcel.2016.09.003DOI Listing
October 2016

Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.

Adv Exp Med Biol 2016 ;907:1-28

Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, La Jolla, CA, USA.

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http://link.springer.com/10.1007/978-3-319-29073-7_1
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http://dx.doi.org/10.1007/978-3-319-29073-7_1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522005PMC
July 2017

Deactivation of the GATA Transcription Factor ELT-2 Is a Major Driver of Normal Aging in C. elegans.

PLoS Genet 2016 Apr 12;12(4):e1005956. Epub 2016 Apr 12.

Departments of Genetics and Developmental Biology, Stanford University Medical Center, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829211PMC
April 2016

Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.

Cell Rep 2016 Apr 7;15(3):666-679. Epub 2016 Apr 7.

Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92037, USA; Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92037, USA; Molecular Engineering Laboratory, A(∗)STAR, Singapore 1190777, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 1190777, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.03.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839292PMC
April 2016

The Inflammatory Transcription Factors NFκB, STAT1 and STAT3 Drive Age-Associated Transcriptional Changes in the Human Kidney.

PLoS Genet 2015 Dec 17;11(12):e1005734. Epub 2015 Dec 17.

Department of Developmental Biology, Stanford University, Stanford, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682820PMC
December 2015

Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions.

Genome Res 2013 Jun 26;23(6):941-53. Epub 2013 Mar 26.

Department of Genetics and Department of Developmental Biology, Stanford University Medical Center, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.152876.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668362PMC
June 2013

Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans.

PLoS Genet 2013 28;9(2):e1003325. Epub 2013 Feb 28.

Department of Genetics, Stanford University Medical Center, Stanford, California, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585033PMC
June 2013

Seeing elegance in gene regulatory networks of the worm.

Curr Opin Genet Dev 2011 Dec 29;21(6):776-86. Epub 2011 Sep 29.

Department of Genetics, Stanford University Medical Center, Stanford, CA, USA.

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http://dx.doi.org/10.1016/j.gde.2011.08.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224770PMC
December 2011

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:
Mark B Gerstein Zhi John Lu Eric L Van Nostrand Chao Cheng Bradley I Arshinoff Tao Liu Kevin Y Yip Rebecca Robilotto Andreas Rechtsteiner Kohta Ikegami Pedro Alves Aurelien Chateigner Marc Perry Mitzi Morris Raymond K Auerbach Xin Feng Jing Leng Anne Vielle Wei Niu Kahn Rhrissorrakrai Ashish Agarwal Roger P Alexander Galt Barber Cathleen M Brdlik Jennifer Brennan Jeremy Jean Brouillet Adrian Carr Ming-Sin Cheung Hiram Clawson Sergio Contrino Luke O Dannenberg Abby F Dernburg Arshad Desai Lindsay Dick Andréa C Dosé Jiang Du Thea Egelhofer Sevinc Ercan Ghia Euskirchen Brent Ewing Elise A Feingold Reto Gassmann Peter J Good Phil Green Francois Gullier Michelle Gutwein Mark S Guyer Lukas Habegger Ting Han Jorja G Henikoff Stefan R Henz Angie Hinrichs Heather Holster Tony Hyman A Leo Iniguez Judith Janette Morten Jensen Masaomi Kato W James Kent Ellen Kephart Vishal Khivansara Ekta Khurana John K Kim Paulina Kolasinska-Zwierz Eric C Lai Isabel Latorre Amber Leahey Suzanna Lewis Paul Lloyd Lucas Lochovsky Rebecca F Lowdon Yaniv Lubling Rachel Lyne Michael MacCoss Sebastian D Mackowiak Marco Mangone Sheldon McKay Desirea Mecenas Gennifer Merrihew David M Miller Andrew Muroyama John I Murray Siew-Loon Ooi Hoang Pham Taryn Phippen Elicia A Preston Nikolaus Rajewsky Gunnar Rätsch Heidi Rosenbaum Joel Rozowsky Kim Rutherford Peter Ruzanov Mihail Sarov Rajkumar Sasidharan Andrea Sboner Paul Scheid Eran Segal Hyunjin Shin Chong Shou Frank J Slack Cindie Slightam Richard Smith William C Spencer E O Stinson Scott Taing Teruaki Takasaki Dionne Vafeados Ksenia Voronina Guilin Wang Nicole L Washington Christina M Whittle Beijing Wu Koon-Kiu Yan Georg Zeller Zheng Zha Mei Zhong Xingliang Zhou Julie Ahringer Susan Strome Kristin C Gunsalus Gos Micklem X Shirley Liu Valerie Reinke Stuart K Kim LaDeana W Hillier Steven Henikoff Fabio Piano Michael Snyder Lincoln Stein Jason D Lieb Robert H Waterston

Science 2010 Dec 22;330(6012):1775-87. Epub 2010 Dec 22.

Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/science.1196914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569PMC
December 2010

Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.

PLoS Genet 2007 May 13;3(5):e85. Epub 2007 Apr 13.

Crick-Jacobs Center for Theoretical and Computational Biology, Salk Institute, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0030085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1877881PMC
May 2007