2020

A Large-Scale Binding and Functional Map of Human RNA Binding Proteins.
Van Nostrand EL*, Freese P*, Pratt GA*, Wang X*, Wei X*, Xiao R*, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu XD, Lécuyer E, Burge CB, Graveley BR, Yeo GW. (*Joint first authors)
Nature (in press)
ENCODE Phase III: Building an Encyclopaedia of candidate Regulatory Elements for Human and Mouse.
Moore J*, Purcaro MJ*, Pratt HE*, Epstein CB*, Shoresh N*, Adrian J*, Kawli T*, Davis CA*, Dobin A*, Kaul R*, Halow J*, Van Nostrand EL*, Freese P*, Gorkin DU*, He Y*, Mackiewicz M*, et al. (*Joint first authors)
Nature (in press)
Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors.
Wheeler EC, Vu AQ, Einstein JM, DiSalvo M, Ahmed N, Van Nostrand EL, Shishkin AA, Jin W, Allbritton NL, Yeo GW.
Nature Methods. 2020 May 11. PMID: 32393832
An In Vivo Genome-Wide CRISPR Screen Identifies the RNA-Binding Protein Staufen2 as a Key Regulator of Myeloid Leukemia.
Bajaj J, Hamilton M, Shima Y, Chambers K, Spinler K, Van Nostrand EL, Yee BA, Blue S, Chen M, Rizzeri D, Chuah C, Oehler VG, Broome HE, Sasik R, Scott-Browne J, Rao A, Yeo GW, Reya T.
Nature Cancer. 2020. 1, 410–422.
Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.
Van Nostrand EL, Pratt GA, Yee BA, Wheeler EC, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, Sundararaman B, Wang R, Fu XD, Graveley BR, Yeo GW.
Genome Biology. 2020 Apr 6;21(1):90. PMID: 32252787

2019

A protein-RNA interaction atlas of the ribosome biogenesis factor AATF.
Kaiser RW, Ignarski M, Van Nostrand EL, Frese CK, Jain M, Cukoski S, Heinen H, Schaechter M, Seufert L, Bunte K, Frommolt P, Keller P, Helm M, Bohl K, Höhne M, Schermer B, Benzing T, Höpker K, Dieterich C, Yeo GW, Müller RU, Fabretti F.
Scientific Reports. 2019 Jul 30;9(1):11071. PMID: 31363146
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.
Yang EW, Bahn JH, Hsiao EY, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, Yeo GW, Xiao X.
Nature Communications. 2019 Mar 22;10(1):1338. PMID: 30902979
RBP-Maps enables robust generation of splicing regulatory maps.
Yee BA, Pratt GA, Graveley BR, Van Nostrand EL†, Yeo GW†. (†Co-corresponding authors)
RNA. 2019 Feb;25(2):193-204. PMID: 30413564
Regulation of RNA editing by RNA-binding proteins in human cells.
Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brummer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X.
Communications Biology. 2019 Jan 14;2:19. PMID: 30652130
Widespread RNA editing dysregulation in Autism Spectrum Disorders.
Tran S, Jun HI, Bahn JH, Azghadi A, Ramaswami G, Van Nostrand EL, Nguyen TB, Hsiao YE, Lee C, Pratt GA, Martínez-Cerdeño V, Hagerman RJ, Yeo GW, Geschwind DH, Xiao X.
Nature Neuroscience. 2019 Jan;22(1):25-36. PMID: 30559470

2018

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins.
Dominguez D, Freese P, Alexis MS, Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Burge CB.
Molecular Cell. 2018 Jun 7;70(5):854-867.e9. PMID: 29883606

2017

Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism.
Scott DD, Trahan C, Zindy PJ, Aguilar LC, Delubac MY, Van Nostrand EL, Adivarahan S, Wei KE, Yeo GW, Zenklusen D, Oeffinger M.
Nucleic Acids Research. 2017 Oct 23. PMID: 29069457
Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions.
Van Nostrand EL, Shishkin AA, Pratt GA, Nguyen TB, Yeo GW.
Methods. 2017 Aug 5. pii: S1046-2023(16)30441-8. PMID: 28790018
Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).
Van Nostrand EL*, Nguyen TB*, Gelboin-Burkhart C, Wang R, Blue SM, Pratt GA, Louie AL, Yeo GW. (*Joint first authors)
Methods Mol Biol. 2017;1648:177-200. PMID: 28766298
Biallelic mutations in the 3' exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing.
Lardelli RM, Schaffer AE, Eggens VR, Zaki MS, Grainger S, Sathe S, Van Nostrand EL, Schlachetzki Z, Rosti B, Akizu N, Scott E, Silhavy JL, Heckman LD, Rosti RO, Dikoglu E, Gregor A, Guemez-Gamboa A, Musaev D, Mande R, Widjaja A, Shaw TL, Markmiller S, Marin-Valencia I, Davies JH, de Meirleir L, Kayserili H, Altunoglu U, Freckmann ML, Warwick L, Chitayat D, Blaser S, Çağlayan AO, Bilguvar K, Per H, Fagerberg C, Christesen HT, Kibaek M, Aldinger KA, Manchester D, Matsumoto N, Muramatsu K, Saitsu H, Shiina M, Ogata K, Foulds N, Dobyns WB, Chi NC, Traver D, Spaccini L, Bova SM, Gabriel SB, Gunel M, Valente EM, Nassogne MC, Bennett EJ, Yeo GW, Baas F, Lykke-Andersen J, Gleeson JG
Nature Genetics. 2017 Mar;49(3):457-464. PMID: 28092684

2016

CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins.
Van Nostrand EL*, Gelboin-Burkhart C*, Wang R, Pratt GA, Blue SM, Yeo GW. (*Joint first authors)
Methods. 2016 Dec 18. pii: S1046-2023(16)30481-9. PMID: 28003131
Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.
Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang HC, Nussbacher JK, Broski SM, Kim HJ, Lardelli R, Sundararaman B, Donohue JP, Javaherian A, Lykke-Andersen J, Finkbeiner S, Bennett CF, Ares M Jr, Burge CB, Taylor JP, Rigo F, Yeo GW.
Neuron. 2016 Nov 23;92(4):780-795. PMID: 27773581
SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.
Brannan KW, Jin W, Huelga SC, Banks CA, Gilmore JM, Florens L, Washburn MP, Van Nostrand EL, Pratt GA, Schwinn MK, Daniels DL, Yeo GW.
Molecular Cell. 2016 Oct 4. PMID: 27720645
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW.
Nature Methods. 2016 Jun;13(6):508-14. PMID: 27018577
Featured in UCSD News, Biotechniques News, Nature Methods News and Views, Molecular Cell Technology Preview,
Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.
Conway AE*, Van Nostrand EL*, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, Burge CB, Jones DL, Yeo GW. (*Joint first authors)
Cell Reports. 2016 Apr 19;15(3):666-79. PMID: 27068461
Deactivation of the GATA Transcription Factor ELT-2 Is a Major Driver of Normal Aging in C elegans.
Mann FG, Van Nostrand EL, Friedland AE, Liu X, Kim SK.
PLoS Genetics. 2016 Apr;12(4):e1005956. PMID: 27070429
Resources for the Comprehensive Discovery of Functional RNA Elements.
Sundararaman B, Zhan L, Blue SM, Stanton R, Elkins K, Olson S, Wei X, Van Nostrand EL, Pratt GA, Huelga SC, Smalec BM, Wang X, Hong EL, Davidson JM, Lécuyer E, Graveley BR, Yeo GW.
Molecular Cell. 2016 Mar 17;61(6):903-13. PMID: 26990993

2015

The Inflammatory Transcription Factors NFκB, STAT1 and STAT3 Drive Age-Associated Transcriptional Changes in the Human Kidney.
O'Brown ZK, Van Nostrand EL, Higgins JP, Kim SK.
PLoS Genetics. 2015 Dec;11(12):e1005734. PMID: 26678048

2013

Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome.
Zeitz MJ, Lerner PP, Ay F, Van Nostrand E, Heidmann JD, Noble WS, Hoffman AR.
Nucleus. 2013 Dec 5;4(6). PMID: 24448439
Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans.
Van Nostrand EL, Sánchez-Blanco A, Wu B, Nguyen A, Kim SK.
PLoS Genetics. 2013;9(2):e1003325. PMID: 23468654
Integrative analysis of C elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions.
Van Nostrand EL, Kim SK.
Genome Research. 2013 Jun;23(6):941-53. PMID: 23531767

2010

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
Gerstein MB*, Lu ZJ*, Van Nostrand EL*, Cheng C*, Arshinoff BI*, Liu T*, Yip KY*, Robilotto R*, Rechtsteiner A*, Ikegami K*, Alves P*, Chateigner A*, Perry M*, Morris M*, Auerbach RK*, Feng X*, Leng J*, Vielle A*, Niu W*, Rhrissorrakrai K*, et al. (*Joint first authors)
Science. 2010 Dec 24;330(6012):1775-87. PMID: 21177976

2007

Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.
Yeo GW, Van Nostrand EL, Liang TY.
PLoS Genetics. 2007 May 25;3(5):e85. PMID: 17530930

2006

General and specific functions of exonic splicing silencers in splicing control.
Wang Z, Xiao X, Van Nostrand E, Burge CB.
Molecular Cell. 2006 Jul 7;23(1):61-70. PMID: 16797197

2005

Identification and analysis of alternative splicing events conserved in human and mouse.
Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB.
Proceedings of the National Academy of Sciences, USA. 2005 Feb 22;102(8):2850-5. PMID: 15708978
Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).
Van Nostrand EL*, Nguyen TB*, Gelboin-Burkhart C, Wang R, Blue SM, Pratt GA, Louie AL, Yeo GW. (*Joint first authors)
Methods Mol Biol. 2017;1648:177-200. PMID: 28766298

This describes an updated adaptor strategy (seCLIP) to enable single-end sequencing
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW.
Nature Methods. 2016 Jun;13(6):508-14. PMID: 27018577

This is the original eCLIP publication, describing the initial paired-end implementation
A Large-Scale Binding and Functional Map of Human RNA Binding Proteins.
Van Nostrand EL*, Freese P*, Pratt GA*, Wang X*, Wei X*, Xiao R*, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu XD, Lécuyer E, Burge CB, Graveley BR, Yeo GW. (*Joint first authors)
Nature (in press)

Our ENCODE publication describing 223 eCLIP datasets profiling targets of 150 RBPs in K562 and HepG2 cell lines, along with knockdown/RNA-seq, in vitro RNA Bind-N-Seq, ChIP-seq, and immunoflourescence analysis of RBP localization.
Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.
Van Nostrand EL, Pratt GA, Yee BA, Wheeler EC, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, Sundararaman B, Wang R, Fu XD, Graveley BR, Yeo GW.
Genome Biology. 2020 Apr 6;21(1):90. PMID: 32252787

Companion work describing analysis of eCLIP signal at multi-copy RNAs and other repetitive elements, as well as meta-gene analysis of binding distributions for 150 RBPs
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW.
Nature Methods. 2016 Jun;13(6):508-14. PMID: 27018577

This is the original eCLIP publication, describing the initial paired-end implementation and 102 eCLIP experiments released as part of the ENCODE consortium