2023

Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation
Xu A, Liu M, Huang MF, Zhang Y, Hu R, Gingold JA, Liu Y, Zhu D, Chien CS, Wang WC, Liao Z, Yuan F, Hsu CW, Tu J, Yu Y, Rosen T, Xiong F, Jia P, Yang YP, Bazer DA, Chen YW, Li W, Huff CD, Zhu JJ, Aguilo F, Chiou SH, Boles NC, Lai CC, Hung MC, Zhao Z, Van Nostrand EL, Zhao R, Lee DF.
Nature Communications 2023 Mar 27;14(1):1694. PMID: 36973285
Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death.
Arif W, Mathur B, Saikali MF, Chembazhi UV, Toohill K, Song YJ, Hao Q, Karimi S, Blue SM, Yee BA, Van Nostrand EL, Bangru S, Guzman G, Yeo GW, Prasanth KV, Anakk S, Cummins CL, Kalsotra A.
Nature Communications 2023 Feb 9;14(1):551. PMID: 36759613
RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins.
Benoit Bouvrette LP, Wang X, Boulais J, Kong J, Syed EU, Blue SM, Zhan L, Olson S, Stanton R, Wei X, Yee B, Van Nostrand EL, Fu XD, Burge CB, Graveley BR, Yeo GW, Lécuyer E.
Nucleic Acids Research 2023 Jan 6;51(D1):D1549-D1557. PMID: 36321651

2022

Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP
Manakov SA^, Shishkin AA^, Yee BA, Shen KA, Cox DC, Park SS, Foster HM, Chapman KB, Yeo GW*, Van Nostrand EL*
BioRXiv
Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq
Blue SM, Yee BA, Pratt GA, Mueller JR, Park SS, Shishkin AA, Starner AC, Van Nostrand EL, Yeo GW.
Nature Protocols 2022 Mar 23. PMID: 35322209
Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML
Krivdova G, Voisin V, Schoof EM, Marhon SA, Murison A, McLeod JL, Gabra MM, Zeng AGX, Aigner S, Yee BA, Shishkin AA, Van Nostrand EL, Hermans KG, Trotman-Grant AC, Mbong N, Kennedy JA, Gan OI, Wagenblast E, De Carvalho DD, Salmena L, Minden MD, Bader GD, Yeo GW, Dick JE, Lechman ER.
Cell Reports 2022 Mar 8;38(10):110481. PMID: 35263585

2021

Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop
Alexander RP, Kitchen RR, Tosar JP, Roth M, Mestdagh P, Max KEA, Rozowsky J, Kaczor-Urbanowicz KE, Chang J, Balaj L, Losic B, Van Nostrand EL, LaPlante E, Mateescu B, White BS, Yu R, Milosavljevic A, Stolovitzky G, Spengler RM.
Frontiers in Genetics 2022 Jan 3;12:778416. PMID: 35047007
ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses
Herzner AM, Khan Z, Van Nostrand EL, Chan S, Cuellar T, Chen R, Pechuan-Jorge X, Komuves L, Solon M, Modrusan Z, Haley B, Yeo GW, Behrens TW, Albert ML.
Journal of Experimental Medicine 2021 Sep 6;218(9):e20201833. PMID: 34297039

2020

Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program
Bieging-Rolett KT, Kaiser AM, Morgens DW, Boutelle AM, Seoane JA, Van Nostrand EL, Zhu C, Houlihan SL, Mello SS, Yee BA, McClendon J, Pierce SE, Winters IP, Wang M, Connolly AJ, Lowe SW, Curtis C, Yeo GW, Winslow MM, Bassik MC, Attardi LD.
Molecular Cell. 2020 Nov 5. PMID: 33157015
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation
Van Nostrand JL, Hellberg K, Luo EC, Van Nostrand EL, Dayn A, Yu J, Shokhirev MN, Dayn Y, Yeo GW, Shaw RJ.
Genes & Development. 2020 Oct 1. PMID: 32912901
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. 2020 Jul. PMID: 32728246
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium, 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. (*Equal contribution)
Nature. 2020 Jul. PMID: 32728249
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
Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq
Blue SM, Yee BA, Pratt GA, Mueller JR, Park SS, Shishkin AA, Starner AC, Van Nostrand EL, Yeo GW.
Nature Protocols 2022 Mar 23. PMID: 35322209

An updated seCLIP protocol, incorporating both experimental improvements as well as a full description of our current analysis pipeline
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. 2020 Jul. PMID: 32728246

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