2025

Ahmed S, Fine JL, Chalmers JJ, Kiriakopulos K, Clarke LA, Suárez CC, Soleimanpour K, Oliveros W, Delfosse K, Mokhtaridoost M, Wong CJ, Gingras AC, Ciruna B, Fabian MR, Blencowe BJ, Maass PG. tRNA-overlapping long non-coding RNA loci repress codon-biased genes. Cell Rep. 2025 Oct 9;44(10):116417.
doi: 10.1016/j.celrep.2025.116417

Choi JH, Shpilman I, Mahmood N, Farhangmehr S, Braunschweig U, Cruz NG, Luo J, Ladak RJ, Pistofidis A, Ragoussis J, Schmeing TM, Jafarnejad SM, Blencowe BJ, Sonenberg N. No evidence that human GIGYF2 interacts with GRB10: implications for human disease. Life Sci Alliance. 2025 Jun 16;8(9):e202503334.
doi: 10.26508/lsa.202503334

Poliński P, Miret Cuesta M, Zamora-Moratalla A, Mantica F, Cantero-Recasens G, Viana C, Sabariego-Navarro M, Normanno D, Iñiguez LP, Morenilla-Palao C, Ordoño P, Bonnal S, Ellis JD, Gómez-Riera R, Fanlo-Ucar H, Yap DS, Martínez De Lagrán M, Fernández-Blanco Á, Rodríguez-Marin C, Permanyer J, Fölsz O, Dominguez-Sala E, Sierra C, Legutko D, Wojnacki J, Musoles Lleo JL, Cosma MP, Muñoz FJ, Blencowe BJ, Herrera E, Dierssen M, Irimia M. A highly conserved neuronal microexon in DAAM1 controls actin dynamics, RHOA/ROCK signaling, and memory formation. Nat Commun. 2025 May 6;16(1):4210.
doi: 10.1038/s41467-025-59430-w

Hu D, Thériault BL, Talebian V, Hoffer L, Owen J, Lim J, Blencowe BJ, Lima-Fernandes E, Saraon P, Marcellus R, Al-Awar R. CDC40 suppression induces CDCA5 splicing defects and anti-proliferative effects in lung cancer cells. Sci Rep. 2025 Jan 2;15(1):315.
doi: 10.1038/s41598-024-83337-z

2024

Nabeel-Shah S, Pu S, Burns JD, Braunschweig U, Ahmed N, Burke GL, Lee H, Radovani E, Zhong G, Tang H, Marcon E, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF. C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes. Mol Cell. 2024 Oct 3;84(19):3810-3825.e10.
doi: 10.1016/j.molcel.2024.08.037

Nabeel-Shah S, Pu S, Burke GL, Ahmed N, Braunschweig U, Farhangmehr S, Lee H, Wu M, Ni Z, Tang H, Zhong G, Marcon E, Zhang Z, Blencowe BJ, Greenblatt JF. Recruitment of the m6A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48. Genome Biol. 2024 Sep 19;25(1):246.
doi: 10.1186/s13059-024-03392-7

Lim JJ, Vining KH, Mooney DJ, Blencowe BJ. Matrix stiffness-dependent regulation of immunomodulatory genes in human MSCs is associated with the lncRNA CYTOR. Proc Natl Acad Sci U S A. 2024 Aug 6;121(32):e2404146121.
doi: 10.1073/pnas.2404146121

Best AJ, Braunschweig U, Wu M, Farhangmehr S, Pasculescu A, Lim JJ, Comsa LC, Jen M, Wang J, Datti A, Wrana JL, Cordes SP, Al-Awar R, Han H, Blencowe BJ. High-throughput sensitive screening of small molecule modulators of microexon alternative splicing using dual Nano and Firefly luciferase reporters. Nat Commun. 2024 Jul 27;15(1):6328.
doi: 10.1038/s41467-024-50399-6

Li JD, Taipale M, Blencowe BJ. Efficient, specific, and combinatorial control of endogenous exon splicing with dCasRx-RBM25. Mol Cell. 2024 Jul 11;84(13):2573-2589.e5.
doi: 10.1016/j.molcel.2024.05.028

Wong RW, Balachandran A, Cheung PK, Cheng R, Pan Q, Stoilov P, Harrigan PR, Blencowe BJ, Branch DR, Cochrane A. Correction: An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing. PLoS Pathog. 2024 Apr 9;20(4):e1012155. doi: 10.1371/journal.ppat.1012155. Erratum for: PLoS Pathog. 2020 Feb 18;16(2):e1008307.
doi: 10.1371/journal.ppat.1008307

Ni Z, Ahmed N, Nabeel-Shah S, Guo X, Pu S, Song J, Marcon E, Burke GL, Tong AHY, Chan K, Ha KCH, Blencowe BJ, Moffat J, Greenblatt JF. Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. Nucleic Acids Res. 2024 May 8;52(8):4483-4501.
doi: 10.1093/nar/gkae240

2023

Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt RJ, Gingras AC, Blencowe BJ. Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors. Mol Cell. 2023 Dec 7;83(23):4222-4238.e10.
doi: 10.1016/j.molcel.2023.10.034

Cui H, Diedrich JK, Wu DC, Lim JJ, Nottingham RM, Moresco JJ, Yates JR 3rd, Blencowe BJ, Lambowitz AM, Schimmel P. Publisher Correction: Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2. Nat Cell Biol. 2023 Jul;25(7):1073. doi: 10.1038/s41556-023-01172-2. Erratum for: Nat Cell Biol. 2023 Apr;25(4):592-603.
doi: 10.1038/s41556-023-01118-8

Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR. RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Sci Rep. 2023 Mar 31;13(1):5238.
doi: 10.1038/s41598-023-32245-9

Sinitcyn P, Richards AL, Weatheritt RJ, Brademan DR, Marx H, Shishkova E, Meyer JG, Hebert AS, Westphall MS, Blencowe BJ, Cox J, Coon JJ. Global detection of human variants and isoforms by deep proteome sequencing. Nat Biotechnol. 2023 Dec;41(12):1776-1786.
doi: 10.1038/s41587-023-01714-x

Chan K, Farias AG, Lee H, Guvenc F, Mero P, Brown KR, Ward H, Billmann M, Aulakh K, Astori A, Haider S, Marcon E, Braunschweig U, Pu S, Habsid A, Yan Tong AH, Christie-Holmes N, Budylowski P, Ghalami A, Mubareka S, Maguire F, Banerjee A, Mossman KL, Greenblatt J, Gray-Owen SD, Raught B, Blencowe BJ, Taipale M, Myers C, Moffat J. Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors. Heliyon. 2023 Jan;9(1):e12744.
doi: 10.1016/j.heliyon.2022.e12744

2022

Song J, Nabeel-Shah S, Pu S, Lee H, Braunschweig U, Ni Z, Ahmed N, Marcon E, Zhong G, Ray D, Ha KCH, Guo X, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF. Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1. Mol Cell. 2022 Sep 1;82(17):3135-3150.e9.
doi: 10.1016/j.molcel.2022.06.031

Han H, Best AJ, Braunschweig U, Mikolajewicz N, Li JD, Roth J, Chowdhury F, Mantica F, Nabeel-Shah S, Parada G, Brown KR, O'Hanlon D, Wei J, Yao Y, Zid AA, Comsa LC, Jen M, Wang J, Datti A, Gonatopoulos-Pournatzis T, Weatheritt RJ, Greenblatt JF, Wrana JL, Irimia M, Gingras AC, Moffat J, Blencowe BJ. Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis. Mol Cell. 2022 Aug 18;82(16):2982-2999.e14.
doi: 10.1016/j.molcel.2022.06.036

Fagg WS, Liu N, Braunschweig U, Pereira de Castro KL, Chen X, Ditmars FS, Widen SG, Donohue JP, Modis K, Russell WK, Fair JH, Weirauch MT, Blencowe BJ, Garcia-Blanco MA. Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate. Nucleic Acids Res. 2022 May 20;50(9):5313-5334.
doi: 10.1093/nar/gkac327

Barutcu AR, Wu M, Braunschweig U, Dyakov BJA, Luo Z, Turner KM, Durbic T, Lin ZY, Weatheritt RJ, Maass PG, Gingras AC, Blencowe BJ. Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns. Mol Cell. 2022 Mar 3;82(5):1035-1052.e9.
doi: 10.1016/j.molcel.2021.12.010

Nabeel-Shah S, Lee H, Ahmed N, Burke GL, Farhangmehr S, Ashraf K, Pu S, Braunschweig U, Zhong G, Wei H, Tang H, Yang J, Marcon E, Blencowe BJ, Zhang Z, Greenblatt JF. SARS-CoV-2 nucleocapsid protein binds host mRNAs and attenuates stress granules to impair host stress response. iScience. 2022 Jan 21;25(1):103562.
doi: 10.1016/j.isci.2021.103562

2021

Dumbović G, Braunschweig U, Langner HK, Smallegan M, Biayna J, Hass EP, Jastrzebska K, Blencowe B, Cech TR, Caruthers MH, Rinn JL. Publisher Correction: Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention. Nat Commun. 2021 Oct 21;12(1):6189. doi: 10.1038/s41467-021-26492-5. Erratum for: Nat Commun. 2021 Jun 3;12(1):3308.
doi: 10.1038/s41467-021-23221-w

Ward HN, Aregger M, Gonatopoulos-Pournatzis T, Billmann M, Ohsumi TK, Brown KR, Blencowe BJ, Moffat J, Myers CL. Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline. Nat Protoc. 2021 Oct;16(10):4766-4798.
doi: 10.1038/s41596-021-00596-0

Dumbović G, Braunschweig U, Langner HK, Smallegan M, Biayna J, Hass EP, Jastrzebska K, Blencowe B, Cech TR, Caruthers MH, Rinn JL. Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention. Nat Commun. 2021 Jun 3;12(1):3308. doi: 10.1038/s41467-021-23221-w. Erratum in: Nat Commun. 2021 Oct 21;12(1):6189.
doi: 10.1038/s41467-021-26492-5

Aynaud MM, Hernandez JJ, Barutcu S, Braunschweig U, Chan K, Pearson JD, Trcka D, Prosser SL, Kim J, Barrios-Rodiles M, Jen M, Song S, Shen J, Bruce C, Hazlett B, Poutanen S, Attisano L, Bremner R, Blencowe BJ, Mazzulli T, Han H, Pelletier L, Wrana JL. A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2. Nat Commun. 2021 Mar 3;12(1):1405.
doi: 10.1038/s41467-021-21653-y

Ha KCH, Sterne-Weiler T, Morris Q, Weatheritt RJ, Blencowe BJ. Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity. Nat Commun. 2021 Jan 12;12(1):335.
doi: 10.1038/s41467-020-20483-8

Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell. 2021 Jan 7;81(1):212.
doi: 10.1016/j.molcel.2020.11.028

2020

Gonatopoulos-Pournatzis T, Blencowe BJ. Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder. Curr Opin Genet Dev. 2020 Dec;65:22-33.
doi: 10.1016/j.gde.2020.03.007

Farini D, Cesari E, Weatheritt RJ, La Sala G, Naro C, Pagliarini V, Bonvissuto D, Medici V, Guerra M, Di Pietro C, Rizzo FR, Musella A, Carola V, Centonze D, Blencowe BJ, Marazziti D, Sette C. A Dynamic Splicing Program Ensures Proper Synaptic Connections in the Developing Cerebellum. Cell Rep. 2020 Jun 2;31(9):107703.
doi: 10.1016/j.celrep.2020.107703

Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, Ha KCH, Weiss A, Billmann M, Durbic T, Myers CL, Blencowe BJ, Moffat J. Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform. Nat Biotechnol. 2020 May;38(5):638-648.
doi: 10.1038/s41587-020-0437-z

Rodrigues DC, Mufteev M, Weatheritt RJ, Djuric U, Ha KCH, Ross PJ, Wei W, Piekna A, Sartori MA, Byres L, Mok RSF, Zaslavsky K, Pasceri P, Diamandis P, Morris Q, Blencowe BJ, Ellis J. Shifts in Ribosome Engagement Impact Key Gene Sets in Neurodevelopment and Ubiquitination in Rett Syndrome. Cell Rep. 2020 Mar 24;30(12):4179-4196.e11.
doi: 10.1016/j.celrep.2020.02.107

Wong RW, Balachandran A, Cheung PK, Cheng R, Pan Q, Stoilov P, Harrigan PR, Blencowe BJ, Branch DR, Cochrane A. An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing. PLoS Pathog. 2020 Feb 18;16(2):e1008307. doi: 10.1371/journal.ppat.1008307. Erratum in: PLoS Pathog. 2024 Apr 9;20(4):e1012155.
doi: 10.1371/journal.ppat.1012155

Gonatopoulos-Pournatzis T, Niibori R, Salter EW, Weatheritt RJ, Tsang B, Farhangmehr S, Liang X, Braunschweig U, Roth J, Zhang S, Henderson T, Sharma E, Quesnel-Vallières M, Permanyer J, Maier S, Georgiou J, Irimia M, Sonenberg N, Forman-Kay JD, Gingras AC, Collingridge GL, Woodin MA, Cordes SP, Blencowe BJ. Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions. Mol Cell. 2020 Mar 19;77(6):1176-1192.e16.
doi: 10.1016/j.molcel.2020.01.006

Capponi S, Stöffler N, Irimia M, Van Schaik FMA, Ondik MM, Biniossek ML, Lehmann L, Mitschke J, Vermunt MW, Creyghton MP, Graybiel AM, Reinheckel T, Schilling O, Blencowe BJ, Crittenden JR, Timmers HTM. Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100. RNA Biol. 2020 Jan;17(1):62-74.
doi: 10.1080/15476286.2019.1667214

2019

Ule J, Blencowe BJ. Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. Mol Cell. 2019 Oct 17;76(2):329-345.
doi: 10.1016/j.molcel.2019.09.017

Barutcu AR, Blencowe BJ, Rinn JL. Differential contribution of steady-state RNA and active transcription in chromatin organization. EMBO Rep. 2019 Oct 4;20(10):e48068.
doi: 10.15252/embr.201948068

Andersen RE, Hong SJ, Lim JJ, Cui M, Harpur BA, Hwang E, Delgado RN, Ramos AD, Liu SJ, Blencowe BJ, Lim DA. The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo. Dev Cell. 2019 May 20;49(4):632-642.e7.
doi: 10.1016/j.devcel.2019.04.032

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Consent insufficient for data release-Response. Science. 2019 May 3;364(6439):446.
doi: 10.1126/science.aax7509

Maslon MM, Braunschweig U, Aitken S, Mann AR, Kilanowski F, Hunter CJ, Blencowe BJ, Kornblihtt AR, Adams IR, Cáceres JF. A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes. EMBO J. 2019 May 2;38(9):e101244.
doi: 10.15252/embj.2018101244

Torres-Méndez A, Bonnal S, Marquez Y, Roth J, Iglesias M, Permanyer J, Almudí I, O'Hanlon D, Guitart T, Soller M, Gingras AC, Gebauer F, Rentzsch F, Blencowe BJ, Valcárcel J, Irimia M. A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nat Ecol Evol. 2019 Apr;3(4):691-701.
doi: 10.1038/s41559-019-0813-6

Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL. ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development. Nucleic Acids Res. 2019 Apr 8;47(6):2856-2870.
doi: 10.1093/nar/gkz010

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Toward unrestricted use of public genomic data. Science. 2019 Jan 25;363(6425):350-352.
doi: 10.1126/science.aaw1280

Quesnel-Vallières M, Weatheritt RJ, Cordes SP, Blencowe BJ. Autism spectrum disorder: insights into convergent mechanisms from transcriptomics. Nat Rev Genet. 2019 Jan;20(1):51-63.
doi: 10.1038/s41576-018-0066-2

2018

Gonatopoulos-Pournatzis T, Wu M, Braunschweig U, Roth J, Han H, Best AJ, Raj B, Aregger M, O'Hanlon D, Ellis JD, Calarco JA, Moffat J, Gingras AC, Blencowe BJ. Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons. Mol Cell. 2018 Nov 1;72(3):510-524.e12.
doi: 10.1016/j.molcel.2018.10.008

Sterne-Weiler T, Weatheritt RJ, Best AJ, Ha KCH, Blencowe BJ. Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop. Mol Cell. 2018 Oct 4;72(1):187-200.e6.
doi: 10.1016/j.molcel.2018.08.018

Parikshak NN, Swarup V, Belgard TG, Irimia M, Ramaswami G, Gandal MJ, Hartl C, Leppa V, de la Torre Ubieta L, Huang J, Lowe JK, Blencowe BJ, Horvath S, Geschwind DH. Author Correction: Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature. 2018 Aug;560(7718):E30. doi: 10.1038/s41586-018-0295-8. Erratum for: Nature. 2016 Dec 15;540(7633):423-427.
doi: 10.1038/nature20612

Sharma E, Blencowe BJ. Orchestrating Ribosomal Subunit Coordination to Control Stem Cell Fate. Cell Stem Cell. 2018 Apr 5;22(4):471-473.
doi: 10.1016/j.stem.2018.03.019

Ha KCH, Blencowe BJ, Morris Q. QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data. Genome Biol. 2018 Mar 28;19(1):45.
doi: 10.1186/s13059-018-1414-4

2017

Tapial J, Ha KCH, Sterne-Weiler T, Gohr A, Braunschweig U, Hermoso-Pulido A, Quesnel-Vallières M, Permanyer J, Sodaei R, Marquez Y, Cozzuto L, Wang X, Gómez-Velázquez M, Rayon T, Manzanares M, Ponomarenko J, Blencowe BJ, Irimia M. An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Genome Res. 2017 Oct;27(10):1759-1768.
doi: 10.1101/gr.220962.117

Gueroussov S, Weatheritt RJ, O'Hanlon D, Lin ZY, Narula A, Gingras AC, Blencowe BJ. Regulatory Expansion in Mammals of Multivalent hnRNP Assemblies that Globally Control Alternative Splicing. Cell. 2017 Jul 13;170(2):324-339.e23.
doi: 10.1016/j.cell.2017.06.037

Blencowe BJ. The Relationship between Alternative Splicing and Proteomic Complexity. Trends Biochem Sci. 2017 Jun;42(6):407-408.
doi: 10.1016/j.tibs.2017.04.001

Muñoz MJ, Nieto Moreno N, Giono LE, Cambindo Botto AE, Dujardin G, Bastianello G, Lavore S, Torres-Méndez A, Menck CFM, Blencowe BJ, Irimia M, Foiani M, Kornblihtt AR. Major Roles for Pyrimidine Dimers, Nucleotide Excision Repair, and ATR in the Alternative Splicing Response to UV Irradiation. Cell Rep. 2017 Mar 21;18(12):2868-2879.
doi: 10.1016/j.celrep.2017.02.066

Han H, Braunschweig U, Gonatopoulos-Pournatzis T, Weatheritt RJ, Hirsch CL, Ha KCH, Radovani E, Nabeel-Shah S, Sterne-Weiler T, Wang J, O'Hanlon D, Pan Q, Ray D, Zheng H, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR, Greenblatt JF, Wrana JL, Moffat J, Blencowe BJ. Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors. Mol Cell. 2017 Feb 2;65(3):539-553.e7.
doi: 10.1016/j.molcel.2017.01.011

Balachandran A, Wong R, Stoilov P, Pan S, Blencowe B, Cheung P, Harrigan PR, Cochrane A. Identification of small molecule modulators of HIV-1 Tat and Rev protein accumulation. Retrovirology. 2017 Jan 26;14(1):7.
doi: 10.1186/s12977-017-0330-0

Barrios-Rodiles M, Ellis JD, Blencowe BJ, Wrana JL. LUMIER: A Discovery Tool for Mammalian Protein Interaction Networks. Methods Mol Biol. 2017;1550:137-148.
doi: 10.1007/978-1-4939-6747-6_11

2016

Quesnel-Vallières M, Dargaei Z, Irimia M, Gonatopoulos-Pournatzis T, Ip JY, Wu M, Sterne-Weiler T, Nakagawa S, Woodin MA, Blencowe BJ, Cordes SP. Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders. Mol Cell. 2016 Dec 15;64(6):1023-1034.
doi: 10.1016/j.molcel.2016.11.033

Parikshak NN, Swarup V, Belgard TG, Irimia M, Ramaswami G, Gandal MJ, Hartl C, Leppa V, Ubieta LT, Huang J, Lowe JK, Blencowe BJ, Horvath S, Geschwind DH. Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature. 2016 Dec 15;540(7633):423-427. doi: 10.1038/nature20612. Epub 2016 Dec 5. Erratum in: Nature. 2018 Aug;560(7718):E30.
doi: 10.1038/s41586-018-0295-8

Weatheritt RJ, Sterne-Weiler T, Blencowe BJ. The ribosome-engaged landscape of alternative splicing. Nat Struct Mol Biol. 2016 Dec;23(12):1117-1123.
doi: 10.1038/nsmb.3317

Tahmasebi S, Jafarnejad SM, Tam IS, Gonatopoulos-Pournatzis T, Matta-Camacho E, Tsukumo Y, Yanagiya A, Li W, Atlasi Y, Caron M, Braunschweig U, Pearl D, Khoutorsky A, Gkogkas CG, Nadon R, Bourque G, Yang XJ, Tian B, Stunnenberg HG, Yamanaka Y, Blencowe BJ, Giguère V, Sonenberg N. Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2. Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12360-12367.
doi: 10.1073/pnas.1615540113

Rodrigues DC, Kim DS, Yang G, Zaslavsky K, Ha KC, Mok RS, Ross PJ, Zhao M, Piekna A, Wei W, Blencowe BJ, Morris Q, Ellis J. MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs. Cell Rep. 2016 Oct 11;17(3):720-734.
doi: 10.1016/j.celrep.2016.09.049

Rodor J, Pan Q, Blencowe BJ, Eyras E, Cáceres JF. The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation. RNA. 2016 Sep;22(9):1411-26.
doi: 10.1261/rna.057158.116

Tsalikis J, Pan Q, Tattoli I, Maisonneuve C, Blencowe BJ, Philpott DJ, Girardin SE. The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress. BMC Genomics. 2016 Aug 26;17(1):680.
doi: 10.1186/s12864-016-2999-1

Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N. Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. Elife. 2016 Aug 9;5:e16797.
doi: 10.7554/eLife.16797

Ip JY, Sone M, Nashiki C, Pan Q, Kitaichi K, Yanaka K, Abe T, Takao K, Miyakawa T, Blencowe BJ, Nakagawa S. Gomafu lncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine. Sci Rep. 2016 Jun 2;6:27204.
doi: 10.1038/srep27204

Ennajdaoui H, Howard JM, Sterne-Weiler T, Jahanbani F, Coyne DJ, Uren PJ, Dargyte M, Katzman S, Draper JM, Wallace A, Cazarez O, Burns SC, Qiao M, Hinck L, Smith AD, Toloue MM, Blencowe BJ, Penalva LO, Sanford JR. IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC. Cell Rep. 2016 May 31;15(9):1876-83.
doi: 10.1016/j.celrep.2016.04.083

Sharma E, Sterne-Weiler T, O'Hanlon D, Blencowe BJ. Global Mapping of Human RNA-RNA Interactions. Mol Cell. 2016 May 19;62(4):618-26.
doi: 10.1016/j.molcel.2016.04.030

Dominguez D, Tsai YH, Weatheritt R, Wang Y, Blencowe BJ, Wang Z. An extensive program of periodic alternative splicing linked to cell cycle progression. Elife. 2016 Mar 25;5:e10288.
doi: 10.7554/eLife.10288

Promponas VJ, Katsani KR, Blencowe BJ, Ouzounis CA. Sequence evidence for common ancestry of eukaryotic endomembrane coatomers. Sci Rep. 2016 Mar 2;6:22311.
doi: 10.1038/srep22311

Zhao DY, Gish G, Braunschweig U, Li Y, Ni Z, Schmitges FW, Zhong G, Liu K, Li W, Moffat J, Vedadi M, Min J, Pawson TJ, Blencowe BJ, Greenblatt JF. SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination. Nature. 2016 Jan 7;529(7584):48-53.
doi: 10.1038/nature16469

2015

Merico D, Roifman M, Braunschweig U, Yuen RK, Alexandrova R, Bates A, Reid B, Nalpathamkalam T, Wang Z, Thiruvahindrapuram B, Gray P, Kakakios A, Peake J, Hogarth S, Manson D, Buncic R, Pereira SL, Herbrick JA, Blencowe BJ, Roifman CM, Scherer SW. Compound heterozygous mutations in the noncoding RNU4ATAC cause Roifman Syndrome by disrupting minor intron splicing. Nat Commun. 2015 Nov 2;6:8718.
doi: 10.1038/ncomms9718

Giampietro C, Deflorian G, Gallo S, Di Matteo A, Pradella D, Bonomi S, Belloni E, Nyqvist D, Quaranta V, Confalonieri S, Bertalot G, Orsenigo F, Pisati F, Ferrero E, Biamonti G, Fredrickx E, Taveggia C, Wyatt CD, Irimia M, Di Fiore PP, Blencowe BJ, Dejana E, Ghigna C. The alternative splicing factor Nova2 regulates vascular development and lumen formation. Nat Commun. 2015 Oct 8;6:8479.
doi: 10.1038/ncomms9479

Gueroussov S, Gonatopoulos-Pournatzis T, Irimia M, Raj B, Lin ZY, Gingras AC, Blencowe BJ. An alternative splicing event amplifies evolutionary differences between vertebrates. Science. 2015 Aug 21;349(6250):868-73.
doi: 10.1126/science.aaa8381

Bagherie-Lachidan M, Reginensi A, Pan Q, Zaveri HP, Scott DA, Blencowe BJ, Helmbacher F, McNeill H. Stromal Fat4 acts non-autonomously with Dchs1/2 to restrict the nephron progenitor pool. Development. 2015 Aug 1;142(15):2564-73.
doi: 10.1242/dev.122648

Tomsic J, He H, Akagi K, Liyanarachchi S, Pan Q, Bertani B, Nagy R, Symer DE, Blencowe BJ, de la Chapelle A. A germline mutation in SRRM2, a splicing factor gene, is implicated in papillary thyroid carcinoma predisposition. Sci Rep. 2015 Jul 2;5:10566.
doi: 10.1038/srep10566

Raj B, Blencowe BJ. Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles. Neuron. 2015 Jul 1;87(1):14-27.
doi: 10.1016/j.neuron.2015.05.004

Hirsch CL, Akdemir ZC, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, Xia Z, Salinger AP, Wilson M, Vizeacoumar F, Datti A, Li W, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SY. Corrigendum: Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev. 2015 Jun 15;29(12):1341. doi: 10.1101/gad.266601.115. Erratum for: Genes Dev. 2015 Apr 15;29(8):803-16.
doi: 10.1101/gad.255109.114

Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, Xia Z, Salinger AP, Wilson M, Vizeacoumar F, Datti A, Li W, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SY. Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev. 2015 Apr 15;29(8):803-16. doi: 10.1101/gad.255109.114. Epub 2015 Apr 15. Erratum in: Genes Dev. 2015 Jun 15;29(12):1341.
doi: 10.1101/gad.266601.115

Quesnel-Vallières M, Irimia M, Cordes SP, Blencowe BJ. Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development. Genes Dev. 2015 Apr 1;29(7):746-59.
doi: 10.1101/gad.256115.114

Blencowe BJ. Reflections for the 20th anniversary issue of RNA journal. RNA. 2015 Apr;21(4):573-5.
doi: 10.1261/rna.051003.115

Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, Blencowe BJ, Frey BJ. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science. 2015 Jan 9;347(6218):1254806.
doi: 10.1126/science.1254806

2014

Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, Barrios-Rodiles M, Sternberg MJ, Cordes SP, Roth FP, Wrana JL, Geschwind DH, Blencowe BJ. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell. 2014 Dec 18;159(7):1511-23.
doi: 10.1016/j.cell.2014.11.035

Liu Y, Noon AP, Aguiar Cabeza E, Shen J, Kuk C, Ilczynski C, Ni R, Sukhu B, Chan K, Barbosa-Morais NL, Hermanns T, Blencowe BJ, Azad A, van der Kwast TH, Catto JW, Zlotta AR, Wrana JL. Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer. Eur Urol. 2014 Dec;66(6):982-6.
doi: 10.1016/j.eururo.2014.07.045

Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 2014 Nov;24(11):1774-86.
doi: 10.1101/gr.177790.114

Raj B, Irimia M, Braunschweig U, Sterne-Weiler T, O'Hanlon D, Lin ZY, Chen GI, Easton LE, Ule J, Gingras AC, Eyras E, Blencowe BJ. A global regulatory mechanism for activating an exon network required for neurogenesis. Mol Cell. 2014 Oct 2;56(1):90-103.
doi: 10.1016/j.molcel.2014.08.011

Mansouri S, Pan Q, Blencowe BJ, Claycomb JM, Frappier L. Epstein-Barr virus EBNA1 protein regulates viral latency through effects on let-7 microRNA and dicer. J Virol. 2014 Oct;88(19):11166-77.
doi: 10.1128/JVI.01785-14

Uddin M, Tammimies K, Pellecchia G, Alipanahi B, Hu P, Wang Z, Pinto D, Lau L, Nalpathamkalam T, Marshall CR, Blencowe BJ, Frey BJ, Merico D, Yuen RK, Scherer SW. Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder. Nat Genet. 2014 Jul;46(7):742-7.
doi: 10.1038/ng.2980

Katsani KR, Irimia M, Karapiperis C, Scouras ZG, Blencowe BJ, Promponas VJ, Ouzounis CA. Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins. Sci Rep. 2014 Apr 11;4:4655.
doi: 10.1038/srep04655

2013

Sebé-Pedrós A, Irimia M, Del Campo J, Parra-Acero H, Russ C, Nusbaum C, Blencowe BJ, Ruiz-Trillo I. Regulated aggregative multicellularity in a close unicellular relative of metazoa. Elife. 2013 Dec 24;2:e01287.
doi: 10.7554/eLife.01287

Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013 Jul 11;499(7457):172-7.
doi: 10.1038/nature12311

Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature. 2013 Jun 13;498(7453):241-5.
doi: 10.1038/nature12270

Colak R, Kim T, Michaut M, Sun M, Irimia M, Bellay J, Myers CL, Blencowe BJ, Kim PM. Distinct types of disorder in the human proteome: functional implications for alternative splicing. PLoS Comput Biol. 2013 Apr;9(4):e1003030.
doi: 10.1371/journal.pcbi.1003030

Braunschweig U, Gueroussov S, Plocik AM, Graveley BR, Blencowe BJ. Dynamic integration of splicing within gene regulatory pathways. Cell. 2013 Mar 14;152(6):1252-69.
doi: 10.1016/j.cell.2013.02.034

Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ, Odom DT. Latent regulatory potential of human-specific repetitive elements. Mol Cell. 2013 Jan 24;49(2):262-72.
doi: 10.1016/j.molcel.2012.11.013

2012

Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ. The evolutionary landscape of alternative splicing in vertebrate species. Science. 2012 Dec 21;338(6114):1587-93.
doi: 10.1126/science.1230612

Khare T, Pai S, Koncevicius K, Pal M, Kriukiene E, Liutkeviciute Z, Irimia M, Jia P, Ptak C, Xia M, Tice R, Tochigi M, Moréra S, Nazarians A, Belsham D, Wong AH, Blencowe BJ, Wang SC, Kapranov P, Kustra R, Labrie V, Klimasauskas S, Petronis A. 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nat Struct Mol Biol. 2012 Oct;19(10):1037-43.
doi: 10.1038/nsmb.2372

Blencowe BJ. An exon-centric perspective. Biochem Cell Biol. 2012 Oct;90(5):603-12.
doi: 10.1139/o2012-019

Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ. A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells. 2012 Aug;30(8):1734-45.
doi: 10.1002/stem.1144

Ellis JD, Barrios-Rodiles M, Colak R, Irimia M, Kim T, Calarco JA, Wang X, Pan Q, O'Hanlon D, Kim PM, Wrana JL, Blencowe BJ. Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell. 2012 Jun 29;46(6):884-92.
doi: 10.1016/j.molcel.2012.05.037

Irimia M, Blencowe BJ. Alternative splicing: decoding an expansive regulatory layer. Curr Opin Cell Biol. 2012 Jun;24(3):323-32.
doi: 10.1016/j.ceb.2012.03.005

Martinez NM, Pan Q, Cole BS, Yarosh CA, Babcock GA, Heyd F, Zhu W, Ajith S, Blencowe BJ, Lynch KW. Alternative splicing networks regulated by signaling in human T cells. RNA. 2012 May;18(5):1029-40.
doi: 10.1261/rna.032243.112

2011

Gabut M, Samavarchi-Tehrani P, Wang X, Slobodeniuc V, O'Hanlon D, Sung HK, Alvarez M, Talukder S, Pan Q, Mazzoni EO, Nedelec S, Wichterle H, Woltjen K, Hughes TR, Zandstra PW, Nagy A, Wrana JL, Blencowe BJ. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell. 2011 Sep 30;147(1):132-46.
doi: 10.1016/j.cell.2011.08.023

Han H, Nutiu R, Moffat J, Blencowe BJ. SnapShot: High-throughput sequencing applications. Cell. 2011 Sep 16;146(6):1044, 1044.e1-2.
doi: 10.1016/j.cell.2011.09.002

Raj B, O'Hanlon D, Vessey JP, Pan Q, Ray D, Buckley NJ, Miller FD, Blencowe BJ. Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis. Mol Cell. 2011 Sep 2;43(5):843-50.
doi: 10.1016/j.molcel.2011.08.014

Voineagu I, Wang X, Johnston P, Lowe JK, Tian Y, Horvath S, Mill J, Cantor RM, Blencowe BJ, Geschwind DH. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature. 2011 May 25;474(7351):380-4.
doi: 10.1038/nature10110

Calarco JA, Zhen M, Blencowe BJ. Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts. RNA. 2011 May;17(5):775-91.
doi: 10.1261/rna.2603911

Ip JY, Schmidt D, Pan Q, Ramani AK, Fraser AG, Odom DT, Blencowe BJ. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res. 2011 Mar;21(3):390-401.
doi: 10.1101/gr.111070.110

Saltzman AL, Pan Q, Blencowe BJ. Regulation of alternative splicing by the core spliceosomal machinery. Genes Dev. 2011 Feb 15;25(4):373-84.
doi: 10.1101/gad.2004811

Ramani AK, Calarco JA, Pan Q, Mavandadi S, Wang Y, Nelson AC, Lee LJ, Morris Q, Blencowe BJ, Zhen M, Fraser AG. Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res. 2011 Feb;21(2):342-8.
doi: 10.1101/gr.114645.110

Lahiry P, Lee LJ, Frey BJ, Rupar CA, Siu VM, Blencowe BJ, Hegele RA. Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing. PLoS One. 2011;6(9):e25400.
doi: 10.1371/journal.pone.0025400

Misquitta-Ali CM, Cheng E, O'Hanlon D, Liu N, McGlade CJ, Tsao MS, Blencowe BJ. Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer. Mol Cell Biol. 2011 Jan;31(1):138-50.
doi: 10.1128/MCB.00709-10

2010

Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, Blencowe BJ, Prasanth SG, Prasanth KV. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell. 2010 Sep 24;39(6):925-38.
doi: 10.1016/j.molcel.2010.08.011

McIlwain DR, Pan Q, Reilly PT, Elia AJ, McCracken S, Wakeham AC, Itie-Youten A, Blencowe BJ, Mak TW. Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay. Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12186-91.
doi: 10.1073/pnas.1007336107

Barash Y, Blencowe BJ, Frey BJ. Model-based detection of alternative splicing signals. Bioinformatics. 2010 Jun 15;26(12):i325-33.
doi: 10.1093/bioinformatics/btq200

van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most "dark matter" transcripts are associated with known genes. PLoS Biol. 2010 May 18;8(5):e1000371.
doi: 10.1371/journal.pbio.1000371

Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ. Deciphering the splicing code. Nature. 2010 May 6;465(7294):53-9.
doi: 10.1038/nature09000

Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T. Regulation of alternative splicing by histone modifications. Science. 2010 Feb 19;327(5968):996-1000.
doi: 10.1126/science.1184208

2009

Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ. A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA. 2009 Dec;15(12):2174-85.
doi: 10.1261/rna.1790509

Calarco JA, Superina S, O'Hanlon D, Gabut M, Raj B, Pan Q, Skalska U, Clarke L, Gelinas D, van der Kooy D, Zhen M, Ciruna B, Blencowe BJ. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell. 2009 Sep 4;138(5):898-910.
doi: 10.1016/j.cell.2009.06.012

Kornblihtt AR, Schor IE, Allo M, Blencowe BJ. When chromatin meets splicing. Nat Struct Mol Biol. 2009 Sep;16(9):902-3.
doi: 10.1038/nsmb0909-902

Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR. Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol. 2009 Jul;27(7):667-70.
doi: 10.1038/nbt.1550

Blencowe BJ, Ahmad S, Lee LJ. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev. 2009 Jun 15;23(12):1379-86.
doi: 10.1101/gad.1788009

2008

Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008 Dec;40(12):1413-5.
doi: 10.1038/ng.259

Aznarez I, Barash Y, Shai O, He D, Zielenski J, Tsui LC, Parkinson J, Frey BJ, Rommens JM, Blencowe BJ. A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome Res. 2008 Aug;18(8):1247-58.
doi: 10.1101/gr.073155.107

Saltzman AL, Kim YK, Pan Q, Fagnani MM, Maquat LE, Blencowe BJ. Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol. 2008 Jul;28(13):4320-30.
doi: 10.1128/MCB.00361-08

Gabut M, Chaudhry S, Blencowe BJ. SnapShot: The splicing regulatory machinery. Cell. 2008 Apr 4;133(1):192.e1.
doi: 10.1016/j.cell.2008.03.010

2007

Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD. Using expression profiling data to identify human microRNA targets. Nat Methods. 2007 Dec;4(12):1045-9.
doi: 10.1038/nmeth1130

Calarco JA, Xing Y, Cáceres M, Calarco JP, Xiao X, Pan Q, Lee C, Preuss TM, Blencowe BJ. Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev. 2007 Nov 15;21(22):2963-75.
doi: 10.1101/gad.1606907

Fortes P, Longman D, McCracken S, Ip JY, Poot R, Mattaj IW, Cáceres JF, Blencowe BJ. Identification and characterization of RED120: a conserved PWI domain protein with links to splicing and 3'-end formation. FEBS Lett. 2007 Jun 26;581(16):3087-97.
doi: 10.1016/j.febslet.2007.05.066

Blencowe BJ, Khanna M. Molecular biology: RNA in control. Nature. 2007 May 24;447(7143):391-3.
doi: 10.1038/447391a

Aznarez I, Zielenski J, Rommens JM, Blencowe BJ, Tsui LC. Exon skipping through the creation of a putative exonic splicing silencer as a consequence of the cystic fibrosis mutation R553X. J Med Genet. 2007 May;44(5):341-6.
doi: 10.1136/jmg.2006.045880

Ip JY, Tong A, Pan Q, Topp JD, Blencowe BJ, Lynch KW. Global analysis of alternative splicing during T-cell activation. RNA. 2007 Apr;13(4):563-72.
doi: 10.1261/rna.457207

Babak T, Blencowe BJ, Hughes TR. Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinformatics. 2007 Jan 30;8:33.
doi: 10.1186/1471-2105-8-33

Calarco JA, Saltzman AL, Ip JY, Blencowe BJ. Technologies for the global discovery and analysis of alternative splicing. Adv Exp Med Biol. 2007;623:64-84.
doi: 10.1007/978-0-387-77374-2_5

Fagnani M, Barash Y, Ip JY, Misquitta C, Pan Q, Saltzman AL, Shai O, Lee L, Rozenhek A, Mohammad N, Willaime-Morawek S, Babak T, Zhang W, Hughes TR, van der Kooy D, Frey BJ, Blencowe BJ. Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol. 2007;8(6):R108.
doi: 10.1186/gb-2007-8-6-r108

2006

Ule J, Stefani G, Mele A, Ruggiu M, Wang X, Taneri B, Gaasterland T, Blencowe BJ, Darnell RB. An RNA map predicting Nova-dependent splicing regulation. Nature. 2006 Nov 30;444(7119):580-6.
doi: 10.1038/nature05304

Blencowe BJ. Alternative splicing: new insights from global analyses. Cell. 2006 Jul 14;126(1):37-47.
doi: 10.1016/j.cell.2006.06.023

Shai O, Morris QD, Blencowe BJ, Frey BJ. Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics. 2006 Mar 1;22(5):606-13.
doi: 10.1093/bioinformatics/btk028

López-Bigas N, Blencowe BJ, Ouzounis CA. Highly consistent patterns for inherited human diseases at the molecular level. Bioinformatics. 2006 Feb 1;22(3):269-77.
doi: 10.1093/bioinformatics/bti781

Pan Q, Saltzman AL, Kim YK, Misquitta C, Shai O, Maquat LE, Frey BJ, Blencowe BJ. Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev. 2006 Jan 15;20(2):153-8.
doi: 10.1101/gad.1382806

Hughes TR, Hiley SL, Saltzman AL, Babak T, Blencowe BJ. Microarray analysis of RNA processing and modification. Methods Enzymol. 2006;410:300-16.
doi: 10.1016/S0076-6879(06)10014-2

2005

McCracken S, Longman D, Marcon E, Moens P, Downey M, Nickerson JA, Jessberger R, Wilde A, Caceres JF, Emili A, Blencowe BJ. Proteomic analysis of SRm160-containing complexes reveals a conserved association with cohesin. J Biol Chem. 2005 Dec 23;280(51):42227-36.
doi: 10.1074/jbc.M507410200

Frey BJ, Mohammad N, Morris QD, Zhang W, Robinson MD, Mnaimneh S, Chang R, Pan Q, Sat E, Rossant J, Bruneau BG, Aubin JE, Blencowe BJ, Hughes TR. Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nat Genet. 2005 Sep;37(9):991-6.
doi: 10.1038/ng1630

Babak T, Blencowe BJ, Hughes TR. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics. 2005 Aug 5;6:104.
doi: 10.1186/1471-2164-6-104

Blencowe BJ. Splicing on the brain. Nat Genet. 2005 Aug;37(8):796-7.
doi: 10.1038/ng0805-796

Rosonina E, Ip JY, Calarco JA, Bakowski MA, Emili A, McCracken S, Tucker P, Ingles CJ, Blencowe BJ. Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol Cell Biol. 2005 Aug;25(15):6734-46.
doi: 10.1128/MCB.25.15.6734-6746.2005

Pan Q, Bakowski MA, Morris Q, Zhang W, Frey BJ, Hughes TR, Blencowe BJ. Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet. 2005 Feb;21(2):73-7.
doi: 10.1016/j.tig.2004.12.004

2004

Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, Frey BJ, Blencowe BJ. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell. 2004 Dec 22;16(6):929-41.
doi: 10.1016/j.molcel.2004.12.004

Babak T, Zhang W, Morris Q, Blencowe BJ, Hughes TR. Probing microRNAs with microarrays: tissue specificity and functional inference. RNA. 2004 Nov;10(11):1813-9.
doi: 10.1261/rna.7119904

Lew JM, Fei YL, Aleck K, Blencowe BJ, Weksberg R, Sadowski PD. CDKN1C mutation in Wiedemann-Beckwith syndrome patients reduces RNA splicing efficiency and identifies a splicing enhancer. Am J Med Genet A. 2004 Jun 15;127A(3):268-76.
doi: 10.1002/ajmg.a.30020

Custódio N, Carvalho C, Condado I, Antoniou M, Blencowe BJ, Carmo-Fonseca M. In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA. 2004 Apr;10(4):622-33.
doi: 10.1261/rna.5258504

Rosonina E, Blencowe BJ. Analysis of the requirement for RNA polymerase II CTD heptapeptide repeats in pre-mRNA splicing and 3'-end cleavage. RNA. 2004 Apr;10(4):581-9.
doi: 10.1261/rna.5207204

Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR. The functional landscape of mouse gene expression. J Biol. 2004;3(5):21.
doi: 10.1186/jbiol16

2003

McCracken S, Longman D, Johnstone IL, Cáceres JF, Blencowe BJ. An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation. J Biol Chem. 2003 Nov 7;278(45):44153-60.
doi: 10.1074/jbc.M306856200

Rosonina E, Bakowski MA, McCracken S, Blencowe BJ. Transcriptional activators control splicing and 3'-end cleavage levels. J Biol Chem. 2003 Oct 31;278(44):43034-40.
doi: 10.1074/jbc.M307289200

Aznarez I, Chan EM, Zielenski J, Blencowe BJ, Tsui LC. Characterization of disease-associated mutations affecting an exonic splicing enhancer and two cryptic splice sites in exon 13 of the cystic fibrosis transmembrane conductance regulator gene. Hum Mol Genet. 2003 Aug 15;12(16):2031-40.
doi: 10.1093/hmg/ddg215

Blencowe BJ. Splicing regulation: the cell cycle connection. Curr Biol. 2003 Feb 18;13(4):R149-51.
doi: 10.1016/s0960-9822(03)00079-4

Szymczyna BR, Bowman J, McCracken S, Pineda-Lucena A, Lu Y, Cox B, Lambermon M, Graveley BR, Arrowsmith CH, Blencowe BJ. Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing. Genes Dev. 2003 Feb 15;17(4):461-75.
doi: 10.1101/gad.1060403

2002

Emili A, Shales M, McCracken S, Xie W, Tucker PW, Kobayashi R, Blencowe BJ, Ingles CJ. Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD. RNA. 2002 Sep;8(9):1102-11.
doi: 10.1017/s1355838202025037

Rosonina E, Blencowe BJ. Gene expression: the close coupling of transcription and splicing. Curr Biol. 2002 Apr 30;12(9):R319-21.
doi: 10.1016/s0960-9822(02)00829-1

Blencowe BJ. Transcription: surprising role for an elusive small nuclear RNA. Curr Biol. 2002 Feb 19;12(4):R147-9.
doi: 10.1016/s0960-9822(02)00711-x

McCracken S, Lambermon M, Blencowe BJ. SRm160 splicing coactivator promotes transcript 3'-end cleavage. Mol Cell Biol. 2002 Jan;22(1):148-60.
doi: 10.1128/MCB.22.1.148-160.2002

2001

Longman D, McGarvey T, McCracken S, Johnstone IL, Blencowe BJ, Cáceres JF. Multiple interactions between SRm160 and SR family proteins in enhancer-dependent splicing and development of C. elegans. Curr Biol. 2001 Dec 11;11(24):1923-33.
doi: 10.1016/s0960-9822(01)00589-9

Boucher L, Ouzounis CA, Enright AJ, Blencowe BJ. A genome-wide survey of RS domain proteins. RNA. 2001 Dec;7(12):1693-701.
PMID: 11780626

Rodrigues JP, Rode M, Gatfield D, Blencowe BJ, Carmo-Fonseca M, Izaurralde E. REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus. Proc Natl Acad Sci U S A. 2001 Jan 30;98(3):1030-5.
doi: 10.1073/pnas.98.3.1030

2000

McGarvey T, Rosonina E, McCracken S, Li Q, Arnaout R, Mientjes E, Nickerson JA, Awrey D, Greenblatt J, Grosveld G, Blencowe BJ. The acute myeloid leukemia-associated protein, DEK, forms a splicing-dependent interaction with exon-product complexes. J Cell Biol. 2000 Jul 24;150(2):309-20.
doi: 10.1083/jcb.150.2.309

Blencowe BJ. Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem Sci. 2000 Mar;25(3):106-10.
doi: 10.1016/s0968-0004(00)01549-8

Blencowe BJ, Baurén G, Eldridge AG, Issner R, Nickerson JA, Rosonina E, Sharp PA. The SRm160/300 splicing coactivator subunits. RNA. 2000 Jan;6(1):111-20.
doi: 10.1017/s1355838200991982

Pre-2000

Li Y, Blencowe BJ. Distinct factor requirements for exonic splicing enhancer function and binding of U2AF to the polypyrimidine tract. J Biol Chem. 1999 Dec 3;274(49):35074-9.
doi: 10.1074/jbc.274.49.35074

Eldridge AG, Li Y, Sharp PA, Blencowe BJ. The SRm160/300 splicing coactivator is required for exon-enhancer function. Proc Natl Acad Sci U S A. 1999 May 25;96(11):6125-30.
doi: 10.1073/pnas.96.11.6125

Blencowe BJ, Ouzounis CA. The PWI motif: a new protein domain in splicing factors. Trends Biochem Sci. 1999 May;24(5):179-80.
doi: 10.1016/s0968-0004(99)01387-0

Blencowe BJ, Lamond AI. Purification and depletion of RNP particles by antisense affinity chromatography. Methods Mol Biol. 1999;118:275-87.
doi: 10.1385/1-59259-676-2:275

Blencowe BJ, Bowman JA, McCracken S, Rosonina E. SR-related proteins and the processing of messenger RNA precursors. Biochem Cell Biol. 1999;77(4):277-91.
PMID: 10546891

Blencowe BJ, Issner R, Nickerson JA, Sharp PA. A coactivator of pre-mRNA splicing. Genes Dev. 1998 Apr 1;12(7):996-1009.
doi: 10.1101/gad.12.7.996

Mortillaro MJ, Blencowe BJ, Wei X, Nakayasu H, Du L, Warren SL, Sharp PA, Berezney R. A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix. Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8253-7.
doi: 10.1073/pnas.93.16.8253

Blencowe BJ, Issner R, Kim J, Mccaw P, Sharp PA. New proteins related to the Ser-Arg family of splicing factors. RNA. 1995 Oct;1(8):852-65.
PMID: 7493330

Nickerson JA, Blencowe BJ, Penman S. The architectural organization of nuclear metabolism. Int Rev Cytol. 1995;162A:67-123.
doi: 10.1016/s0074-7696(08)61229-2

Blencowe BJ, Barabino SM. Antisense affinity depletion of RNP particles. Application to spliceosomal snRNPs. Methods Mol Biol. 1995;37:67-76.
doi: 10.1385/0-89603-288-4:67

Blencowe BJ, Nickerson JA, Issner R, Penman S, Sharp PA. Association of nuclear matrix antigens with exon-containing splicing complexes. J Cell Biol. 1994 Nov;127(3):593-607.
doi: 10.1083/jcb.127.3.593

Crispino JD, Blencowe BJ, Sharp PA. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP. Science. 1994 Sep 23;265(5180):1866-9.
doi: 10.1126/science.8091213

Blencowe BJ, Carmo-Fonseca M, Behrens SE, Lührmann R, Lamond AI. Interaction of the human autoantigen p150 with splicing snRNPs. J Cell Sci. 1993 Jul;105 (Pt 3):685-97.
doi: 10.1242/jcs.105.3.685

Ouzounis CA, Blencowe BJ. Bacterial DNA replication initiation factor priA is related to proteins belonging to the 'DEAD-box' family. Nucleic Acids Res. 1991 Dec 25;19(24):6953.
doi: 10.1093/nar/19.24.6953

Lamm GM, Blencowe BJ, Sproat BS, Iribarren AM, Ryder U, Lamond AI. Antisense probes containing 2-aminoadenosine allow efficient depletion of U5 snRNP from HeLa splicing extracts. Nucleic Acids Res. 1991 Jun 25;19(12):3193-8.
doi: 10.1093/nar/19.12.3193

Barabino SM, Blencowe BJ, Ryder U, Sproat BS, Lamond AI. Targeted snRNP depletion reveals an additional role for mammalian U1 snRNP in spliceosome assembly. Cell. 1990 Oct 19;63(2):293-302.
doi: 10.1016/0092-8674(90)90162-8

Sibbald PR, Blencowe BJ. A completely conserved rat U6 snRNA pseudogene coding sequence is sandwiched between a cytochrome c retropseudogene and a LINE-like sequence. Nucleic Acids Res. 1990 Feb 25;18(4):1063.
doi: 10.1093/nar/18.4.1063

Lamond AI, Barabino S, Blencowe BJ, Sproat B, Ryder U. Studying pre-mRNA splicing using antisense 2-OMe RNA oligonucleotides. Mol Biol Rep. 1990;14(2-3):201.
doi: 10.1007/BF00360473

Barabino SM, Sproat BS, Ryder U, Blencowe BJ, Lamond AI. Mapping U2 snRNP--pre-mRNA interactions using biotinylated oligonucleotides made of 2'-OMe RNA. EMBO J. 1989 Dec 20;8(13):4171-8.
doi: 10.1002/j.1460-2075.1989.tb08602.x

Blencowe BJ, Sproat BS, Ryder U, Barabino S, Lamond AI. Antisense probing of the human U4/U6 snRNP with biotinylated 2'-OMe RNA oligonucleotides. Cell. 1989 Nov 3;59(3):531-9.
doi: 10.1016/0092-8674(89)90036-6