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Items: 1 to 50 of 145

1.

Autism spectrum disorder: insights into convergent mechanisms from transcriptomics.

Quesnel-Vallières M, Weatheritt RJ, Cordes SP, Blencowe BJ.

Nat Rev Genet. 2019 Jan;20(1):51-63. doi: 10.1038/s41576-018-0066-2. Review.

PMID:
30390048
2.

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons.

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.

Mol Cell. 2018 Nov 1;72(3):510-524.e12. doi: 10.1016/j.molcel.2018.10.008.

PMID:
30388412
3.

Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop.

Sterne-Weiler T, Weatheritt RJ, Best AJ, Ha KCH, Blencowe BJ.

Mol Cell. 2018 Oct 4;72(1):187-200.e6. doi: 10.1016/j.molcel.2018.08.018. Epub 2018 Sep 13.

PMID:
30220560
4.

Author Correction: Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism.

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.

Nature. 2018 Aug;560(7718):E30. doi: 10.1038/s41586-018-0295-8.

PMID:
29995847
5.

Orchestrating Ribosomal Subunit Coordination to Control Stem Cell Fate.

Sharma E, Blencowe BJ.

Cell Stem Cell. 2018 Apr 5;22(4):471-473. doi: 10.1016/j.stem.2018.03.019.

PMID:
29625061
6.

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data.

Ha KCH, Blencowe BJ, Morris Q.

Genome Biol. 2018 Mar 28;19(1):45. doi: 10.1186/s13059-018-1414-4.

7.

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms.

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.

Genome Res. 2017 Oct;27(10):1759-1768. doi: 10.1101/gr.220962.117. Epub 2017 Aug 30.

8.

Regulatory Expansion in Mammals of Multivalent hnRNP Assemblies that Globally Control Alternative Splicing.

Gueroussov S, Weatheritt RJ, O'Hanlon D, Lin ZY, Narula A, Gingras AC, Blencowe BJ.

Cell. 2017 Jul 13;170(2):324-339.e23. doi: 10.1016/j.cell.2017.06.037.

9.

The Relationship between Alternative Splicing and Proteomic Complexity.

Blencowe BJ.

Trends Biochem Sci. 2017 Jun;42(6):407-408. doi: 10.1016/j.tibs.2017.04.001. Epub 2017 May 5. No abstract available.

PMID:
28483376
10.

Major Roles for Pyrimidine Dimers, Nucleotide Excision Repair, and ATR in the Alternative Splicing Response to UV Irradiation.

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.

Cell Rep. 2017 Mar 21;18(12):2868-2879. doi: 10.1016/j.celrep.2017.02.066.

11.

LUMIER: A Discovery Tool for Mammalian Protein Interaction Networks.

Barrios-Rodiles M, Ellis JD, Blencowe BJ, Wrana JL.

Methods Mol Biol. 2017;1550:137-148. doi: 10.1007/978-1-4939-6747-6_11.

PMID:
28188528
12.

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors.

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.

Mol Cell. 2017 Feb 2;65(3):539-553.e7. doi: 10.1016/j.molcel.2017.01.011.

13.

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders.

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.

Mol Cell. 2016 Dec 15;64(6):1023-1034. doi: 10.1016/j.molcel.2016.11.033.

14.

Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism.

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.

Nature. 2016 Dec 15;540(7633):423-427. doi: 10.1038/nature20612. Epub 2016 Dec 5. Erratum in: Nature. 2018 Aug;560(7718):E30.

PMID:
27919067
15.

The ribosome-engaged landscape of alternative splicing.

Weatheritt RJ, Sterne-Weiler T, Blencowe BJ.

Nat Struct Mol Biol. 2016 Dec;23(12):1117-1123. doi: 10.1038/nsmb.3317. Epub 2016 Nov 7.

16.

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2.

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.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12360-12367. Epub 2016 Oct 24.

17.

Preferential binding of a stable G3BP ribonucleoprotein complex to intron-retaining transcripts in mouse brain and modulation of their expression in the cerebellum.

Martin S, Bellora N, González-Vallinas J, Irimia M, Chebli K, de Toledo M, Raabe M, Eyras E, Urlaub H, Blencowe BJ, Tazi J.

J Neurochem. 2016 Nov;139(3):349-368. doi: 10.1111/jnc.13768. Epub 2016 Oct 18.

18.

MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs.

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.

Cell Rep. 2016 Oct 11;17(3):720-734. doi: 10.1016/j.celrep.2016.09.049.

19.

The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress.

Tsalikis J, Pan Q, Tattoli I, Maisonneuve C, Blencowe BJ, Philpott DJ, Girardin SE.

BMC Genomics. 2016 Aug 26;17:680. doi: 10.1186/s12864-016-2999-1.

20.

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians.

Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N.

Elife. 2016 Aug 9;5. pii: e16797. doi: 10.7554/eLife.16797.

21.

The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation.

Rodor J, Pan Q, Blencowe BJ, Eyras E, Cáceres JF.

RNA. 2016 Sep;22(9):1411-26. doi: 10.1261/rna.057158.116. Epub 2016 Jun 30.

22.

Gomafu lncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine.

Ip JY, Sone M, Nashiki C, Pan Q, Kitaichi K, Yanaka K, Abe T, Takao K, Miyakawa T, Blencowe BJ, Nakagawa S.

Sci Rep. 2016 Jun 2;6:27204. doi: 10.1038/srep27204.

23.

IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC.

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.

Cell Rep. 2016 May 31;15(9):1876-83. doi: 10.1016/j.celrep.2016.04.083. Epub 2016 May 19.

24.

Global Mapping of Human RNA-RNA Interactions.

Sharma E, Sterne-Weiler T, O'Hanlon D, Blencowe BJ.

Mol Cell. 2016 May 19;62(4):618-26. doi: 10.1016/j.molcel.2016.04.030. Epub 2016 May 12.

25.

An extensive program of periodic alternative splicing linked to cell cycle progression.

Dominguez D, Tsai YH, Weatheritt R, Wang Y, Blencowe BJ, Wang Z.

Elife. 2016 Mar 25;5. pii: e10288. doi: 10.7554/eLife.10288.

26.

Sequence evidence for common ancestry of eukaryotic endomembrane coatomers.

Promponas VJ, Katsani KR, Blencowe BJ, Ouzounis CA.

Sci Rep. 2016 Mar 2;6:22311. doi: 10.1038/srep22311.

27.

SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination.

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.

Nature. 2016 Jan 7;529(7584):48-53. doi: 10.1038/nature16469. Epub 2015 Dec 23.

PMID:
26700805
28.

Compound heterozygous mutations in the noncoding RNU4ATAC cause Roifman Syndrome by disrupting minor intron splicing.

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.

Nat Commun. 2015 Nov 2;6:8718. doi: 10.1038/ncomms9718.

29.

The alternative splicing factor Nova2 regulates vascular development and lumen formation.

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.

Nat Commun. 2015 Oct 8;6:8479. doi: 10.1038/ncomms9479.

30.

An alternative splicing event amplifies evolutionary differences between vertebrates.

Gueroussov S, Gonatopoulos-Pournatzis T, Irimia M, Raj B, Lin ZY, Gingras AC, Blencowe BJ.

Science. 2015 Aug 21;349(6250):868-73. doi: 10.1126/science.aaa8381.

31.

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles.

Raj B, Blencowe BJ.

Neuron. 2015 Jul 1;87(1):14-27. doi: 10.1016/j.neuron.2015.05.004. Review.

32.

A germline mutation in SRRM2, a splicing factor gene, is implicated in papillary thyroid carcinoma predisposition.

Tomsic J, He H, Akagi K, Liyanarachchi S, Pan Q, Bertani B, Nagy R, Symer DE, Blencowe BJ, de la Chapelle A.

Sci Rep. 2015 Jul 2;5:10566. doi: 10.1038/srep10566.

33.

Stromal Fat4 acts non-autonomously with Dchs1/2 to restrict the nephron progenitor pool.

Bagherie-Lachidan M, Reginensi A, Pan Q, Zaveri HP, Scott DA, Blencowe BJ, Helmbacher F, McNeill H.

Development. 2015 Aug 1;142(15):2564-73. doi: 10.1242/dev.122648. Epub 2015 Jun 26.

34.

Corrigendum: Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming.

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.

Genes Dev. 2015 Jun 15;29(12):1341. doi: 10.1101/gad.266601.115. No abstract available.

35.

Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming.

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.

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.

36.

Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development.

Quesnel-Vallières M, Irimia M, Cordes SP, Blencowe BJ.

Genes Dev. 2015 Apr 1;29(7):746-59. doi: 10.1101/gad.256115.114.

37.

Reflections for the 20th anniversary issue of RNA journal.

Blencowe BJ.

RNA. 2015 Apr;21(4):573-5. doi: 10.1261/rna.051003.115. No abstract available.

38.

A highly conserved program of neuronal microexons is misregulated in autistic brains.

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.

Cell. 2014 Dec 18;159(7):1511-23. doi: 10.1016/j.cell.2014.11.035.

39.

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

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.

Science. 2015 Jan 9;347(6218):1254806. doi: 10.1126/science.1254806. Epub 2014 Dec 18.

40.

Widespread intron retention in mammals functionally tunes transcriptomes.

Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ.

Genome Res. 2014 Nov;24(11):1774-86. doi: 10.1101/gr.177790.114. Epub 2014 Sep 25.

41.

A global regulatory mechanism for activating an exon network required for neurogenesis.

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.

Mol Cell. 2014 Oct 2;56(1):90-103. doi: 10.1016/j.molcel.2014.08.011. Epub 2014 Sep 11.

42.

Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer.

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.

Eur Urol. 2014 Dec;66(6):982-6. doi: 10.1016/j.eururo.2014.07.045. Epub 2014 Sep 6.

PMID:
25199720
43.

Epstein-Barr virus EBNA1 protein regulates viral latency through effects on let-7 microRNA and dicer.

Mansouri S, Pan Q, Blencowe BJ, Claycomb JM, Frappier L.

J Virol. 2014 Oct;88(19):11166-77. doi: 10.1128/JVI.01785-14. Epub 2014 Jul 16.

44.

Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder.

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.

Nat Genet. 2014 Jul;46(7):742-7. doi: 10.1038/ng.2980. Epub 2014 May 25.

PMID:
24859339
45.

Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins.

Katsani KR, Irimia M, Karapiperis C, Scouras ZG, Blencowe BJ, Promponas VJ, Ouzounis CA.

Sci Rep. 2014 Apr 11;4:4655. doi: 10.1038/srep04655.

46.

Regulated aggregative multicellularity in a close unicellular relative of metazoa.

Sebé-Pedrós A, Irimia M, Del Campo J, Parra-Acero H, Russ C, Nusbaum C, Blencowe BJ, Ruiz-Trillo I.

Elife. 2013 Dec 24;2:e01287. doi: 10.7554/eLife.01287.

47.

A compendium of RNA-binding motifs for decoding gene regulation.

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.

Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.

48.

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.

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.

Nature. 2013 Jun 13;498(7453):241-5. doi: 10.1038/nature12270. Epub 2013 Jun 5.

49.

Distinct types of disorder in the human proteome: functional implications for alternative splicing.

Colak R, Kim T, Michaut M, Sun M, Irimia M, Bellay J, Myers CL, Blencowe BJ, Kim PM.

PLoS Comput Biol. 2013 Apr;9(4):e1003030. doi: 10.1371/journal.pcbi.1003030. Epub 2013 Apr 25.

50.

Dynamic integration of splicing within gene regulatory pathways.

Braunschweig U, Gueroussov S, Plocik AM, Graveley BR, Blencowe BJ.

Cell. 2013 Mar 14;152(6):1252-69. doi: 10.1016/j.cell.2013.02.034. Review.

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