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Items: 1 to 50 of 75

1.

CD133-directed CAR T-cells for MLL leukemia: on-target, off-tumor myeloablative toxicity.

Bueno C, Velasco-Hernandez T, Gutiérrez-Agüera F, Zanetti SR, Baroni ML, Sánchez-Martínez D, Molina O, Closa A, Agraz-Doblás A, Marín P, Eyras E, Varela I, Menéndez P.

Leukemia. 2019 Feb 18. doi: 10.1038/s41375-019-0418-8. [Epub ahead of print] No abstract available.

PMID:
30778134
2.

Corrigendum: Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks.

Sebestyén E, Singh B, Miñana B, Pagès A, Mateo F, Pujana MA, Valcárcel J, Eyras E.

Genome Res. 2018 Sep;28(9):1426. doi: 10.1101/gr.242214.118. No abstract available.

3.

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L.

Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052.

4.

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.

Dotu I, Adamson SI, Coleman B, Fournier C, Ricart-Altimiras E, Eyras E, Chuang JH.

PLoS Comput Biol. 2018 Mar 29;14(3):e1006078. doi: 10.1371/journal.pcbi.1006078. eCollection 2018 Mar.

5.

Genome Sequencing and RNA-Motif Analysis Reveal Novel Damaging Noncoding Mutations in Human Tumors.

Singh B, Trincado JL, Tatlow PJ, Piccolo SR, Eyras E.

Mol Cancer Res. 2018 Jul;16(7):1112-1124. doi: 10.1158/1541-7786.MCR-17-0601. Epub 2018 Mar 28.

PMID:
29592900
6.

SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.

Trincado JL, Entizne JC, Hysenaj G, Singh B, Skalic M, Elliott DJ, Eyras E.

Genome Biol. 2018 Mar 23;19(1):40. doi: 10.1186/s13059-018-1417-1.

7.

Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1.

Cifdaloz M, Osterloh L, Graña O, Riveiro-Falkenbach E, Ximénez-Embún P, Muñoz J, Tejedo C, Calvo TG, Karras P, Olmeda D, Miñana B, Gómez-López G, Cañon E, Eyras E, Guo H, Kappes F, Ortiz-Romero PL, Rodríguez-Peralto JL, Megías D, Valcárcel J, Soengas MS.

Nat Commun. 2017 Dec 21;8(1):2249. doi: 10.1038/s41467-017-02353-y.

8.

The discovery potential of RNA processing profiles.

Pagès A, Dotu I, Pallarès-Albanell J, Martí E, Guigó R, Eyras E.

Nucleic Acids Res. 2018 Feb 16;46(3):e15. doi: 10.1093/nar/gkx1115.

9.

The Functional Impact of Alternative Splicing in Cancer.

Climente-González H, Porta-Pardo E, Godzik A, Eyras E.

Cell Rep. 2017 Aug 29;20(9):2215-2226. doi: 10.1016/j.celrep.2017.08.012.

10.

IRFinder: assessing the impact of intron retention on mammalian gene expression.

Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJ, Bomane A, Cosson B, Eyras E, Rasko JE, Ritchie W.

Genome Biol. 2017 Mar 15;18(1):51. doi: 10.1186/s13059-017-1184-4.

11.

The role of alternative splicing in cancer.

Singh B, Eyras E.

Transcription. 2017 Mar 15;8(2):91-98. doi: 10.1080/21541264.2016.1268245. Epub 2016 Dec 22.

12.

Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers.

Pérez-Guijarro E, Karras P, Cifdaloz M, Martínez-Herranz R, Cañón E, Graña O, Horcajada-Reales C, Alonso-Curbelo D, Calvo TG, Gómez-López G, Bellora N, Riveiro-Falkenbach E, Ortiz-Romero PL, Rodríguez-Peralto JL, Maestre L, Roncador G, de Agustín Asensio JC, Goding CR, Eyras E, Megías D, Méndez R, Soengas MS.

Nat Commun. 2016 Nov 18;7:13418. doi: 10.1038/ncomms13418.

13.

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.

14.

The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development.

Rodor J, FitzPatrick DR, Eyras E, Cáceres JF.

RNA Biol. 2017 Jan 2;14(1):45-57. doi: 10.1080/15476286.2016.1247148. Epub 2016 Oct 20.

15.

The prognostic potential of alternative transcript isoforms across human tumors.

Trincado JL, Sebestyén E, Pagés A, Eyras E.

Genome Med. 2016 Aug 17;8(1):85. doi: 10.1186/s13073-016-0339-3.

16.

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.

17.

The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators.

Llorian M, Gooding C, Bellora N, Hallegger M, Buckroyd A, Wang X, Rajgor D, Kayikci M, Feltham J, Ule J, Eyras E, Smith CW.

Nucleic Acids Res. 2016 Oct 14;44(18):8933-8950. Epub 2016 Jun 17.

18.

Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks.

Sebestyén E, Singh B, Miñana B, Pagès A, Mateo F, Pujana MA, Valcárcel J, Eyras E.

Genome Res. 2016 Jun;26(6):732-44. doi: 10.1101/gr.199935.115. Epub 2016 Apr 13. Erratum in: Genome Res. 2018 Sep;28(9):1426.

19.

Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing.

Falaleeva M, Pages A, Matuszek Z, Hidmi S, Agranat-Tamir L, Korotkov K, Nevo Y, Eyras E, Sperling R, Stamm S.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):E1625-34. doi: 10.1073/pnas.1519292113. Epub 2016 Mar 8.

20.

A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing.

Kremsky I, Bellora N, Eyras E.

PLoS One. 2015 Jul 24;10(7):e0132448. doi: 10.1371/journal.pone.0132448. eCollection 2015.

21.

Leveraging transcript quantification for fast computation of alternative splicing profiles.

Alamancos GP, Pagès A, Trincado JL, Bellora N, Eyras E.

RNA. 2015 Sep;21(9):1521-31. doi: 10.1261/rna.051557.115. Epub 2015 Jul 15.

22.

A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells.

González-Vallinas J, Pagès A, Singh B, Eyras E.

BMC Genomics. 2015 Jul 14;16:523. doi: 10.1186/s12864-015-1704-0.

23.

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, Barta A, Nimmo HG, Brown JW.

New Phytol. 2015 Oct;208(1):96-101. doi: 10.1111/nph.13545. Epub 2015 Jun 25.

24.

A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins.

Agirre E, Bellora N, Alló M, Pagès A, Bertucci P, Kornblihtt AR, Eyras E.

BMC Biol. 2015 May 2;13:31. doi: 10.1186/s12915-015-0141-5.

25.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A.

Nucleic Acids Res. 2015 Jul 1;43(W1):W589-98. doi: 10.1093/nar/gkv350. Epub 2015 Apr 20.

26.

Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB.

Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J, Smith CW.

EMBO J. 2015 Mar 4;34(5):653-68. doi: 10.15252/embj.201489852. Epub 2015 Jan 19.

27.

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer.

Sebestyén E, Zawisza M, Eyras E.

Nucleic Acids Res. 2015 Feb 18;43(3):1345-56. doi: 10.1093/nar/gku1392. Epub 2015 Jan 10.

28.

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells.

Alló M, Agirre E, Bessonov S, Bertucci P, Gómez Acuña L, Buggiano V, Bellora N, Singh B, Petrillo E, Blaustein M, Miñana B, Dujardin G, Pozzi B, Pelisch F, Bechara E, Agafonov DE, Srebrow A, Lührmann R, Valcárcel J, Eyras E, Kornblihtt AR.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15622-9. doi: 10.1073/pnas.1416858111. Epub 2014 Oct 13.

29.

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.

30.

Drosha Regulates Gene Expression Independently of RNA Cleavage Function.

Gromak N, Dienstbier M, Macias S, Plass M, Eyras E, Cáceres JF, Proudfoot NJ.

Cell Rep. 2014 Jun 12;7(5):1753-1754. doi: 10.1016/j.celrep.2014.05.047. Epub 2014 Jun 12. No abstract available.

31.

The translational landscape of the splicing factor SRSF1 and its role in mitosis.

Maslon MM, Heras SR, Bellora N, Eyras E, Cáceres JF.

Elife. 2014 May 6:e02028. doi: 10.7554/eLife.02028. [Epub ahead of print]

32.

Regulation of FAS exon definition and apoptosis by the Ewing sarcoma protein.

Paronetto MP, Bernardis I, Volpe E, Bechara E, Sebestyén E, Eyras E, Valcárcel J.

Cell Rep. 2014 May 22;7(4):1211-26. doi: 10.1016/j.celrep.2014.03.077. Epub 2014 May 10.

33.

Methods to study splicing from high-throughput RNA sequencing data.

Alamancos GP, Agirre E, Eyras E.

Methods Mol Biol. 2014;1126:357-97. doi: 10.1007/978-1-62703-980-2_26.

PMID:
24549677
34.

Approaches to link RNA secondary structures with splicing regulation.

Plass M, Eyras E.

Methods Mol Biol. 2014;1126:341-56. doi: 10.1007/978-1-62703-980-2_25.

PMID:
24549676
35.

Drosha regulates gene expression independently of RNA cleavage function.

Gromak N, Dienstbier M, Macias S, Plass M, Eyras E, Cáceres JF, Proudfoot NJ.

Cell Rep. 2013 Dec 26;5(6):1499-510. doi: 10.1016/j.celrep.2013.11.032. Epub 2013 Dec 19. Erratum in: Cell Rep. 2014 Jun 12;7(5):1753-4.

36.

RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation.

Bechara EG, Sebestyén E, Bernardis I, Eyras E, Valcárcel J.

Mol Cell. 2013 Dec 12;52(5):720-33. doi: 10.1016/j.molcel.2013.11.010.

37.

The Microprocessor controls the activity of mammalian retrotransposons.

Heras SR, Macias S, Plass M, Fernandez N, Cano D, Eyras E, Garcia-Perez JL, Cáceres JF.

Nat Struct Mol Biol. 2013 Oct;20(10):1173-81. doi: 10.1038/nsmb.2658. Epub 2013 Sep 1.

38.

The 5' untranslated region of the serotonin receptor 2C pre-mRNA generates miRNAs and is expressed in non-neuronal cells.

Zhang Z, Falaleeva M, Agranat-Tamir L, Pages A, Eyras E, Sperling J, Sperling R, Stamm S.

Exp Brain Res. 2013 Oct;230(4):387-94. doi: 10.1007/s00221-013-3458-8. Epub 2013 Mar 15.

39.

Nucleosome-driven transcription factor binding and gene regulation.

Ballaré C, Castellano G, Gaveglia L, Althammer S, González-Vallinas J, Eyras E, Le Dily F, Zaurin R, Soronellas D, Vicent GP, Beato M.

Mol Cell. 2013 Jan 10;49(1):67-79. doi: 10.1016/j.molcel.2012.10.019. Epub 2012 Nov 21.

40.

Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling.

Nadal-Ribelles M, Conde N, Flores O, González-Vallinas J, Eyras E, Orozco M, de Nadal E, Posas F.

Genome Biol. 2012 Nov 18;13(11):R106. doi: 10.1186/gb-2012-13-11-r106.

41.

Predictive models of gene regulation from high-throughput epigenomics data.

Althammer S, Pagès A, Eyras E.

Comp Funct Genomics. 2012;2012:284786. doi: 10.1155/2012/284786. Epub 2012 Aug 13.

42.

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor.

Macias S, Plass M, Stajuda A, Michlewski G, Eyras E, Cáceres JF.

Nat Struct Mol Biol. 2012 Aug;19(8):760-6. doi: 10.1038/nsmb.2344. Epub 2012 Jul 15.

43.

RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae.

Plass M, Codony-Servat C, Ferreira PG, Vilardell J, Eyras E.

RNA. 2012 Jun;18(6):1103-15. doi: 10.1261/rna.030767.111. Epub 2012 Apr 26.

44.

Use of ChIP-Seq data for the design of a multiple promoter-alignment method.

Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C.

Nucleic Acids Res. 2012 Apr;40(7):e52. doi: 10.1093/nar/gkr1292. Epub 2012 Jan 9.

45.

Key contribution of CPEB4-mediated translational control to cancer progression.

Ortiz-Zapater E, Pineda D, Martínez-Bosch N, Fernández-Miranda G, Iglesias M, Alameda F, Moreno M, Eliscovich C, Eyras E, Real FX, Méndez R, Navarro P.

Nat Med. 2011 Dec 4;18(1):83-90. doi: 10.1038/nm.2540.

PMID:
22138752
46.

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.

Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E.

Bioinformatics. 2011 Dec 15;27(24):3333-40. doi: 10.1093/bioinformatics/btr570. Epub 2011 Oct 12.

47.

Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing.

Meyer M, Plass M, Pérez-Valle J, Eyras E, Vilardell J.

Mol Cell. 2011 Sep 16;43(6):1033-9. doi: 10.1016/j.molcel.2011.07.030.

48.

Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression.

Shen M, Eyras E, Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S.

Nucleic Acids Res. 2011 Dec;39(22):9720-30. doi: 10.1093/nar/gkr684. Epub 2011 Aug 31.

49.

Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation.

Fernández N, Fernandez-Miragall O, Ramajo J, García-Sacristán A, Bellora N, Eyras E, Briones C, Martínez-Salas E.

Nucleic Acids Res. 2011 Oct;39(19):8572-85. doi: 10.1093/nar/gkr560. Epub 2011 Jul 8.

50.

Databases and resources for human small non-coding RNAs.

Agirre E, Eyras E.

Hum Genomics. 2011 Mar;5(3):192-9. Review.

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