Publications

For a complete list please see Eyras’ Google Scholar

2017

Singh B, Eyras E. The role of alternative splicing in cancer. Transcription. 2017 Mar 15;8(2):91-98.

Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJ, Bomane A, Cosson B, Eyras E, Rasko JE, Ritchie W. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biol. 2017 Mar 15;18(1):51.

Rodor J, FitzPatrick DR, Eyras E, Cáceres JF. The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development. RNA Biol. 2017 Jan 2;14(1):45-57.

2016

Llorian M, Gooding C, Bellora N, Hallegger M, Buckroyd A, Wang X, Rajgor D, Kayikci M, Feltham J, Ule J, Eyras E, Smith CW. The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators. Nucleic Acids Res. 2016 Jun 17. pii: gkw560. [article]

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. Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers. Nat Commun. 2016 Nov 18;7:13418.

Trincado JL, Sebestyén E, Pagés A, Eyras E. The prognostic potential of alternative transcript isoforms across human tumors. Genome Med. 2016 Aug 17;8(1):85.

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.

Sebestyén E, Singh B, Miñana B, Pagès A, Mateo F, Pujana MA, Valcárcel J, Eyras E. Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks. Genome Res. 2016 Jun;26(6):732-44. [article]

Falaleeva M, Pages A, Matuszek Z, Hidmi S, Agranat-Tamir L, Korotkov K, Nevo Y, Eyras E, Sperling R, Stamm S. Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing. Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):E1625-34. [article]

Martin S, Bellora N, González-Vallinas J, Irimia M, Chebli K, de Toledo M, Raabe M, Eyras E, Urlaub H, Blencowe BJ, Tazi J. Preferential binding of a stable G3BP ribonucleoprotein complex to intron-retaining transcripts in mouse brain and modulation of their expression in the cerebellum. J Neurochem. 2016 Nov;139(3):349-368.

2015

Kremsky I, Bellora N, Eyras E. A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing. PLoS One. 2015 Jul 24;10(7):e0132448. [open access] [ProfileSeq software]

Alamancos GP, Pagès A, Trincado JL, Bellora N, Eyras E. Leveraging transcript quantification for fast computation of alternative splicing profiles. RNA 2015 21(9):1521-31. [open access] [SUPPA software]

Gonzalez-Vallinas J, Pagés A, Singh B, Eyras E. A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells. BMC Genomics 2015 16:523  [ bioRxiv ] [enhancers data]

Agirre E, Bellora N, Alló M, Pagès A, Bertucci P, Kornblihtt AR, Eyras E. A
chromatin code for alternative splicing involving a putative association between
CTCF and HP1α proteins. BMC Biol. 2015 May 2;13(1):31. [ Pubmed ]

Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule
J, Smith CW. Nuclear matrix protein Matrin3 regulates alternative splicing and
forms overlapping regulatory networks with PTB. EMBO J. 2015 Mar 4;34(5):653-68. [ Pubmed ]

Sebestyén E, Zawisza M, Eyras E. Detection of recurrent alternative splicing
switches in tumor samples reveals novel signatures of cancer. Nucleic Acids Res.
2015 Feb 18;43(3):1345-56 [ Pubmed ]

2014

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*. Argonaute-1 binds transcriptional enhancers and controls constitutive and
alternative splicing in human cells. Proc Natl Acad Sci U S A. 2014 Nov
4;111(44):15622-9. (* co-corresponding) [ Pubmed ]

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. (2014) A global regulatory mechanism for activating an exon network required for neurogenesis. Mol Cell. 56(1):90-103 [ Pubmed ]

Paronetto MP, Bernardis I, Volpe E, Bechara E, Sebestyén E, Eyras E, Valcárcel J. Regulation of FAS exon definition and apoptosis by the Ewing sarcoma protein. Cell Rep. 2014 May 22;7(4):1211-26 [ Pubmed ] (Datasets)

Alamancos GP, Agirre E, Eyras E. Methods to study splicing from high-throughput RNA sequencing data. Methods Mol Biol. 2014;1126:357-97 [ Pubmed ] (http://arxiv.org/abs/1304.5952)

Maslon MM, Heras SR, Bellora N, Eyras E, Cáceres JF. The translational landscape of the splicing factor SRSF1 and its role in mitosis. eLife 2014;10.7554/eLife.02028 [ Pubmed ]

Plass M, Eyras E. Approaches to link RNA secondary structures with splicing regulation. Methods Mol Biol. 2014;1126:341-56 [ Pubmed ] [preprint]

2013

Gromak N, Dienstbier M, Macias S, Plass M, Eyras E, Cáceres JF, Proudfoot NJ. Drosha regulates gene expression independently of RNA cleavage function. Cell Rep. 2013 Dec 26;5(6):1499-510 [ Pubmed ]

Bechara EG, Sebestyén E, Bernardis I, Eyras E, Valcárcel J. RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation. Mol. Cell. 2013 Dec 12;52(5):720-33 [ Pubmed ] (Datasets)

Heras SR, Macias S, Plass M, Fernandez N, Cano D, Eyras E, Garcia-Perez JL, Cáceres JF, (2013) The Microprocessor controls the activity of mammalian retrotransposons. NSMB 20(10):1173-81 [ Pubmed ]

Zhang Z, Falaleeva A, Agranat-Tamir L, Pagès A, Eyras E, Sperling J, Sperling R and Stamm A. (2013) The 5’ untranslated region of the serotonin receptor 2C pre-mRNA generates miRNAs and is expressed in non-neuronal cells. Experimental Brain Research, 2013 Mar 15 [ Pubmed ]

Ballaré C, Castellano G, Gaveglia L, Althammer S, González-Vallinas J, Eyras E, Le Dily F, Zaurin R, Soronellas D, Vicent GP, Beato M. Nucleosome-driven transcription factor binding and gene regulation. Molecular Cell 2013 49(1):67-79 [ Pubmed ]

2012

Plass M, Codony-Servat C, Ferreira PG, Vilardell J, Eyras E. RNA secondary structure mediates alternative 3′ss selection in Saccharomyces cerevisiae. RNA. 2012 Jun;18(6):1103-15 [ Pubmed ]

Althammer S, Pagès A, Eyras E. Predictive models of gene regulation from high-throughput epigenomics data. Comp Funct Genomics. 2012;2012:284786 [ Pubmed ]

Nadal-Ribelles M, Conde N, Flores O, González-Vallinas J, Eyras E, Orozco M, de Nadal E, Posas F. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biol. 2012 13(11):R106 [ Pubmed ]

Macias S, Plass M, Stajuda A, Michlewski G, Eyras E, Cáceres JF. DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. Nat Struct Mol Biol. 2012 19(8):760-6. [ Pubmed ] (Datasets)

Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C. Use of ChIP-Seq data for the design of a multiple promoter-alignment method. Nucleic Acids Res. 2012 40(7):e52 [ Pubmed ]

2011

Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics. 2011 Dec 15;27(24):3333-40 [ Pubmed ]

Agirre E, Eyras E. Databases and resources for human small non-coding RNAs. Hum. Genomics. 2011 Mar;5(3):192-9. Review [ Pubmed ]

2010

Alló M, Schor IE, Muñoz MJ, de la Mata M, Agirre E, Valcárcel J, Eyras E, Kornblihtt AR. Chromatin and alternative splicing. Cold Spring Harb Symp Quant Biol. 2010;75:103-11 [ Pubmed ]

Corvelo A, Hallegger M, Smith CW, Eyras E. Genome-wide association between branch point properties and alternative splicing. PLoS Comput Biol. 2010 6(11):e1001016 [ Pubmed ]

Gal-Mark N, Schwartz S, Ram O, Eyras E*, Ast G. The pivotal roles of TIA proteins in 5′ splice-site selection of alu exons and across evolution. PLoS Genet. 2009 5(11):e1000717. (* co-corresponding author) [ Pubmed ]

2009

Alló M, Buggiano V, Fededa JP, Petrillo E, Schor I, de la Mata M, Agirre E, Plass M, Eyras E, Elela SA, Klinck R, Chabot B, Kornblihtt AR. Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat Struct Mol Biol. 2009 16(7):717-24 [ Pubmed ]

Bovine Genome Sequencing and Analysis Consortium (includes E. Eyras). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 324(5926):522-8 [ Pubmed ]

Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E et al. ASTD: The Alternative Splicing and Transcript Diversity database. Genomics. 2009 93(3):213-20. [ Pubmed ]

Irimia M, Eyras E. Evolution of Splicing. In “Adaptation and Evolution: 150 years after the Origin of Species”. Dopazo H & Navarro A Editors. 2009. Spanish Society of Evolutionary Biology (SESBE). ISBN 978-84-92910-06-09.

2008

Plass M, Agirre E, Reyes D, Camara F, Eyras E. Co-evolution of the branch site and SR proteins in eukaryotes. Trends Genet. 2008 Dec;24(12):590-4 [ Pubmed ]

Corvelo A, Eyras E. Exon creation and establishment in human genes. Genome Biol. 2008;9(9):R141 [ Pubmed ]

Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, Ast G. Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res. 2008 18(1):88-103 [ Pubmed ]

For a complete list please see Eyras’ Google Scholar