Publications

List of group publications. Add more info here.

2013

Bava FA, Eliscovich C, Ferreira PG, Miñana B, Ben-Dov C, Guigó R, Valcárcel J, Méndez R.  2013.  CPEB1 coordinates alternative 3'-UTR formation with translational regulation. Nature. 495:121–125. Abstract
Ferreira PG, Patalano S, Chauhan R, Ffrench-Constant R, Gabaldon T, Guigo R, Sumner S.  2013.  Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol. 14:R20. Abstract
Knowles D, Röder M, Merkel A, Guigó R.  2013.  Grape RNA-Seq analysis pipeline environment. Bioinformatics. 10.1093/bioinformatics/btt016 Abstract

2012

Johnson R.  2012.  Long non-coding RNAs in Huntington's disease neurodegeneration.. Neurobiol. Dis.. 46:245–254. Abstract
Pervouchine DD, Knowles DG, Guigó R.  2012.  Intron-Centric Estimation of Alternative Splicing from RNA-seq data. Bioinformatics. 29(2):273-274. Abstract
Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R et al..  2012.  Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.. Genome Res.. 22:1231–1242. Abstract
Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M.  2012.  Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res.. 40:10073–10083. Abstract
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E et al..  2012.  Modeling gene expression using chromatin features in various cellular contexts.. Genome Biol.. 13:R53. Abstract
Marco-Sola S, Sammeth M, Guigó R, Ribeca P.  2012.  The GEM mapper: fast, accurate and versatile alignment by filtration. Nat. Methods. 9:1185–1188. Abstract
Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L, Lowy E et al..  2012.  The genome of melon (Cucumis melo L.).. Proc. Natl. Acad. Sci. U.S.A.. 109:11872–11877. Abstract
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Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al..  2012.  GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res.. 22:1760–1774.
Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigo R.  2012.  Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res.. 22:1616–1625.
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F et al..  2012.  Landscape of transcription in human cells. Nature. 489:101–108.
Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Dunham I, Kundaje A, Aldred SF, Collins PJ et al..  2012.  An integrated encyclopedia of DNA elements in the human genome. Nature. 489:57–74.
Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y et al..  2012.  Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res.. 22:1658–1667.
Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T et al..  2012.  Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res.. 22:1698–1710.
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al..  2012.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res.. 22:1775–1789.
Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T et al..  2012.  An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol.. 13:418.
Johnson R, Richter N, Bogu GK, Bhinge A, Teng SW, Choo SH, Andrieux LO, de Benedictis C, Jauch R, Stanton LW.  2012.  A genome-wide screen for genetic variants that modify the recruitment of REST to its target genes. PLoS Genet.. 8:e1002624. Abstract
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Consortium TTG, Institute KDNAR, Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y et al..  2012.  The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 485:635–641. Abstract
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Mariotti M, Ridge PG, Zhang Y, Lobanov AV, Pringle TH, Guigo R, Hatfield DL, Gladyshev VN.  2012.  Composition and evolution of the vertebrate and Mammalian selenoproteomes. PLoS ONE. 7:e33066.
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Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A et al..  2012.  BLUEPRINT to decode the epigenetic signature written in blood. Nat. Biotechnol.. 30:224–226.
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Derrien T, Guigo R, Johnson R.  2012.  The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter". Front Genet.. 2(107):1–6. Abstract
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Ng SY, Johnson R, Stanton LW.  2012.  Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors.. EMBO J.. 31:522–533. Abstract
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Derrien T, Estell, Marco Sola S, Knowles DG, Raineri E, Guigo R, Ribeca P.  2012.  Fast computation and applications of genome mappability.. PLoS ONE. 7:e30377. Abstract
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Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al..  2012.  Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells. PLoS ONE. 7:e28213. Abstract
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2011

Maxwell CA, Benítez J, Gómez-Baldó L, Osorio A, Bonifaci N, Fernández-Ramires R, Costes SV, Guinó E, Chen H, Evans GJ et al..  2011.  Interplay between BRCA1 and RHAMM Regulates Epithelial Apicobasal Polarization and May Influence Risk of Breast Cancer. PLoS Biol.. 9:e1001199. Abstract
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Gonzalez-Porta M, Calvo M, Sammeth M, Guigo R.  2011.  Estimation of alternative splicing variability in human populations. Genome research. 22:528-538. Abstract
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Kedzierska AM, Drton M, Guigo R, Casanellas M.  2011.  SPIn: model selection for phylogenetic mixtures via linear invariants.. Molecular biology and evolution. Abstract
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Consortium ENCODEP, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E et al..  2011.  A user's guide to the encyclopedia of DNA elements (ENCODE).. PLoS Biol.. 9:e1001046. Abstract
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Martin D, Pantoja C, Miñán AF, Valdes-Quezada C, Moltó E, Matesanz F, Bogdanović O, de la Calle-Mustienes E, Domínguez O, Taher L et al..  2011.  Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat. Struct. Mol. Biol.. 18:708–714. Abstract
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Puente XS, Pinyol M, Quesada V, Conde L, Ordonez GR, Villamor N, Escaramis G, Jares P, Bea S, González-Díaz M et al..  2011.  Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. Abstract
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Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigo R, Hubbard T, Harrow J.  2011.  The origins, evolution and functional potential of alternative splicing in vertebrates. Molecular biology and evolution. Abstract
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Orom UA, Derrien T, Guigo R, Shiekhattar R.  2011.  Long Noncoding RNAs as Enhancers of Gene Expression. Cold Spring Harbor symposia on quantitative biology. Abstract
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Derrien T, Guigó R.  2011.  [Long non-coding RNAs with enhancerlike function in human cells.]. Medecine sciences : M/S. 27:359–361.
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2010

Nikolaou C, Althammer S, Beato M, Guigo R.  2010.  Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae. Epigenetics & chromatin. 3:20. Abstract
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Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Câmara F et al..  2010.  Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.. Science. 330:86–88. Abstract
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Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q et al..  2010.  Long Noncoding RNAs with Enhancer-like Function in Human Cells. Cell. 143:46–58. Abstract
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Mariotti M, Guigó R.  2010.  Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics (Oxford, England). Abstract
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Manichanh C, Reeder J, Gibert P, Varela E, Llopis M, Antolin M, Guigo R, Knight R, Guarner F.  2010.  Reshaping the gut microbiome with bacterial transplantation and antibiotic intake.. Genome research. Abstract
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Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET.  2010.  Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 464:773–777. Abstract
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Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK et al..  2010.  Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proceedings of the National Academy of Sciences of the United States of America. 10.1073:1003391107. Abstract
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Novoa I, Gallego J, Ferreira PG, Mendez R.  2010.  Mitotic cell-cycle progression is regulated by CPEB1 and CPEB4-dependent translational control. Nature cell biology. 12(5):447-456. Abstract
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Consortium ICG.  2010.  International network of cancer genome projects. Nature. 464:993–998. Abstract
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Tilgner H, Guigó R.  2010.  From chromatin to splicing: RNA-processing as a total artwork. Epigenetics : official journal of the DNA Methylation Society. 5(3):180-184. Abstract
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Horner DS, Pavesi G, Castrignanò T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G.  2010.  Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief. Bioinformatics. 11:181–197. Abstract
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Consortium TIAG.  2010.  Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS biology. 8:e1000313. Abstract
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2009

Ferreira PG, Silva CG, Azevedo PJ, Brito RM.  2009.  Spatial Clustering of Molecular Dynamics Trajectories in Protein Unfolding Simulations. :156–166.
Sammeth M.  2009.  Complete alternative splicing events are bubbles in splicing graphs. J. Comput. Biol.. 16:1117–1140. Abstract
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Thornton J, including Guigó BSNR.  2009.  Annotations for all by all - the BioSapiens network.. Genome Biol.. 10:401. Abstract
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Makrythanasis P, Kapranov P, Bartoloni L, Reymond A, Deutsch S, Guigó R, Denoeud F, Drenkow J, Rossier C, Ariani F et al..  2009.  Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls.. Hum. Mutat.. 30:E866–E879. Abstract
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Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcárcel J, Guigó R.  2009.  Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol.. 16:996–1001. Abstract
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Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R.  2009.  Identifying protein-coding genes in genomic sequences.. Genome Biol.. 10:201. Abstract
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Chapple CE, Guigó R, Krol A.  2009.  SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.. Bioinformatics. 25:674–675. Abstract
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Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M et al..  2009.  ASTD: The Alternative Splicing and Transcript Diversity database.. Genomics. 93:213–220. Abstract
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Takeuchi A, Schmitt D, Chapple C, Babaylova E, Karpova G, Guigo R, Krol A, Allmang C.  2009.  A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins.. Nucleic Acids Res.. 37:2126–2141. Abstract
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Boj SF, Servitja JM, Martin D, Rios M, Talianidis I, Guigo R, Ferrer J.  2009.  Functional targets of the monogenic diabetes transcription factors HNF-1alpha and HNF-4alpha are highly conserved between mice and humans.. Diabetes. 58:1245–1253. Abstract
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Sequencing BG, Consortium A, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE et al..  2009.  The genome sequence of taurine cattle: a window to ruminant biology and evolution.. Science. 324:522–528. Abstract
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Servitja JM, Pignatelli M, Maestro MA, Cardalda C, Boj SF, Lozano J, Blanco E, Lafuente A, McCarthy MI, Sumoy L et al..  2009.  Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver.. Mol. Cell. Biol.. 29:2945–2959. Abstract
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Pignatelli M, Serras F, Moya A, Guigó R, Corominas M.  2009.  CROC: finding chromosomal clusters in eukaryotic genomes.. Bioinformatics. 25:1552–1553. Abstract
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Castellano S, Andrés AM, Bosch E, Bayes M, Guigó R, Clark AG.  2009.  Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins.. Mol. Biol. Evol.. 26:2031–2040. Abstract
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Arman M, Aguilera-Montilla N, Mas V, Puig-Kröger A, Pignatelli M, Guigó R, Corbí AL, Lozano F.  2009.  The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells.. Mol. Immunol.. 46:2226–2235. Abstract
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Buschbeck M, Uribesalgo I, Wibowo I, Rué P, Martin D, Gutierrez A, Morey L, Guigó R, López-Schier H, Di Croce L.  2009.  The histone variant macroH2A is an epigenetic regulator of key developmental genes.. Nat. Struct. Mol. Biol.. 16:1074–1079. Abstract
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2008

Castellano S, Gladyshev VN, Guigó R, Berry MJ.  2008.  SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.. Nucleic Acids Res.. 36:D332–D338. Abstract
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Weng Z, Guigó R.  2008.  In silico meets in vivo.. Genome Biol.. 9:302. Abstract
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Consortium STAR, Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J et al..  2008.  SNP and haplotype mapping for genetic analysis in the rat.. Nat. Genet.. 40:560–566. Abstract
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Consortium BM, Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D et al..  2008.  Interoperability with Moby 1.0–it's better than sharing your toothbrush!. Brief. Bioinformatics. 9:220–231. Abstract
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Sammeth M, Foissac S, Guigó R.  2008.  A general definition and nomenclature for alternative splicing events.. PLoS Comput. Biol.. 4:e1000147. Abstract
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Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J.  2008.  A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.. Nucleic Acids Res.. 36:5180–5188. Abstract
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Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR et al..  2008.  Efficient targeted transcript discovery via array-based normalization of RACE libraries.. Nat. Methods. 5:629–635. Abstract
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Chapple CE, Guigó R.  2008.  Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes.. PLoS ONE. 3:e2968. Abstract
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Blanco E, Pignatelli M, Beltran S, Punset A, Pérez-Lluch S, Serras F, Guigó R, Corominas M.  2008.  Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila.. Genome Biol.. 9:R134. Abstract
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Piqué M, López JM, Foissac S, Guigó R, Méndez R.  2008.  A combinatorial code for CPE-mediated translational control.. Cell. 132:434–448. Abstract
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2007

Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M et al..  2007.  Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.. Genome Res.. 17:839–851. Abstract
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Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A et al..  2007.  The implications of alternative splicing in the ENCODE protein complement.. Proc. Natl. Acad. Sci. U.S.A.. 104:5495–5500. Abstract
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Blanco E, Parra G, Guigó R.  2007.  Using geneid to identify genes.. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Chapter 4:Unit4.3. Abstract
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Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V.  2007.  Improving gene annotation using peptide mass spectrometry.. Genome Res.. 17:231–239. Abstract
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Blanco E, Guigó R, Messeguer X.  2007.  Multiple non-collinear TF-map alignments of promoter regions.. BMC Bioinformatics. 8:138. Abstract
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Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J et al..  2007.  Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.. Genome Res.. 17:746–759. Abstract
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Kerhornou A, Guigó R.  2007.  BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations.. Bioinformatics. 23:1831–1833. Abstract
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Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A et al..  2007.  Structured RNAs in the ENCODE selected regions of the human genome.. Genome Res.. 17:852–864. Abstract
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Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R et al..  2007.  The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.. Genome Res.. 17:732–745. Abstract
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Consortium DG12, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W et al..  2007.  Evolution of genes and genomes on the Drosophila phylogeny.. Nature. 450:203–218. Abstract
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Lyle R, Prandini P, Osoegawa K, ten Hallers B, Humphray S, Zhu B, Eyras E, Castelo R, Bird CP, Gagos S et al..  2007.  Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.. Genome Res.. 17:1690–1696. Abstract
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Consortium ENCODEP, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al..  2007.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.. Nature. 447:799–816. Abstract
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2006

Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, Thomson TM, Antonarakis SE, Guigó R.  2006.  Tandem chimerism as a means to increase protein complexity in the human genome.. Genome Res.. 16:37–44. Abstract
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Mularoni L, Guigó R, Albà MM.  2006.  Mutation patterns of amino acid tandem repeats in the human proteome.. Genome Biol.. 7:R33. Abstract
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Blanco E, Farré D, Albà MM, Messeguer X, Guigó R.  2006.  ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.. Nucleic Acids Res.. 34:D63–D67. Abstract
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Blanco E, Messeguer X, Smith TF, Guigó R.  2006.  Transcription factor map alignment of promoter regions.. PLoS Comput. Biol.. 2:e49. Abstract
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Reese MG, Guigó R.  2006.  EGASP: Introduction.. Genome Biol.. 7 Suppl 1:S1.1–S1.3.
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Guigó R, Valcárcel J.  2006.  Unweaving the meanings of messenger RNA sequences.. Mol. Cell. 23:150–151. Abstract
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Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Ségurens B, Daubin V, Anthouard V, Aiach N et al..  2006.  Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.. Nature. 444:171–178. Abstract
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Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al..  2006.  GENCODE: producing a reference annotation for ENCODE.. Genome Biol.. 7 Suppl 1:S4.1–S4.9. Abstract
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Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E et al..  2006.  EGASP: the human ENCODE Genome Annotation Assessment Project.. Genome Biol.. 7 Suppl 1:S2.1–S231. Abstract
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2005

Szafranski K, Lehmann R, Parra G, Guigo R, Glöckner G.  2005.  Gene organization features in A/T-rich organisms.. J. Mol. Evol.. 60:90–98. Abstract
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Abril JF, Castelo R, Guigó R.  2005.  Comparison of splice sites in mammals and chicken.. Genome Res.. 15:111–119. Abstract
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López-Bigas N, Audit B, Ouzounis C, Parra G, Guigó R.  2005.  Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett.. 579:1900–1903. Abstract
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Castelo R, Reymond A, Wyss C, Câmara F, Parra G, Antonarakis SE, Guigó R, Eyras E.  2005.  Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.. Nucleic Acids Res.. 33:1935–1939. Abstract
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Taskov K, Chapple C, Kryukov GV, Castellano S, Lobanov AV, Korotkov KV, Guigó R, Gladyshev VN.  2005.  Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome? Nucleic Acids Res.. 33:2227–2238. Abstract
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Eyras E, Reymond A, Castelo R, Bye JM, Câmara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C et al..  2005.  Gene finding in the chicken genome.. BMC Bioinformatics. 6:131. Abstract
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Izquierdo JM, Majós N, Bonnal S, Martínez C, Castelo R, Guigó R, Bilbao D, Valcárcel J.  2005.  Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition.. Mol. Cell. 19:475–484. Abstract
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Guigó R, Reese MG.  2005.  EGASP: collaboration through competition to find human genes.. Nat. Methods. 2:575–577. Abstract
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Castellano S, Lobanov AV, Chapple C, Novoselov SV, Albrecht M, Hua D, Lescure A, Lengauer T, Krol A, Gladyshev VN et al..  2005.  Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family.. Proc. Natl. Acad. Sci. U.S.A.. 102:16188–16193. Abstract
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2004

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE et al..  2004.  Genome sequence of the Brown Norway rat yields insights into mammalian evolution.. Nature. 428:493–521. Abstract
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Brent MR, Guigó R.  2004.  Recent advances in gene structure prediction.. Curr. Opin. Struct. Biol.. 14:264–272. Abstract
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Castresana J, Guigó R, Albà MM.  2004.  Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome.. J. Mol. Evol.. 59:72–79. Abstract
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Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A et al..  2004.  Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.. Nature. 431:946–957. Abstract
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Castelo R, Guigó R.  2004.  Splice site identification by idlBNs.. Bioinformatics. 20 Suppl 1:i69–i76. Abstract
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Consortium ENCODEP.  2004.  The ENCODE (ENCyclopedia Of DNA Elements) Project.. Science. 306:636–640. Abstract
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Consortium ICGS.  2004.  Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.. Nature. 432:695–716. Abstract
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2003

Beltran S, Blanco E, Serras F, Pérez-Villamil B, Guigó R, Artavanis-Tsakonas S, Corominas M.  2003.  Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster.. Proc. Natl. Acad. Sci. U.S.A.. 100:3293–3298. Abstract
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Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigó R.  2003.  Comparative gene prediction in human and mouse.. Genome Res.. 13:108–117. Abstract
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Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, Zehtab O, Guigó R, Gladyshev VN.  2003.  Characterization of mammalian selenoproteomes.. Science. 300:1439–1443. Abstract
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Abril JF, Guigó R, Wiehe T.  2003.  gff2aplot: Plotting sequence comparisons.. Bioinformatics. 19:2477–2479. Abstract
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Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C et al..  2003.  Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.. Proc. Natl. Acad. Sci. U.S.A.. 100:1140–1145. Abstract
Pubmed

2002

Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R et al..  2002.  The genome sequence of the malaria mosquito Anopheles gambiae.. Science. 298:129–149. Abstract
Pubmed
Glöckner G, Eichinger L, Szafranski K, Pachebat JA, Bankier AT, Dear PH, Lehmann R, Baumgart C, Parra G, Abril JF et al..  2002.  Sequence and analysis of chromosome 2 of Dictyostelium discoideum.. Nature. 418:79–85. Abstract
Pubmed
Consortium MGS, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M et al..  2002.  Initial sequencing and comparative analysis of the mouse genome.. Nature. 420:520–562. Abstract
Pubmed

2001

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al..  2001.  The sequence of the human genome.. Science. 291:1304–1351. Abstract
Pubmed

2000

Guigó R, Agarwal P, Abril JF, Burset M, Fickett JW.  2000.  An assessment of gene prediction accuracy in large DNA sequences.. Genome Res.. 10:1631–1642. Abstract
Pubmed

1996

Burset M, Guigó R.  1996.  Evaluation of gene structure prediction programs.. Genomics. 34:353–367. Abstract
Pubmed

1992

Guigó R, Knudsen S, Drake N, Smith T.  1992.  Prediction of gene structure.. J. Mol. Biol.. 226:141–157. Abstract
Pubmed
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