Publications
List of group publications. Add more info here.
2012
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.
Pubmed
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.
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Gonzalez-Porta, M, Calvo M, Sammeth M, Guigo R.
2011. Estimation of alternative splicing variability in human populations. Genome research. Abstract
Pubmed
Kedzierska, AM., Drton M, Guigo R, Casanellas M.
2011. SPIn: model selection for phylogenetic mixtures via linear invariants.. Molecular biology and evolution. Abstract
Pubmed
Consortium, ENCODE P, 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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Derrien, T, Guigó R.
2011. [Long non-coding RNAs with enhancerlike function in human cells.]. Medecine sciences : M/S. 27:359–361.
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Mariotti, M, Guigó R.
2010. Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics (Oxford, England). Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Consortium, I C G.
2010. International network of cancer genome projects. Nature. 464:993–998. Abstract
Pubmed
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
Pubmed
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
Pubmed
Consortium, T I A G.
2010. Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS biology. 8:e1000313. Abstract
Pubmed
2009
Sammeth, M.
2009. Complete alternative splicing events are bubbles in splicing graphs. J. Comput. Biol.. 16:1117–1140. Abstract
Pubmed
Thornton, J, including Guigó BS NR.
2009. Annotations for all by all - the BioSapiens network.. Genome Biol.. 10:401. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Sequencing, B G, 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
Pubmed
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
Pubmed
Pignatelli, M, Serras F, Moya A, Guigó R, Corominas M.
2009. CROC: finding chromosomal clusters in eukaryotic genomes.. Bioinformatics. 25:1552–1553. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Sammeth, M, Foissac S, Guigó R.
2008. A general definition and nomenclature for alternative splicing events.. PLoS Comput. Biol.. 4:e1000147. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Blanco, E, Guigó R, Messeguer X.
2007. Multiple non-collinear TF-map alignments of promoter regions.. BMC Bioinformatics. 8:138. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Consortium, D G12, 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
Pubmed
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
Pubmed
Mularoni, L, Guigó R, Albà MM..
2006. Mutation patterns of amino acid tandem repeats in the human proteome.. Genome Biol.. 7:R33. Abstract
Pubmed
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
Pubmed
Blanco, E, Messeguer X, Smith TF., Guigó R.
2006. Transcription factor map alignment of promoter regions.. PLoS Comput. Biol.. 2:e49. Abstract
Pubmed
Guigó, R, Valcárcel J.
2006. Unweaving the meanings of messenger RNA sequences.. Mol. Cell. 23:150–151. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Abril, JF., Castelo R, Guigó R.
2005. Comparison of splice sites in mammals and chicken.. Genome Res.. 15:111–119. Abstract
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
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
Pubmed
Guigó, R, Reese MG..
2005. EGASP: collaboration through competition to find human genes.. Nat. Methods. 2:575–577. Abstract
Pubmed
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
Pubmed
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
Pubmed
Brent, MR., Guigó R.
2004. Recent advances in gene structure prediction.. Curr. Opin. Struct. Biol.. 14:264–272. Abstract
Pubmed
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
Pubmed
Castelo, R, Guigó R.
2004. Splice site identification by idlBNs.. Bioinformatics. 20 Suppl 1:i69–i76. Abstract
Pubmed
Consortium, ENCODE P.
2004. The ENCODE (ENCyclopedia Of DNA Elements) Project.. Science. 306:636–640. Abstract
Pubmed
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
Pubmed
2003
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
Pubmed
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
Pubmed
Kryukov, GV., Castellano S, Novoselov SV., Lobanov AV., Zehtab O, Guigó R, Gladyshev VN..
2003. Characterization of mammalian selenoproteomes.. Science. 300:1439–1443. Abstract
Pubmed
Abril, JF., Guigó R, Wiehe T.
2003. gff2aplot: Plotting sequence comparisons.. Bioinformatics. 19:2477–2479. Abstract
Pubmed
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, M G S, 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
