Publications
List of group publications. Add more info here.
2010
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
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Consortium, I C G.
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, T I A G.
2010. Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS biology. 8:e1000313. Abstract
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2009
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 BS NR.
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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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
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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
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
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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
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
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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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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
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
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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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
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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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, Messeguer X, Smith TF., Guigó R.
2006. Transcription factor map alignment of promoter regions.. PLoS Comput. Biol.. 2:e49. Abstract
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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
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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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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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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Eyras, E, Reymond A, Castelo R, Bye JM., Camara 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
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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
Pubmed
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
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
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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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Brent, MR., Guigó R.
2004. Recent advances in gene structure prediction.. Curr. Opin. Struct. Biol.. 14:264–272. 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, ENCODE P.
2004. The ENCODE (ENCyclopedia Of DNA Elements) Project.. Science. 306:636–640. 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
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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
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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
