Pukkila PJ. et al (including Guigo R.). Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A. 107(26):11889-94. (2010). PubMed ID: 20547848.abstract
Tilgner H, Guigó R.. From chromatin to splicing: RNA-processing as a total artwork. Epigenetics. Apr 27;5(3) (2010). PubMed ID: 20305391.abstract
Bayes M, Estivill X et al. "International network of cancer genome projects" Nature 464(7291):993-8 (2010). abstract
Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET.. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 2010 464(7289):773-7 (2010). PubMed ID: 20220756.abstract
International Aphid Genome Consortium (including Gabaldon T and Guigo R). Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol. 8(2):e1000313. (2010). PubMed ID: 20186266.abstract
Buschbeck M, Uribesalgo I, Wibowo I, Rué P, Martin D, Gutierrez A, Morey L, Guigó R, López-Schier H, Di Croce L. "The histone variant macroH2A is an epigenetic regulator of key developmental genes". Nat Struct Mol Biol. 16(10):1074-9. Epub 2009 Sep 6. (2009). PubMed ID: 19734898.abstract
Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcárcel J, Guigó R.. Nucleosome positioning as a determinant of exon recognition Nat Struct Mol Biol 2009 Sep;16(9):996-1001. (2009). PubMed ID: 19684599.abstract
Castellano S, Andrés AM, Bosch E, Bayes M, Guigó R, Clark AG.. "Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins." Mol Biol Evol. 2009 Sep; 26 (9): 2031-40. Epub 2009 Jun 1. (2009). PubMed ID: 19487332.abstract
Makrythanasis P, Kapranov P, Bartoloni L, Reymond A, Deutsch S, Guigó R, Denoeud F, et al. Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Hum Mutat. 30(9):E866-79. (2009). PubMed ID: 19562714.abstract
Arman M, Aguilera-Montilla N, Mas V, Puig-Kröger A, Pignatelli M, Guigó R, Corbí AL, Lozano F.. The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells. Mol Immunol. 2009 Jul;46(11-12):2226-35. Epub 2009 May 14. (2009). PubMed ID: 19446338.
Pignatelli M, Serras F, Moya A, Guigó R, Corominas M.. CROC: finding chromosomal clusters in eukaryotic genomes. Bioinformatics. 2009 Jun 15;25(12):1552-3. Epub 2009 Apr 23. (2009). PubMed ID: 19389737.abstract
Servitja JM, Pignatelli M, Maestro MA, Cardalda C, Boj SF, Lozano J, Blanco E, Lafuente A, McCarthy MI, Sumoy L, Guigó R, Ferrer J.. Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver. Mol Cell Biol. 2009 Jun;29(11):2945-59. Epub 2009 Mar 16. (2009). PubMed ID: 19289501.abstract
Boj SF, Servitja JM, Martin D, Rios M, Talianidis I, Guigo R, Ferrer J.. Functional targets of the monogenic diabetes transcription factors HNF-1alpha and HNF-4alpha are highly conserved between mice and humans. Diabetes. 2009 May;58(5):1245-53. Epub 2009 Feb 2. (2009). PubMed ID: 19188435.abstract
Bovine Genome Sequencing and Analysis Consortium (including Guigo, R.). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24;324(5926):522-8. (2009). PubMed ID: 19390049.abstract
Takeuchi A, Schmitt D, Chapple C, Babaylova E, Karpova G, Guigo R, Krol A, Allmang C.. A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins. Nucleic Acids Res. 2009 Apr;37(7):2126-41. Epub 2009 Feb 17. (2009). PubMed ID: 19223320.abstract
Chapple CE, Guigó R, Krol A.. SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements. Bioinformatics. 2009 Mar 1;25(5):674-5. Epub 2009 Jan 29. (2009). PubMed ID: 19179357.abstract
D. Gautheret et al. (including R. Guigo). "ASTD: The Alternative Splicing and Transcript Diversity database." Genomics Genomics. 2009 Mar;93(3):213-20. Epub 2008 Dec 24. (2009). PubMed ID: 19059335.
Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R.. Identifying protein-coding genes in genomic sequences. Genome Biol. 2009;10(1):201. Epub 2009 Jan 30. (2009). PubMed ID: 19226436.
Lacroix V, Sammeth M, Guigo R, et al.. Exact Transcriptome Reconstruction from Short Sequence Reads Source: ALGORITHMS IN BIOINFORMATICS, WABI 2008 Book Series: LECTURE NOTES IN BIOINFORMATICS Volume: 5251 Pages: 50-63 Published: 2008 (2008).
Blanco E, Pignatelli M, Beltran S, Punset A, Pérez-Lluch S, Serras F, Guigó R, Corominas M.. Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila. Genome Biol. 2008 Sep 10;9(9):R134 (2008). abstract
Manichanh C, Chapple CE, Frangeul L, et al. (including Guigo R). A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library NUCLEIC ACIDS RESEARCH 36;16.Pages: 5180-5188 (2008). abstract
C.E. Chapple and R. Guigó. "Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes." PLoS ONE (2008).
Sammeth M, Foissac S, Guigo R.. "A General Definition and Nomenclature for Alternative Splicing Events" PLOS COMPUTATIONAL BIOLOGY Vol.4;Issue: 8 (2008). abstract
Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud F, Calvo M, et al. "Efficient targeted transcript discovery via array-based normalization of RACE libraries" Nat Methods. 2008 May 25 (AOP) (2008). abstract
STAR Consortium (including Guigo R). SNP and haplotype mapping for genetic analysis in the rat. Nat Genet 2008 May;40(5):560-6 (2008). abstract
BioMoby Consortium (including Guigo R). Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform. 2008 May;9(3):220-31. Epub 2008 Jan 31. 2008 May;9(3):220-31. Epub 2008 Jan 31. (2008). abstract
Sammeth M, Valiente G, Guigó R.. "Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs"/ Book: Research in Computational Molecular Biology. Volum SpringerLink Volume 4955/2008. Pages 372-395 (2008). abstract
Weng Z, Guigó R.. “In silico meets in vivo” Genome Biol. 2008 Feb 25;9(2):302 (2008). abstract
Piqué M, López JM, Foissac S, Guigó R and Méndez R. A Combinatorial Code for CPE-Mediated Translational Control Cell Vol 132, 434-448 (2008).
Castellano S, Gladyshev VN, Guigó R, Berry MJ.. SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements Nucleic Acids Res. 2008 Jan;36:D332-8. Epub 2008 Jan 3. (2008). abstract
Drosophila 12 Genomes Consortium (Guigo R and Chapple C). "Evolution of genes and genomes on the Drosophila phylogeny" Nature 450(7167):203-18 (2007).
Lyle R, Prandini P, Osoegawa K, ten Hallers B, Humphray S, Zhu B, Eyras E, Castelo R, Bird CP, Gagos S, Scott C, Cox A, Deutsch S, Ucla C, Cruts M, et al. "Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21" Genome Res. 17(11):1690-6. Epub 2007 Sep 25 (2007).
Kerhornou A, Guigó R.. "BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations" Bionformatics 23(14):1831-3. Epub 2007 May 12 (2007).
The ENCODE Project Consortium (Alioto TS, Estivill X, Foissac S, Guigo R). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 447:799-816 (2007). abstract
Washietl S, Pedersen JS, Korbel JO, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigo R. Structured RNAs in the ENCODE selected regions of the human genome Genome Res. 17(6):852-64. (2007). abstract
Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, et al. "The DART classification of unannotated transcription within the ENCODE regions: associating transcription with and novel loci./ known and novel loci" Genome Res. 17(6):732-45. (2007). abstract
Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions/ ENCODE regions. Genome Res. 17(6):746-59 (2007). abstract
Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Gingeras TR, Guigo R, et al.. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res. 17(6):839-51. (2007). abstract
Blanco E, Parra G, Guigó R.. Using geneid to Identify Genes Current Protocols in Bioinformatics Chapter 4:Unit 4.3. (2007).
Blanco E, Guigo R, Messeguer X.. Multiple Non-Collinear TF-map Alignments of Promoter Regions BMC Bioinformatics 8(1):138 (2007). abstract
M.L. Tress et al. (including R. Guigó). "The implications of alternative splicing in the ENCODE protein complement" Proc Natl Acad Sci U S A. 104(13):5495-500 (2007). abstract
Tanner S, Shen Z, Ng J, Florea L, Guigo R, Briggs SP, Bafna V.. Improving gene annotation using peptide mass spectrometry. Genome Res. 17(2):231-9 (2007). abstract
Aury JM,Jaillon O,Duret L,NoelB, Jubin C,Porcel BM,Segurens B,Daubin V,Anthouard V,Aiach N,Arnaiz O,Billaut A,Beisson J,Blanc I,Bouhouche K,Camara F, et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444(7116):171-8 (2006). abstract
Guigo R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, et al. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 7 Suppl 1:S2.1-31. (2006). abstract
Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 7 Suppl 1:S4.1-9. Epub 2006 Aug 7 (2006). abstract
Guigó R, Valcarcel J. "Unweaving the meanings of messenger RNA sequences" Mol Cell. 2006 Jul 21. Review. 23(2):150-1 (2006). abstract
Blanco E, Messeguer X, Smith TF, Guigo R. "Transcription factor map alignment of promoter regions" PLoS Comput Biol. 2(5):e49- (2006). abstract
Mularoni L, Guigo R, Alba MM. "Mutation patterns of amino acid tandem repeats in the human proteome". Genome Biol. 7(4):R33:- (2006). abstract
Enrique Blanco, Domènec Farré, M. Mar Albà, Xavier Messeguer and Roderic Guigó. "ABS: a database of Annotated regulatory Binding Sites from orthologous promoters" Nucleic Acids Research 34:D63-67 (2006). abstract
Genís Parra, Alexandre Reymond, Noura Dabbouseh, Emmanouil, T. Dermitzakis,Robert Castelo, Timothy M. Thomson, Stylianos E. Antonarakis, and et al. "Tandem chimerism as a means to increase protein complexity in the human genome." Genome Res 16 (1):37-44 (2006). abstract
Sergi Castellano, Alexey V. Lobanov, Charles Chapple, Sergey V. Novoselov, Mario Albrecht, Deame Hua, et al. "Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family Proc Natl Acad Sci U S A. PNAS 102(45):16188-16193 (2005). abstract
Izquierdo JM, Majos N, Bonnal S, Martinez C, Castelo R, Guigo R, Bilbao D, Valcarcel J. Regulation of Fas Alternative Splicing by Antagonistic Effects of TIA-1 and PTB on Exon Definition Molecular Cell 19(4):475-484 (2005). abstract
Guigo R, Reese MG. EGASP: collaboration through competition to find human genes. Nat Methods 2(8):575-577 (2005). abstract
Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, et al. "Gene finding in the chicken genome." BMC Bioinformatics. 6:131 (2005). abstract
Taskov K, Chapple C, Kryukov GV, Castellano S, Lobanov AV, Korotkov KV, Guigo R, Gladyshev VN.. "Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?" Nucleic Acids Res. 33(7):2227-2238 (2005). abstract
Castelo R, Reymond A, Wyss C, Camara F, Parra G, Antonarakis SE, Guigo R, Eyras E.. "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(6):1935-1939 (2005). abstract
Lopez-Bigas N, Audit B, Ouzounis C, Parra G, Guigo R.. "Are splicing mutations the most frequent cause of hereditary disease?" FEBS Lett 579(9):1900-1903 (2005). abstract
Szafranski K, Lehmann R, Parra G, Guigo R, Glockner G.. "Gene organization features in A/T-rich organisms." J Mol Evol. 60(1):90-98 (2005). abstract
Abril JF, Castelo R, Guigo R. "Comparison of splice sites in mammals and chicken". Genome Res. 15:111-119 (2005). abstract
Guigó R and Zhang MQ. "Gene predictions and Annotations. In A. Ruvinsky and J. Marshall Graves editors: Mammalian Genomics" CAB International 15:111-119 (2004).
E. Eyras, R. Castelo, J.F. Abril, S. Castellano, F. Camara, G. Parra and R. Guigó et al. "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution." Nature 432(7018):695-716 (2004). abstract
The ENCODE Project Consortium (including Denoeud F, Lagarde J, Wesselink J J, Castelo R, Eyras E, and Guigó R). "The ENCODE (ENCyclopedia of DNA Elements) Project". Science 306:636-640 (2004).
Jaillon O et al (including Castellano S, Parra G, Chapple C and Guigó R). "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype." Nature 431:946-957 (2004).
Castelo R and Guigó R. "Splice Site Identification by idlBNs". Bioinformatics 20:169-176 (2004).
Castresana J, Guigó R and Albà M. "Clustering of Genes Coding for DNA Binding Proteins in a Region of Atypical Evolution of the Human Genome". J Mol Evol 59:72-79 (2004).
J.M. Hancock and M.J. Zvelebil editors.. "Dictionary of Bioinformatics and Computational Biology" Wiley-Liss, ISBN:0-471-43622-4:- (2004).
Brent MR and Guigó R. "Recent advances in gene structure prediction" Current Opinion in Structural Biology 14:264-272 (2004).
Albà M, Guigó R. "Comparative analysis of amino acid repeats in rodents and humans and relationship to GC content". Genome Res 14(4):549-54 (2004).
Rat Genome Sequencing Project Consortium (including Câmara F, Albà M, Abril J F, Eyras E and Guigó R). "Genome sequence of the brown Norway rat yields insights into mammalian evolution." Nature 428:493-521 (2004).
Castellano S, Novoselov, Kryukov, Lescure, Blanco E, Krol, Gladyshev, Guigó R. "Reconsidering the evolutionary distribution of selenoproteins: identification of a novel family in fish, birds and diatoms". EMBO Reports 5(1):71-7 (2004).
Abril JF, Guigó R and Wiehe T. "gff2aplot: Plotting sequence comparisons". Bioinformatics 19:2477-2479 (2003).
Guigó R, Wiehe T. "Gene Prediction Accuracy in Large DNA Sequences." In M.Y. Galperin and E.V. Koonin, editors:Frontiers in Computational Genomics. Chapter 1, Pp:1-33. (Functional Genomics Series, Volume 3) Caister Aca 3:- (2003).
Kryukov G V, Castellano S, Novoselov SV, Lobanov A V, Zehtab O, Guigó R and Gladyshev V N. "Characterization of mammalian selenoproteomes.". Science 300:1439-1443 (2003).
Beltran S, Blanco E, Serras F, Pèrez-VillamilB, Guigó R, Artavanis-Tsakonas S and Corominas M. "Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster". Proc Nat Acad Sci (USA) 100:3293-3298 (2003).
Guigó R, Dermitzakis E T, Agarwal P, Ponting C P, Parra G, Reymond A, Abril J F, Keibler E, Lyle R, Ucla C, Antonarakis S E and Brent M R. "Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes". Proc Nat Acad Sci(USA) 100:1140-1145 (2003).
Parra G, Agarwal P, Abril J F, Wiehe T, Fickett J W and Guigó R. "Comparative gene prediction in human and mouse". Genome Res 13:108-117 (2003).
Mouse Genome Sequencing Consortium (including Abril J F, Parra G and Guigó R. "Initial sequencing and comparative analysis of the mouse genome". Nature 420:520-562 (2002).
Holt R A et al (including Abril J F and Guigó R).. "The Genome Sequence of the Malaria Mosquito Anopheles gambiae". Science 298:129-149 (2002).
Glökner G, Eichinger L, Szafranski K, Pachebat J A, Bankier A T, Dear, R. Lehmann, Baumgart C, Parra G, Abril J F, Guigó R, Kumpf K, Tunggal B, the Di et al. "Sequence and Analysis of Chromosome 2 of Dictyostelium discoideum". Nature 418:79-85 (2002).
Venter JC et al (including Guigo R.). "The Sequence of the Human Genome" Science 291(5507):1304-1351 (2001).
Burset M and Guigo R.. "Evaluacion of gene structure prediction programs." Genomics 34(3):353.357 (1996).
Guigo R, Knudsen S, Drake N and Smith TF. "Prediction of gene structure" Journal of Molecular Biology 226:141-157 (1992).
Guigo R, Knudsen S, Drake N and Smith TF. "Prediction of gene structure" Journal of Molecular Biology 226:141-157 (1992).
Burset M, Guigo R.. "Evaluation of gene structure prediction programs" Genomics 34(3):353-357 (1992).
Drosophila 12 Genomes Consortium (including R Guigo). "Evolution of genes and genomes on the Drosophila phylogeny" Nature Vol 450; 203-218 (0207). abstract
