PUBLICATIONS


Publications In Press

  • J.F. Abril, S. Castellano and R. Guigó
    "Comparative gene prediction."
    In M.D. Adams editor:
    Comparative Genomics: A Guide to the Analysis of Eukaryotic Genomes.
    Humana Press, 2006 (in press). ISBN: 1-58829-339-4.   [sgp2]   [gff2aplot]

Publications in 2009

  • H. Tilgner, C. Nikolaou, S. Althammer, M. Sammeth, M. Beato, J. Valcarcel and R. Guigó
    "Nucleosome positioning as a determinant of exon recognition."
    Nat Struct Mol Biol. (2009) Published online before print Aug 16, 2009  [Abstract]   [PDF]  [PubMed]  

  • P. Makrythanasis, P. Kapranov, L. Bartoloni, A. Reymond, Deutsch S, R. Guigó , F. Denoeud, J. Drenkow, C. Rossier, F. Ariani, V. Capra, L. Excoffier, A. Renieri, T.R. Gingeras and S.E. Antonarakis
    "Variation in Novel Exons (RACEfrags) of the MECP2 Gene in Rett Syndrome Patients and Controls."
    Hum Mutat. (2009) Published online before print June 26, 2009  [Abstract]   [PDF]  [PubMed]  

  • S. Castellano, A.M. Andres, E. Bosch, M. Bayes, R. Guigó and A.G. Clark
    "Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins."
    Mol Biol Evol. 26(9):2031-2040. (2009) Published online before print June 1, 2009  [Abstract]   [PDF]  [PubMed]  

  • M. Arman, N. Aguilera-Montilla, V. Mas, A. Puig-Kroger, M. Pignatelli, R. Guigó , A.L. Corbi and F. Lozano
    "The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells."
    Mol Immunol doi:10.1016/j.molimm.2009.04.018 (2009) Published online before print May 13, 2009  [Abstract]   [PDF]  [PubMed]  

  • "The Bovine Genome Sequencing and Analysis Consortium" including (T. Alioto, F. Camara and R. Guigó)
    "The genome sequence of taurine cattle: a window to ruminant biology and evolution."
    Science 24(5926):522-528 (2009) [Abstract]   [PDF]   [PubMed]   [SUPPLEMENTARY]  

  • M. Pignatelli, F. Serras, A. Moya, R. Guigó and M. Corominas
    "CROC: Finding Chromosomal Clusters in Eukaryotic Genomes."
    Bioinformatics doi:10.1093/bioinformatics/btp248 (2009) Published online before print Apr 23, 2009  [Abstract]   [PubMed]  

  • J.M. Servitja, M. Pignatelli, M.A. Maestro, C. Cardalda, S.F. Boj, J. Lozano, E. Blanco, A. Lafuente, M.I. McCarthy, L. Sumoy, R. Guigó and J. Ferrer
    "Hnf1{alpha} (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver."
    Mol. Cell. Biol. doi:10.1128/MCB.01389-08 (2009) Published online before print Mar 16, 2009  [Abstract]   [PubMed]  

  • S.F. Boj, J.M. Servitja, D. Martin, M. Rios, I. Talianidis, R. Guigó and J. Ferrer
    "The functional targets of the monogenic diabetes transcription factors HNF1{alpha} and HNF4{alpha} are highly conserved between mice and humans."
    Diabetes 0:db08-0812v2-0 (2009) Published online before print Feb 10, 2009  [Abstract]   [PubMed]   [SUPPLEMENTARY]  

  • C.E. Chapple, R. Guigó and A. Krol
    "SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements."
    Bioinformatics doi:10.1093/bioinformatics/btp020 (2009) Published online before print Jan 29, 2009  [Abstract]   [PDF]   [PubMed]   [SUPPLEMENTARY]  

  • J. Thornton for "the BioSapiens Network" (including R. Guigó)
    "Annotations for all by all - the BioSapiens network."
    Genome Biology 10:401-4 (2009) [Abstract]  [PDF]  

  • J. Harrow, A. Nagy, A. Reymond, T. Alioto, L. Patthy, S.E. Antonarakis and R. Guigó
    "Identifying protein-coding genes in genomic sequences."
    Genome Biology 10(1):201 (2009) Published online before print Jan 30, 2009  [Abstract]  [PREVIEW PDF]   [PubMed]  

Publications in 2008

  • A. Coghlan et al. (including T. Alioto, F. Camara and R. Guigó as part of "The nGASP Consortium")
    "nGASP - the nematode genome annotation assessment project."
    BMC Bioinformatics 9(1):549 (2008) Published online before print Dec 19, 2008  [Abstract]   [PDF]   [PubMed]  

  • G. Koscielny, V.L. Texier, C. Gopalakrishnan, V. Kumanduri, J.J. Riethoven, F. Nardone, E. Stanley, C. Fallsehr, O. Hofmann, M. Kull, E. Harrington, S. Boué, E. Eyras, M. Plass, F. Lopez, W. Ritchie, V. Moucadel, T. Ara, H. Pospisil, A. Herrmann, J. Reich G, R. Guigó, P. Bork, M.V. Doeberitz, J. Vilo, W. Hide, R. Apweiler, T.A. Thanaraj and D. Gautheret
    "ASTD: The Alternative Splicing and Transcript Diversity database."
    Genomics (2008) doi:10.1016/j.ygeno.2008.11.003 Published online before print Dec 23, 2008 [Abstract]   [PDF]  [PubMed]  

  • M. Plass, E. Agirre, D. Reyes, F. Camara and E. Eyras
    "Co-evolution of the branch site and SR proteins in eukaryotes."
    Trends in Genetics doi:10.1016/j.tig.2008.10.004 (2008) Published online before print Nov 5, 2008  [Abstract]   [PDF]   [PubMed]  

  • E. Blanco, E. Pignatelli, M. Beltran, S. Punset, A. Perez-Lluch, S. Serras, R. Guigó and M. Corominas
    "Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila."
    Genome Biology 9(9):R134 (2008) Published online before print Sept 10, 2008  [Abstract]   [PDF]   [PubMed]  

  • C.E. Chapple and R. Guigó
    "Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes."
    PLoS ONE 3(8):e2968 (2008) Published online before print Aug 18, 2008  [Abstract]   [PDF]   [PubMed]  

  • V. Lacroix, M. Sammeth, R. Guigó and A. Bergeron
    "Exact Transcriptome Reconstruction from Short Sequence Reads."
    8th Workshop on Algorithms in Bioinformatics (WABI), September 15-17 (2008) [Accepted Papers]   [Submitted PDF]  

  • T.S. Alioto, R. Guigó, E. Picardi and G. Pesole
    "GenePC and ASPIC Integrate Gene Predictions with Expressed Sequence Alignments To Predict Alternative Transcripts."
    Proceedings of 6th Asia-Pacific Bioinformatics Conference (Kyoto, Japan), January 14-17:363-72 (2008) [Accepted Papers]   [PDF]  

  • M. Sammeth , S. Foissac and R. Guigó
    "A general definition and nomenclature for alternative splicing events."
    PLoS Comput. Biol. 4(8):e1000147 (2008) [Abstract]   [PDF]   [PubMed]  

  • C. Manichanh, C.E. Chapple, L. Frangeul, R. Guigó and J. Dore
    "A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library."
    Nucleic Acids Research 10.1093/nar/gkn496:1-9 (2008) Published online before print Aug 5, 2008 [Abstract]   [PDF]  [PubMed]  

  • S. Djebali ,P. Kapranov ,S. Foissac ,J. Lagarde ,A. Reymond , C. Ucla, C. Wyss, J. Drenkow, E. Dumais, R.R. Murray, C. Lin, D. Szeto, F. Denoeud, M. Calvo, A. Frankish, J. Harrow, P. Makrythanasis, M. Vidal, K. Salehi-Ashtiani, S.E. Antonarakis, T.R. Gingeras and R. Guigó
    "Efficient targeted transcript discovery via array-based normalization of RACE libraries."
    Nature Methods 5(7):629-35 (2008) Published online before print May 25, 2008 [Abstract]   [PDF]  [PubMed]  

  • "The STAR Consortium" (including M. Shikhagaie and R. Guigó)
    "SNP and haplotype mapping for genetic analysis in the rat."
    Nature Genetics 40(5):560-6 (2008) [Abstract]   [Full Text]   [PubMed]   [SUPPLEMENTARY]  

  • Z. Weng and R. Guigó
    "In silico meets in vivo."
    Genome Biology 9(2):302 (2008), Published online before print Feb 25, 2008  [Abstract]   [PubMed]  

  • M. Piqué, J.M. López, S. Foissac, R. Guigó and R. Méndez
    "A combinatorial code for CPE-mediated translational control."
    Cell 132(3):335-37 (2008) [Abstract]   [PDF]   [PubMed]   [SUPPLEMENTARY]  

  • "The BioMoby Consortium" (including R. Guigó)
    "Interoperability with Moby 1.0--it's better than sharing your toothbrush!"
    Briefings in Bioinformatics 9(3):220-31 (2008), Published online before print Jan 31, 2008  [Abstract]   [PDF]   [PubMed]   [SUPPLEMENTARY]  

  • S. Castellano,V.N. Gladyshev, R. Guigó and M.J. Berry
    "SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements."
    Nucleic Acids Research 36(Database issue):D332-38 (2008), Published online before print Jan 3, 2008  [Abstract]   [PDF]   [PubMed]   [SUPPLEMENTARY]   [SelenoDB]  

Publications in 2007

  • A.G. Clark et al. (including R. Guigó and C. Chapple )
    "Evolution of genes and genomes on the Drosophila phylogeny."
    Nature 450(7167):203-18 (2007) [Abstract]   [PDF]   [PubMed]  

  • R. Lyle, P. Prandini, K. Osoegawa, B. ten Hallers, S. Humphray, B. Zhu, E. Eyras, R. Castelo, C.P. Bird, S. Gagos, C. Scott, A. Cox, S. Deutsch, C. Ucla, M. Cruts, S. Dahoun, X. She, F. Bena, S.Y. Wang, C. Van Broeckhoven, E.E. Eichler, R. Guigó, J. Rogers, P.J. de Jong, A. Reymond and S.E. Antonarakis
    "Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21."
    Genome Research 17(11):1690-6 (2007), Published online before print September 25, 2007  [Abstract]   [PDF]   [PubMed]   [Datasets]  

  • "The ENCODE Project Consortium" (including R. Guigó, J. Lagarde, S. Foissac, R. Castelo, T.S. Alioto, J.F. Abril and F. Denoeud )
    "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project."
    Nature 447(7146):799-816 (2007)   [Abstract]   [PDF]  [PubMed]  

  • S. Washietl, J.S. Pedersen, J.O. Korbel, C. Stocsits, A.R. Gruber, J. Hackermuller, J. Hertel, M. Lindemeyer, K. Reiche, A. Tanzer, C. Ucla, C. Wyss , S.E. Antonarakis, F. Denoeud, J. Lagarde, J. Drenkow, P. Kapranov, T.R. Gingeras, R. Guigó, M. Snyder, M.B Gerstein, A. Reymond, I.L. Hofacker and P.F. Stadler
    "Structured RNAs in the ENCODE selected regions of the human genome."
    Genome Research 17(6):852-64 (2007) [Abstract]   [PDF]   [PubMed]  

  • D. Zheng, A. Frankish, R. Baertsch, P. Kapranov, A. Reymond, S.W. Choo, Y. Lu, F. Denoeud, S.E. Antonarakis, M. Snyder, Y Ruan, C.L. Wei, T.R. Gingeras, R. Guigó, J. Harrow and M.B Gerstein
    "Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution."
    Genome Research 17(6):839-51 (2007) [Abstract]   [PDF]   [PubMed]   [Datasets]  

  • F. Denoeud, P. Kapranov, C. Ucla, A. Frankish, R. Castelo, J. Drenkow, J. Lagarde, T.S. Alioto, C. Manzano, J. Chrast, S. Dike, C. Wyss, C.N. Henrichsen, N. Holroyd, M.C. Dickson, R. Taylor, Z. Hance, S. Foissac, R.M. Myers, J. Rogers, T. Hubbard, J. Harrow, R. Guigó, T.R. Gingeras, S.E. Antonarakis and A. Reymond
    "Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions."
    Genome Research 17(6):746-59 (2007) [Abstract]   [PDF]   [PubMed]   [Datasets]  

  • A. Mellmann, T. Weniger, C. Berssenbrugge, J. Rothganger, M. Sammeth, J. Stoyea and D. Harmsen
    "Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms."
    BMC Microbiology 7:98 (2007) [Abstract]   [PDF]   [PubMed]  

  • S. Foissac and M. Sammeth
    "ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets."
    Nucleic Acids Research 35(Web Server issue):W297-9 (2007), Published online before print May 7, 2007  [Abstract]   [PDF]   [PubMed]   [ASTALAVISTA]  

  • J.S. Rozowsky, D. Newburger, F. Sayward, J. Wu, G. Jordan, J.O. Korbel, U. Nagalakshmi, J. Yang, D. Zheng, R. Guigó , T.R. Gingeras, S. Weissman, P. Miller, M. Snyder, and M.B. Gerstein
    "The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci."
    Genome Research 17(6):732-45 (2007) [Abstract]   [PDF]   [PubMed]   [Datasets]  

  • A. Kerhornou and R. Guigó
    "BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations."
    Bioinformatics 23(14):1831-33 (2007), Published online before print May 12, 2007  [Abstract]   [PDF]   [PubMed]  

  • E. Blanco, R. Guigó and X. Messeguer.
    "Multiple Non-collinear TF-Map Alignments of Promoter Regions."
    BMC Bioinformatics 8:138 (2007) [Open Access]  

  • S. Tanner, Z. Shen, J. Ng, L. Florea, R. Guigó, S.P. Briggs and V. Bafna
    "Improving gene annotation using peptide mass spectrometry."
    Genome Research 17(2):231-9 (2007), Published online before print December 22, 2006   [Abstract]   [PDF]   [PubMed]   [Datasets]  

  • M.L. Tress et al. (including R. Guigó, J. Lagarde and F. Denoeud )
    "The implications of alternative splicing in the ENCODE protein complement."
    Proc. Nat. Acad. Sci. 104(13):5495-500 (2007) Published online before print March 19, 2007  [Abstract]   [PDF]   [PubMed]   [Datasets]  

  • T.S. Alioto
    "U12DB: a database of orthologous U12-type spliceosomal introns."
    Nucleic Acids Research, 35(DataBase Issue):D110-D115 ( 2006)   [Abstract]   [PDF]   [PubMed]   [U12DB]
    [NAR Advance Access originally published online on November 1, 2006]

Publications in 2006

  • J.M. Aury, O. Jaillon, L. Duret, B. Noel, C. Jubin, B.M. Porcel, B. Segurens, V. Daubin, V. Anthouard, N. Aiach, O. Arnaiz, A. Billaut, J. Beisson, I. Blanc, K. Bouhouche, F. Câmara, S. Duharcourt, R. Guigó, D. Gogendeau, M. Katinka, A.M. Keller, R. Kissmehl, C. Klotz, F. Koll, A. Le Mouel, G. Lepere, S. Malinsky, M. Nowacki, J.K. Nowak, H. Plattner, J. Poulain, F. Ruiz, V. Serrano, M. Zagulski, P. Dessen, M. Betermier, J. Weissenbach, C. Scarpelli, V. Schachter, L. Sperling, E. Meyer, J. Cohen and P.M. Wincker
    "Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia."
    Nature, 444(7116):171-187 (2006)   [Abstract]   [PDF]   [PubMed]

  • M.G. Reese and R. Guigó
    "EGASP: Introduction."
    Genome Biology, 7(Suppl 1):S1 (2006)   [Full Text]   [PDF]   [PubMed]   [GENCODE]   [EGASP]
    NEW   We are pleased to announce that the EGASP Genome Biology supplement is now available via AMAZON.   NEW

  • R. Guigó, P. Flicek, J.F. Abril, A. Reymond, J. Lagarde, F. Denoeud, S. Antonarakis, M. Ashburner, V.B. Bajic, E. Birney, R. Castelo, E. Eyras, C. Ucla, T.R. Gingeras, J. Harrow, T. Hubbard, S. Lewis and M.G. Reese
    "EGASP: The human ENCODE GENOME ANNOTATION ASSESSMENT PROJECT."
    Genome Biology, 7(Suppl 1):S2 (2006)   [Full Text]   [PDF]   [PubMed]   [EGASP]

  • J. Harrow, F. Denoeud, A. Frankish, A. Reymond, C.-K. Chen, J. Chrast, J. Lagarde, J.G.R. Gilbert, R. Storey, D. Swarbreck, C. Rossier, C. Ucla, T. Hubbard, S.E. Antonarakis and R. Guigó
    "GENCODE: producing a reference annotation for ENCODE."
    Genome Biology, 7(Suppl 1):S4 (2006)   [Full Text]   [PDF]   [PubMed]   [GENCODE]

  • R. Guigó and J. Valcárcel
    PREVIEW: "Unweaving the meanings of messenger RNA sequences."
    Molecular Cell, 23(2):150-151 (2006)   [Abstract]   [Full Text]   [PubMed]

  • E. Blanco.
    "Meta-Alignment of Biological Sequences."
    PhD Thesis, Departament de Llenguatges i Sistemes Informàtics at Universitat Politècnica de Catalunya, 2006.
    [Thesis Web Site]

  • E. Blanco, X. Messeguer, T. Smith and R. Guigó
    "Transcription Factor Map Alignment of Promoter Regions."
    PLoS Computational Biology, 2(5):e49 (2006)   [Open Access Article]   [PubMed]   [Datasets]

  • L. Mularoni, R. Guigó and M.M. Albà
    "Mutation patterns of amino acid tandem repeats in the human proteome."
    Genome Biology, 7(4):R33 (2006)   [Full Text]   [PDF]   [PubMed]

  • G. Parra, A. Reymond, N. Dabbouseh, E.T. Dermitzakis, R. Castelo, T.M. Thompson, S.E. Antonarakis, and R. Guigó
    "Tandem chimerism as a means to increase protein complexity in the human genome."
    Genome Research, 19(8):475-484 ( 2006)   [Abstract]   [From the cover]   [PubMed]
    [Published online before print in Dec 2005]

  • E. Blanco, D. Farré, M.M. Albà, X. Messeguer and R. Guigó
    "ABS: a database of Annotated regulatory Binding Sites from orthologous promoters."
    Nucleic Acids Research, 34(Suppl 1:Database Issue):D63-D67 (2006)   [Abstract]   [NAR Open Access Article PDF]   [PubMed]   [ABS]

Publications in 2005

  • S. Castellano, A.V. Lobanov, C. Chapple, S.V. Novoselov, M. Albrecht, D. Hua, A. Lescure, T. Lengauer, A. Krol, V.N. Gladyshev and R. Guigó
    "Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family."
    PNAS, 102(45):16188-16193 (2005)   [Abstract]   [From the cover]   [PubMed]
    [Commentary by R.J. Stillwell and M.J. Berry]

  • R. Guigó, F. Morán, A. Valencia and J.F. Abril
    EDITORIAL: "ECCB/JBI 2005."
    Bioinformatics, 21(Suppl2):ii1-ii2 (2005)
    [ECCB/JBI - Computational Biology 2005]   [Proceedings Table of Contents]
    [Editorial PDF]   [PubMed]   [Organization PDF]   [PubMed]

  • J.M. Izquierdo, N. Majós, S. Bonnal, C. Martínez, R. Castelo, R. Guigó, D. Bilbao and J. Valcárcel
    "Regulation of Fas Alternative Splicing by Antagonistic Effects of TIA-1 and PTB on Exon Definition."
    Molecular Cell, 19(8):475-484 (2005)   [Abstract]   [PubMed]

  • R. Guigó and M.G. Reese
    COMMENTARY: "EGASP: collaboration through competition to find human genes."
    Nature Methods, 2(8):575-577 (2005)   [Abstract]   [PubMed]

  • E. Eyras, A. Reymond, R. Castelo, J.M. Bye, F. Câmara, P. Flicek, E.J. Huckle, G. Parra, D.D. Shteynberg, C. Wyss, J. Rogers, S.E. Antonarakis, E. Birney, R. Guigó and M.R. Brent
    "Gene finding in the chicken genome."
    BMC Bioinformatics, 6(1):131 (2005)   [Abstract]   [BMC Open Access Article PDF]   [PubMed]
    [BMC electronic publication ahead of print]

  • J.F. Abril.
    "Comparative Analysis of Eukaryotic Gene Sequence Features."
    PhD Thesis, Departament de Ciéncies Experimentals i de la Salut at Universitat Pompeu Fabra, 2005.

  • K. Taskov, C. Chapple, G.V. Kryukov, S. Castellano, A.V. Lobanov, K.V. Korotkov, R. Guigó and V.N. Gladyshev
    "Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome ?"
    Nucleic Acids Research, 33(7):2227-38 (2005)   [Abstract]   [NAR Open Access Article PDF]   [PubMed]

  • N. López-Bigas, B. Audit, C. Ouzounis, G. Parra and R. Guigó
    "Are splicing mutations the most frequent cause of hereditary disease ?"
    FEBS Letters, 579(9):1900-3 (2005)   [Abstract]   [PubMed]

  • R. Castelo, A. Reymond, C. Wyss, F. Câmara, G. Parra, S.E. Antonarakis, R. Guigó and E. Eyras
    "Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely-expressed human genes."
    NAR, 33(6):1935-1939 (2005)   [Abstract]   [NAR Open Access Article PDF]   [Supplementary Material]

  • K. Szafranski, R. Lehmann, G. Parra, R. Guigó and G. Glöckner
    "Gene Organization Features in A/T-Rich Organisms."
    Journal of Molecular Evolution, 60(1):90-98 (2005)   [Abstract]   [Full Text]

  • J.F. Abril, R. Castelo and R. Guigó
    "Comparison of splice sites in mammals and chicken."
    Genome Research, 15(1):111-119 (2005)   [Abstract]   [Full Text]   [Datasets]
    [Published online before print in Dec 2004]

Publications in 2004

  • R. Guigó and M.Q. Zhang
    "Gene predictions and Annotations."
    In A. Ruvinsky and J. Marshall Graves editors:
    Mammalian Genomics.
    CAB International, 2004. ISBN: 0-851-99910-7.   [geneid]   [sgp2]

  • M.B. Wahl, R.B. Caldwell, A.M. Kierzek, H. Arakawa, E. Eyras, N. Hubner, C. Jung, M. Soeldenwagner, M. Cervelli, Y-D. Wang, V. Liebscher and J-M. Buerstedde
    "Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line."
    BMC Genomics, 5:98 (21 December 2004)   [Abstract]   [PDF]

  • International Chicken Genome Sequencing Consortium
    (including E. Eyras, R. Castelo, J.F. Abril, S. Castellano, F. Câmara, G. Parra and R. Guigó)
    "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution."
    Nature, 432(7018):695-716 (2004)   [Abstract]   [Full Text]

  • G. Parra.
    "Computational Identification of Genes: ab initio and comparative approaches."
    PhD Thesis, Departament de Ciéncies Experimentals i de la Salut at Universitat Pompeu Fabra, 2004.

  • The ENCODE Project Consortium
    (including F. Denoeud, J. Lagarde, J.J. Wesselink, R. Castelo, E. Eyras and R. Guigó).
    "The ENCODE (ENCyclopedia Of DNA Elements) Project."
    Science, 306(5696):636-640 (2004)   [Abstract]   [Full Text]   [GENCODE Project]

  • O. Jaillon et al (including S. Castellano, G. Parra, C. Chapple and R. Guigó).
    "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype."
    Nature, 431(7011):946-957 (2004)   [Abstract]   [Full Text]

  • The International Human Genome Sequencing Consortium (Includes E. Eyras).
    "Finishing the euchromatic sequence of the human genome."
    Nature 431, 931-45 (21 October 2004)   [Abstract]   [Full Text]

  • E. Blanco and R. Guigó.
    "Predictive Methods using DNA Sequences."
    In A.D. Baxevanis and B.F.F. Oullette, editors:
    Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. 3rd Edition. Chapter 5.
    John Wiley & Sons Inc., New York, 2004. ISBN: 0-471-47878-4.   [Table of Contents]   [geneid]

  • J. Castresana, R. Guigó and M. Albà.
    "Clustering of Genes Coding for DNA Binding Proteins in a Region of Atypical Evolution of the Human Genome."
    Journal of Molecular Evolution, 59(1):72-79 (2004)   [Abstract]

  • S. Castellano.
    "Towards the Characterization of the Eukaryotic Selenoproteome: A Computational Approach."
    PhD Thesis, Departament de Ciéncies Experimentals i de la Salut at Universitat Pompeu Fabra, 2004.

  • R. Castelo and R. Guigó.
    "Splice Site Identification by idlBNs."
    Bioinformatics, 20(Suppl1):I69-I76 (2004)   [PubMed]   [PDF]   [Datasets]

  • Dictionary of Bioinformatics and Computational Biology.
    (R. Guigó contributor)
    J.M. Hancock and M.J. Zvelebil editors.
    Wiley-Liss, 2004. ISBN: 0-471-43622-4.   [Description]

  • M.R. Brent and R. Guigó.
    "Recent advances in gene structure prediction."
    Current Opinion in Structural Biology, 14(3):264-272 (2004)   [PubMed]   [Abstract]

  • M. Albà and R. Guigó.
    "Comparative analysis of amino acid repeats in rodents and humans."
    Genome Research, 14(4):549-554 (2004)   [Abstract]   [Full text]

  • Rat Genome Sequencing Project Consortium
    (including F. Câmara, M. Albà, J.F. Abril, E. Eyras and R. Guigó).
    "Genome sequence of the brown Norway rat yields insights into mammalian evolution."
    Nature, 428(6982):493-521 (2004)   [Abstract]   [Full text]

  • R. Castelo and M.D. Perlman.
    "Learning Essential Graph Markov Models from Data."
    In J.A. Gàmez, S. Moral and A. Salmerón, editors:
    Advances in Bayesian Networks. Chapter 14, Pp:255-270.
    (Series: Studies in Fuzziness and Soft Computing, Volume 146)
    Springer-Verlag, Berlin, Germany, 2004. ISBN: 3-540-20876-3.   [Table of Contents]

  • S. Castellano, S.V. Novoselov, G.V. Kryukov, A. Lescure, E. Blanco, A. Krol. V.N. Gladyshev and R. Guigó.
    "Reconsidering the evolution of eukaryotic selenoproteins: a novel non-mammalian family with scattered phylogenetic distribution."
    EMBO reports, 5(1):71-77 (2004)   [PubMed]   [Abstract]   [Full text]   [Datasets]   [Commentary to this paper]

Publications in 2003

  • J.F. Abril, R. Guigó and T. Wiehe.
    "gff2aplot: Plotting sequence comparisons."
    Bioinformatics 19(18):2477-2479 (2003)   [PubMed]   [Abstract]   [gff2aplot]

  • R. Guigó and T. Wiehe.
    "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 Academic Press, United Kingdom, 2003. ISBN: 0-9542464-4-6.   [Table of Contents]

  • R. Castelo and T. Kocka.
    "On inclusion-driven learning of Bayesian Networks."
    Journal of Machine Learning Research 4(Sep):527-574 (2003)   [Abstract]

  • G.V. Kryukov, S. Castellano, S.V. Novoselov, A.V. Lobanov, O. Zehtab, R. Guigó and V.N. Gladyshev
    "Characterization of mammalian selenoproteomes."
    Science 300(5624):1439-1443 (2003)   [PubMed]   [Abstract]   [Full Text]   [Datasets]

  • E. Blanco, G. Parra and R. Guigó.
    "Using geneid to Identify Genes."
    In A. D. Baxevanis and D. B. Davison, chief editors:
    Current Protocols in Bioinformatics. Volume 1, Unit 4.3.
    John Wiley & Sons Inc., New York, 2002. ISBN: 0-471-25093-7.   [Table of Contents]   [geneid]

  • S. Beltran, E. Blanco, F. Serras, B. Pèrez-Villamil, R. Guigó, S. Artavanis-Tsakonas and M. Corominas.
    "Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster."
    Proc. Nat. Acad. Sci. 100(6):3293-3298 (2003)   [PubMed]   [Abstract]   [Full Text]

  • R. Guigó, E.T. Dermitzakis, P. Agarwal, C.P. Ponting, G. Parra, A. Reymond, J.F. Abril, E. Keibler, R. Lyle, C. Ucla, S.E. Antonarakis and M.R. Brent.
    "Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes."
    Proc. Nat. Acad. Sci. 100(3):1140-1145 (2003)   [PubMed]   [Abstract]   [Full Text]   [Datasets]

  • G. Parra, P. Agarwal, J.F. Abril, T. Wiehe, J.W. Fickett and R. Guigó.
    "Comparative gene prediction in human and mouse."
    Genome Research 13(1):108-117 (2003)   [PubMed]   [Abstract]   [Datasets]   [sgp2]

Publications in 2002

  • Mouse Genome Sequencing Consortium (including J.F. Abril, G. Parra and R. Guigó).
    "Initial sequencing and comparative analysis of the mouse genome."
    Nature 420(6915):520-562 (2002)   [PubMed]   [Abstract]   [Full text]

  • R.A. Holt et al (including J.F. Abril and R. Guigó).
    "The Genome Sequence of the Malaria Mosquito Anopheles gambiae."
    Science 298(5591):129-149 (2002)   [PubMed]   [Abstract]   [Poster]   [gff2ps]

  • R. Guigó and D. Gusfield editors.
    "Algorithms in Bioinformatics."
    Proceedings of the Second International Workshop, WABI 2002.
      (Lecture Notes in Computer Science, Volume 2452)
    Springer-Verlag, Berlin Heidelberg, 2002. ISBN: 3-540-44211-1.   [Table of Contents]

  • G. Glökner, L. Eichinger, K. Szafranski, J.A. Pachebat, A.T. Bankier, P.H. Dear, R. Lehmann, C. Baumgart, G. Parra, J.F. Abril, R. Guigó, K. Kumpf, B. Tunggal, the Dictyostelium Genome Sequencing Consortium, E. Cox, M.A. Quail, M. Platzer, A. Rosenthal and A.A. Noegel.
    "Sequence and Analysis of Chromosome 2 of Dictyostelium discoideum."
    Nature 418(6893):79-85 (2002)   [PubMed]   [Abstract]   [Datasets]

  • M. Burset.
    "Estudi Computacional de l'Especificació dels Llocs d'Splicing."
    Written in Catalan [ Computational analysis of the splice sites definition ].
    PhD Thesis, Department of Genetics of the School of Biology at Universitat de Barcelona, 2002.
    [6.2Mb gziped PostScript file]   [5.1Mb gziped PDF file]

Publications in 2001

  • M.J. Betts, R. Guigó, P. Agarwal and R.B. Russell.
    "Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution?"
    EMBO Journal 20(19):5354-5360 (2001)   [PubMed]   [Abstract]

  • T. Wiehe, S. Gebauer-Jung, T. Mitchell-Olds and R. Guigó.
    "SGP-1: Prediction and Validation of Homologous Genes Based on Sequence Alignments."
    Genome Research 11(9):1574-1583 (2001)   [PubMed]   [Abstract]

  • S. Castellano, N. Morozova, M. Morey, M.J. Berry, F. Serras, M. Corominas and R. Guigó.
    "in silico identification of novel selenoproteins in the Drosophila melanogaster genome."
    EMBO Reports 2(8):697-702 (2001)   [PubMed]   [Abstract]   [Full Text]   [Datasets]

  • J.C. Venter et al (including J.F. Abril and R. Guigó).
    "The Sequence of the Human Genome."
    Science 291(5507):1304-1351 (2001)   [PubMed]   [Abstract]   [Poster]   [gff2ps]

  • M. Burset, I.A. Seledtsov and V.V. Solovyev.
    "SpliceDB: Database of canonical and non-canonical mammalian splice sites."
    Nucleic Acid Research 29(1):255-259 (2001)   [PubMed]   [Abstract]

Publications in 2000

  • T. Wiehe, R. Guigó, and W. Miller.
    "Genome Sequence Comparisons: Hurdles in the Fast Lane to Functional Genomics."
    Briefings in Bioinformatics 1(4):381-388 (2000)   [PubMed]

  • M. Burset, I.A. Seledtsov and V.V. Solovyev.
    "Analysis of canonical and non-canonical splice sites in mammalian genomes."
    Nucleic Acid Research 28(21):4364-4375 (2000)   [PubMed]   [Abstract]

  • T. Thomson, J.J. Lozano, R. Carrió, F. Serras, N. Loukili, M. Valeri, B. Cormand, M.P. del R\x{00ED}o, J.F. Abril, M. Burset, E. Sancho, J. Merino, A. Macaya, M. Corominas and R. Guigó.
    "Fusion of the human gene for the polyubiquitination co-effector uev-1 with kua, a newly identified gene."
    Genome Research 10(11):1743-1756 (2000)   [PubMed]   [Abstract]

  • J.F. Abril and R. Guigó.
    "gff2ps: visualizing genomic annotations."
    Bioinformatics 16(8):743-744 (2000)   [PubMed]   [Abstract]   [gff2ps]

  • R. Guigó, P. Agarwal, J.F. Abril, M. Burset and J.W. Fickett.
    "An Assessment of Gene Prediction Accuracy in Large DNA Sequences."
    Genome Research 10(10):1631-1642 (2000)   [PubMed]   [Abstract]   [Datasets]

  • G. Parra, E. Blanco, and R. Guigó.
    "Geneid in Drosophila."
    Genome Research 10(4):511-515 (2000)   [PubMed]   [Abstract]   [Datasets]   [geneid]

  • M.G. Reese, G. Hartzell, N.L. Harris, U. Ohler, J.F. Abril and S.E. Lewis.
    "Genome Annotation Assessment in Drosophila melanogaster."
    Genome Research 10(4):483-501 (2000)   [PubMed]   [Abstract]   [Datasets]   [Poster]

  • M.D. Adams et al (including J.F. Abril).
    "The Genome Sequence of Drosophila melanogaster."
    Science 287(5461):2185-2195 (2000)   [PubMed]   [Abstract]   [Poster]   [gff2ps]

  • R. Guigó, M. Burset, P. Agarwal, J.F. Abril, R.F. Smith and J.W. Fickett.
    "Sequence Similarity Based Gene Prediction."
    In S. Suhai editor:
    Genomics and Proteomics: Functional and Computational Aspects. Pp:95-105.
    Plenum Publishing Corporation, 2000. ISBN: 0-306-46312-1.   [Table of Contents]

  • R. Guigó.
    "La biologia computacional."
    In J. Bertranpetit editor:
    La Biologia a l'alba d'un nou mil·leni. Pp:93-102.
    Treballs de la Societat Catalana de Biologia, Volum 50, 2000.

Publications in 1999

  • R. Guigó.
    "DNA composition, codon usage and exon prediction."
    In M. Bishop, editor:
    Genetic Databases. Pp:53-80.
    Academic Press, 1999. ISBN: 0-12-101625-0.   [Table of Contents]

Publications in 1998

  • R. Guigó.
    "Assembling genes from predicted exons in linear time with dynamic programming."
    Journal of Computational Biology, 5(4):681-702 (1998)   [PubMed]

Publications in 1997

  • J.J. Lozano, E. López de Briñas, N.B. Centeno, R. Guigó, and F. Sanz.
    "Three-dimensional modeling of human cytochrome p450 1a2 and its interaction with caffeine and carcinogenic aromatic amines."
    Journal of Computer Aided Molecular Design, 11(4):395-408 (1997)   [PubMed]   [Abstract]

  • R. Guigó.
    "Computational gene identification."
    Journal of Molecular Medicine, 75(6):389-393 (1997)   [PubMed]

  • R. Guigó.
    "Computational gene identification: An open problem."
    Computers and Chemistry, 21(4):215-222 (1997)   [PubMed]

Publications in 1996

  • M. Burset and R. Guigó.
    "Evaluation of gene structure prediction programs."
    Genomics, 34(3):353-357 (1996)   [PubMed]   [Abstract]

  • R. Guigó, I. Muchnik, and T.F. Smith.
    "Reconstruction of ancient molecular phylogeny."
    Molecular Phylogenetics and Evolution, 6:189-213 (1996)   [PubMed]   [Abstract]

  • J. W. Fickett and R. Guigó.
    "Computational gene identification."
    In S.R. Swindell, R.R. Miller and G. Myers, editors:
    Internet for the Molecular Biologist. Pp:73-100.
    Horizon Scientific Press, Oxford, United Kingdom, 1996. ISBN: 1-898486-10-7.   [Table of Contents]

Publications in 1995

  • R. Guigó and J. W. Fickett.
    "Distinctive sequence features in protein coding, genic non-coding, and intergenic human DNA."
    Journal of Molecular Biology, 253(1):51-60 (1995)   [PubMed]   [Abstract]

  • E. López de Briñas, J.J. Lozano, R. Guigó, F. Manaut and F. Sanz.
    "Secondary structure Prediction. A tool in the alignment of cytochrome P450 1A2 sequence with those of cytochromes P450 CAM, P450 BM3, and P450 TERP."
    In F. Sanz, J. Giraldo, F. Manaut, editors:
    QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications. Pp:601-604.
    J.R. Prous Science Publisher, Barcelona, 1995.

Other Publications

  • R. Guigó. "Genomics: Halfway between Biology and Computing."  Teraflop, 73:20-21, November/2003.

  • R. Guigó. "La pedra de Rosetta del genoma."  El Periódico, 07/12/2002.

  • R. Guigó. "Genómica: la Biología como una ciencia de la información."  Informe Quiral 2000. Pp:25-31, June/2001.

  • R. Guigó. "Esperances i malsons del genoma humà."  L'Avui, 23/04/2001.

  • J.F. Abril and R. Guigó. "La Cartografía del Ser Humano."  El Mundo (magazine "El Cultural"), 21/02/2001.

  • R. Guigó. "El eco del genoma."  El Periódico, 15/02/2001.

  • R. Guigó. "Els límits de la nostra presó."  El Periódico, 02/07/2000.

  • R. Guigó. "Bioinformática ¿ una ciencia sin científicos ?"  Quark, 18:51-55, June/2000.

  • R. Guigó. "La computació i el projecte genoma humà."  Teraflop, 10:2, October/1995.

Posters

  • S.J. Furney, D.G. Higgins, C.A. Ouzounis and N. López-Bigas
    "Structural and Functional Properties of Genes Involved in Human Cancer."
    IVth ECCB/VIth JBI (Computational Biology ECCB/JBI'05), Madrid, Spain (2005)
    [235Kb gzipped PDF file]

  • J.J. Wesselink and R. Guigó
    "Cross-species Alignment of Alternative Transcripts of Splicing Regulatory Proteins."
    IVth ECCB/VIth JBI (Computational Biology ECCB/JBI'05), Madrid, Spain (2005)
    [485Kb gzipped PDF file]

  • M. Sammeth, E. Eyras and R. Guigó
    "Alignning Intron-Exon Structures of Alternatively Spliced Genes."
    IVth ECCB/VIth JBI (Computational Biology ECCB/JBI'05), Madrid, Spain (2005)
    [1.9Mb gzipped PDF file]

  • F. Denoeud, R. Guigó, J. Lagarde, J.F. Abril, J. Ashurst, A. Frankish, D. Swarbreck, J. Gilbert, S. Antonarakis, A. Reymond, C. Ucla, T. Hubbard, E. Birney, P. Good and the Gencode consortium
    "Gene Finding in the ENCODE Project."
    IVth ECCB/VIth JBI (Computational Biology ECCB/JBI'05), Madrid, Spain (2005)
    [1.1Mb gzipped PDF file]

  • J.F. Abril and R. Guigó
    "Large-scale display of genomic annotation data sets with gff2ps."
    IVth ECCB/VIth JBI (Computational Biology ECCB/JBI'05), Madrid, Spain (2005)
    [6.2Mb gzipped PDF file]

  • E. Blanco, M. Pignatelli, X. Messeguer and R. Guigó
    "Deconstructing the Position Weight Matrices to Detect Regulatory Elements."
    CSHL - Systems Biology "Global Regulation of Gene Expression", New York, USA (2005)
    [499Kb gzipped PostScript file]

  • J. Lagarde, J.F. Abril, F. Denoeud, R. Guigó and the GENCODE Consortium
    "ENr334: Computational Gene Predictions, VEGA Annotations and GENCODE Experimental Validations."
    CSHL - Genomics Workshop "Identification of Functional Elements in Mammalian Genomes", New York, USA (Nov, 2004)
    [117Kb gzipped PostScript file]  [169Kb gzipped PDF file]

  • S. Castellano, C. Chapple and R. Guigó
    "Annotation of Eukaryotic Selenoproteins: Finding the Needle in the Haystack"
    CSHL - The Biology of Genomes, New York, USA (2004)
    [121Kb gzipped PostScript file]

  • E. Blanco, X. Messeguer and R. Guigó
    "Novel computational methods to characterize regulatory regions."
    CSHL - Systems Biology "Genomic approaches to transcriptional regulation", New York, USA (2004)
    [387Kb gzipped PostScript file]

  • E. Blanco, X. Messeguer and R. Guigó
    "Alignment of Promoter Regions by Mapping Nucleotide Sequences into Arrays of Transcription Factor Binding Motifs."
    VIIth RECOMB, Berlin, Germany (2003)
    [255Kb gzipped PostScript file]

  • J.F. Abril, M. Albà, E. Blanco, M. Burset, F. Câmara, S. Castellano, R. Castelo, O. Gonzalez, G. Parra and R. Guigó
    "Understanding the Eukaryotic Genome Sequence."
    Inaugural Symposium of the Center for Genomic Regulation, Barcelona, Spain (2002)
    [1.5Mb gzipped PDF file]

  • "Annotation of the Anopheles gambiae Genome Sequence."
    In R.A. Holt et al (including J.F. Abril and R. Guigó).
    "The Genome Sequence of the Malaria Mosquito Anopheles gambiae."
    Science 298(5591):129-149 ( 2002)
    [Link to this Figure on Science website]  [1.5Mb gzipped PostScript file]  [2.9Mb gzipped PDF file]

  • S. Castellano, G.V. Kryukov, S.V. Novoselov, A.V. Lobanov, V.N. Gladyshev and R. Guigó
    "The Eukaryotic SelenoProteome."
    CSHL - Translational Control, New York, USA (2002)
    [204Kb gzipped PostScript file]

  • E. Blanco, G. Parra, S. Castellano, J.F. Abril, M. Burset, X. Fustero, X. Messeguer and R. Guigó
    "Gene Prediction in the Post-Genomic Era."
    IXth ISMB, Copenhagen, Denmark (2001)
    [695Kb gzipped PostScript file]

  • S. Castellano, M. Morozova, M. Morey, M.J. Berry, F. Serras, M. Corominas and R. Guigó
    "Genome-wide Search for Selenoproteins in Eukaryotes."
    CSHL - Genome Sequencing & Biology, New York, USA (2001)
    [1.9Mb gzipped PostScript file]

  • G. Glöckner, L. Eichinger, K. Szafranski, P. Dear, J. Pachebat, K. Kumpf, R. Lehmann, J.F. Abril, G. Parra, R. Guigó, B. Tunggal, E. Cox, M.A. Quail, M. Platzer, A. Rosenthal, A.A. Noegel and the Dictyostelium Genome Sequencing Consortium.
    "Sequence and Analysis of Chromosome 2 from the Model Organism Dictyostelium discoideum."
    CSHL - Genome Sequencing & Biology, New York, USA (2001)
    [Link to Dictyostelium team at IMB-Jena]

  • "Annotation of the Celera Human Genome Assembly."
    In J.C. Venter et al (including J.F. Abril and R. Guigó).
    "The Sequence of the Human Genome."
    Science 291(5507):1304-1351 (2001)
    [Link to this Figure on Science website]  [2.7Mb gzipped PostScript file]  [10Mb gzipped PDF file]

  • J.F. Abril, E. Blanco, M. Burset, S. Castellano, X. Fustero, G. Parra and R. Guigó
    "Genome Informatics Research Laboratory: Main Research Topics."
    Ist Jornadas de Bioinformática, Cartagena, Spain (2000)
    [1.2Mb gzipped PostScript file]

  • "Drosophila Genome Annotation Assessment Project"
    In M.G. Reese, G. Hartzell, N.L. Harris, U. Ohler, J.F. Abril and S.E. Lewis.
    "Genome Annotation Assessment in Drosophila melanogaster."
    Genome Research 10(4):483-501 (2000)
    [Link to this Poster from Genome Research website]  [466Kb gzipped PostScript file]  [2.2Mb gzipped PDF file]

  • "Coding Content of the Drosophila Genome."
    In M.D. Adams et al (including J.F. Abril).
    "The Genome Sequence of Drosophila melanogaster."
    Science 287(5461):2185-2195 (2000)
    [Link to this Figure on Science website]  [1.1Kb gzipped PostScript file]  [1.7Mb gzipped PDF file]

  • T. Wiehe, J.F. Abril, M. Burset, S. Gebauer-Jung and R. Guigó
    "Comparative Genomics: At the Crossroads of Evolutionary Biology and Genome Sequence Analysis."
    VIIth ESEB, Barcelona, Spain (1999)
    [267Kb gzipped PostScript file]

  • T. Wiehe, J.F. Abril, M. Burset, S. Gebauer-Jung and R. Guigó
    "Gene Prediction and Validation Based on Homologous Genomic Sequences."
    VIIth ISMB, Heidelberg, Germany (1999)
    [161Kb gzipped PostScript file]

  • J.F. Abril, T. Wiehe, M. Burset and R. Guigó
    "Tools to Visualize Genome Annotations."
    IIIth RECOMB, Lyon, France (1999)
    [136Kb gzipped PostScript file]

  • M. Burset, J.F. Abril and R. Guigó
    "GeneID-3, from DNA Sequence to Protein Function."
    Vth ISMB, Halkidiki, Greece (1997)


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