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JOSEP F. ABRIL's PUBLICATIONS
  
   
Summary


Publications In Press

  • E. Blanco and J.F. Abril
    "Computational Gene Annotation in New Genome Assemblies."
    In D. Posada editor:
    Bioinformatics for DNA Sequence Analysis Book [Methods in Molecular Biology Series]
    Humana Press (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 (in press).

Publications Since 2006

  • Emili Saló, J.F. Abril, T. Adell, F. Cebriá, K. Eckelt, E. Fernández-Taboada, M. Handberg-Thorsager, M. Iglesias, M.D. Molina and G. Rodríguez-Esteban
    "Planarian regeneration: achievements and future directions after 20 years of research."
    Int. J. Dev. Biol., in press (2008)   [Abstract]
    [Published online before print in Apr 2008]

  • S. Levy, G. Sutton, P.C. Ng, L. Feuk, A.L. Halpern, B.P. Walenz, N. Axelrod, J. Huang, E.F. Kirkness, G. Denisov, Y. Lin, J.R. Macdonald, A.W. Pang, M. Shago, T.B. Stockwell, A. Tsiamouri, V. Bafna, V. Bansal, S.A. Kravitz, D.A. Busam, K.Y. Beeson, T.C. McIntosh, K.A. Remington, J.F. Abril, J. Gill, J. Borman, Y.H. Rogers, M.E. Frazier, S.W. Scherer, R.L. Strausberg and J.C. Venter
    "The Diploid Genome Sequence of an Individual Human."
    PLoS Biology, 5(10):e254 (2007)   [Full Text]   [PDF]   [PubMed]   [Interactive map]   [PDF Map]

  • ENCODE Project Consortium (including J.F. Abril)
    "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project."
    Nature, 447(7146):S2 (2007)   [Full Text]   [PDF]   [PubMed]   [ENCODE Project]   [GENCODE]

  • 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]   [Datasets]

Publications from 2001 to 2005

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

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

  • International Chicken Genome Sequencing Consortium (including J.F. Abril)
    "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution."
    Nature, 432(7018):695-716 (2004)   [PubMed]   [Abstract]   [Full Text]

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

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

  • 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 ]   [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) [Abstract]   [Datasets]   [sgp2]

  • Mouse Genome Sequencing Consortium (including J.F. Abril).
    "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).
    "The Genome Sequence of the Malaria Mosquito Anopheles gambiae."
    Science 298(5591):129-149 (2002)   [PubMed]   [Abstract]   [2.9Mb gzipped PDF file genome map]   [gff2ps]

  • 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]

  • J.C. Venter et al (including J.F. Abril).
    "The Sequence of the Human Genome."
    Science 291(5507):1304-1351 (2001)   [PubMed]   [Abstract]   [10Mb gzipped PDF file genome map]   [gff2ps]

Publications until 2000

  • 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.
    Plenum Publishing Corporation, 2000. ISBN: 0-306-46312-1.   [Table of Contents]

  • T. Thomson, J.J. Lozano, R. Carrió, F. Serras, N. Loukili, M. Valeri, B. Cormand, M.P. del Río, 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]

  • M.G. Reese, G. Hartzell, N.L. Harris, U. Ohler, J.F. Abril and S.E. Lewis.
    "Genome Annotation Assesment in Drosophila melanogaster."
    Genome Research 10(4):483-501(2000)   [PubMed]   [Abstract]   [Datasets]   [2.2Mb gzipped PDF file GASP poster]

  • M.D. Adams et al (including J.F. Abril).
    "The Genome Sequence of Drosophila melanogaster."
    Science 287(5461):2185-2195(2000)   [PubMed]   [Abstract]   [2.2Mb gzipped PDF file genome map]   [gff2ps]

Posters Since 2006

  • K. Eckelt, J.F. Abril, F. Crebrià and E. Saló
    "Identification of Eye Genes in the Flatworm Schmidtea mediterranea with a Genome-Derived Microchip."


  • J.F. Abril, E. Fernàndez-Taboada and E. Saló
    "Neoblast-Specific Functional Screening in Schmidtea mediterranea: a Proteomics Approach."
    15th ISMB / 6th ECCB, Wien, Austria (2007)

Posters from 2001 to 2005

  • 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]

  • 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. 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]

  • 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).
    "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]

  • 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."
    IX th   ISMB, Copenhagen, Denmark (2001)
    [695Kb 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).
    "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]

Posters until 2000

  • J.F. Abril, E. Blanco, M. Burset, S. Castellano, X. Fustero, G. Parra and R. Guigó
    "Genome Informatics Research Laboratory: Main Research Topics."
    I st   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 Assesment 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."
    VII th   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."
    VII th   ISMB, Heidelberg, Germany (1999)
    [161Kb gzipped PostScript file]

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

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

Other Publications

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

 
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