Search Results - (Author, Cooperation:R. Guigo)

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  1. 1
    Staff View
    Publication Date:
    2015-12-04
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  2. 2
    X. S. Puente ; M. Pinyol ; V. Quesada ; L. Conde ; G. R. Ordonez ; N. Villamor ; G. Escaramis ; P. Jares ; S. Bea ; M. Gonzalez-Diaz ; L. Bassaganyas ; T. Baumann ; M. Juan ; M. Lopez-Guerra ; D. Colomer ; J. M. Tubio ; C. Lopez ; A. Navarro ; C. Tornador ; M. Aymerich ; M. Rozman ; J. M. Hernandez ; D. A. Puente ; J. M. Freije ; G. Velasco ; A. Gutierrez-Fernandez ; D. Costa ; A. Carrio ; S. Guijarro ; A. Enjuanes ; L. Hernandez ; J. Yague ; P. Nicolas ; C. M. Romeo-Casabona ; H. Himmelbauer ; E. Castillo ; J. C. Dohm ; S. de Sanjose ; M. A. Piris ; E. de Alava ; J. San Miguel ; R. Royo ; J. L. Gelpi ; D. Torrents ; M. Orozco ; D. G. Pisano ; A. Valencia ; R. Guigo ; M. Bayes ; S. Heath ; M. Gut ; P. Klatt ; J. Marshall ; K. Raine ; L. A. Stebbings ; P. A. Futreal ; M. R. Stratton ; P. J. Campbell ; I. Gut ; A. Lopez-Guillermo ; X. Estivill ; E. Montserrat ; C. Lopez-Otin ; E. Campo
    Nature Publishing Group (NPG)
    Published 2011
    Staff View
    Publication Date:
    2011-06-07
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Amino Acid Sequence ; Animals ; Carrier Proteins/genetics ; DNA Mutational Analysis ; Genome, Human/*genetics ; Humans ; Karyopherins/genetics ; Leukemia, Lymphocytic, Chronic, B-Cell/*genetics ; Molecular Sequence Data ; Mutation/*genetics ; Myeloid Differentiation Factor 88/chemistry/genetics ; Receptor, Notch1/genetics ; Receptors, Cytoplasmic and Nuclear/genetics ; Reproducibility of Results
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  3. 3
    F. A. Bava ; C. Eliscovich ; P. G. Ferreira ; B. Minana ; C. Ben-Dov ; R. Guigo ; J. Valcarcel ; R. Mendez
    Nature Publishing Group (NPG)
    Published 2013
    Staff View
    Publication Date:
    2013-02-26
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    3' Untranslated Regions/*genetics ; Alternative Splicing/*genetics ; Cell Cycle Proteins/genetics ; Cell Nucleus/metabolism ; Cell Proliferation ; Cell Transformation, Neoplastic ; Cytoplasm/metabolism ; HeLa Cells ; Humans ; Models, Genetic ; Nuclear Proteins/metabolism ; Poly A/genetics/metabolism ; Polyadenylation/genetics ; Protein Biosynthesis/*genetics ; RNA, Messenger/genetics/metabolism ; Ribonucleoproteins/metabolism ; Transcription Factors/*metabolism ; mRNA Cleavage and Polyadenylation Factors/*metabolism
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  4. 4
    S. Djebali ; C. A. Davis ; A. Merkel ; A. Dobin ; T. Lassmann ; A. Mortazavi ; A. Tanzer ; J. Lagarde ; W. Lin ; F. Schlesinger ; C. Xue ; G. K. Marinov ; J. Khatun ; B. A. Williams ; C. Zaleski ; J. Rozowsky ; M. Roder ; F. Kokocinski ; R. F. Abdelhamid ; T. Alioto ; I. Antoshechkin ; M. T. Baer ; N. S. Bar ; P. Batut ; K. Bell ; I. Bell ; S. Chakrabortty ; X. Chen ; J. Chrast ; J. Curado ; T. Derrien ; J. Drenkow ; E. Dumais ; J. Dumais ; R. Duttagupta ; E. Falconnet ; M. Fastuca ; K. Fejes-Toth ; P. Ferreira ; S. Foissac ; M. J. Fullwood ; H. Gao ; D. Gonzalez ; A. Gordon ; H. Gunawardena ; C. Howald ; S. Jha ; R. Johnson ; P. Kapranov ; B. King ; C. Kingswood ; O. J. Luo ; E. Park ; K. Persaud ; J. B. Preall ; P. Ribeca ; B. Risk ; D. Robyr ; M. Sammeth ; L. Schaffer ; L. H. See ; A. Shahab ; J. Skancke ; A. M. Suzuki ; H. Takahashi ; H. Tilgner ; D. Trout ; N. Walters ; H. Wang ; J. Wrobel ; Y. Yu ; X. Ruan ; Y. Hayashizaki ; J. Harrow ; M. Gerstein ; T. Hubbard ; A. Reymond ; S. E. Antonarakis ; G. Hannon ; M. C. Giddings ; Y. Ruan ; B. Wold ; P. Carninci ; R. Guigo ; T. R. Gingeras
    Nature Publishing Group (NPG)
    Published 2012
    Staff View
    Publication Date:
    2012-09-08
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Alleles ; Cell Line ; DNA/*genetics ; DNA, Intergenic/genetics ; *Encyclopedias as Topic ; Enhancer Elements, Genetic ; Exons/genetics ; Gene Expression Profiling ; Genes/genetics ; Genome, Human/*genetics ; Genomics ; Humans ; *Molecular Sequence Annotation ; Polyadenylation/genetics ; Protein Isoforms/genetics ; RNA/biosynthesis/genetics ; RNA Editing/genetics ; RNA Splicing/genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, RNA ; Transcription, Genetic/*genetics ; Transcriptome/*genetics
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  5. 5
    T. Lappalainen ; M. Sammeth ; M. R. Friedlander ; P. A. t Hoen ; J. Monlong ; M. A. Rivas ; M. Gonzalez-Porta ; N. Kurbatova ; T. Griebel ; P. G. Ferreira ; M. Barann ; T. Wieland ; L. Greger ; M. van Iterson ; J. Almlof ; P. Ribeca ; I. Pulyakhina ; D. Esser ; T. Giger ; A. Tikhonov ; M. Sultan ; G. Bertier ; D. G. MacArthur ; M. Lek ; E. Lizano ; H. P. Buermans ; I. Padioleau ; T. Schwarzmayr ; O. Karlberg ; H. Ongen ; H. Kilpinen ; S. Beltran ; M. Gut ; K. Kahlem ; V. Amstislavskiy ; O. Stegle ; M. Pirinen ; S. B. Montgomery ; P. Donnelly ; M. I. McCarthy ; P. Flicek ; T. M. Strom ; H. Lehrach ; S. Schreiber ; R. Sudbrak ; A. Carracedo ; S. E. Antonarakis ; R. Hasler ; A. C. Syvanen ; G. J. van Ommen ; A. Brazma ; T. Meitinger ; P. Rosenstiel ; R. Guigo ; I. G. Gut ; X. Estivill ; E. T. Dermitzakis
    Nature Publishing Group (NPG)
    Published 2013
    Staff View
    Publication Date:
    2013-09-17
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Alleles ; Cell Line, Transformed ; Exons/genetics ; Gene Expression Profiling ; Genetic Variation/*genetics ; Genome, Human/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics ; RNA, Messenger/analysis/genetics ; *Sequence Analysis, RNA ; Transcriptome/*genetics
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  6. 6
    Staff View
    Publication Date:
    2015-05-09
    Publisher:
    American Association for the Advancement of Science (AAAS)
    Print ISSN:
    0036-8075
    Electronic ISSN:
    1095-9203
    Topics:
    Biology
    Chemistry and Pharmacology
    Computer Science
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Alternative Splicing ; Female ; Gene Expression Profiling ; *Gene Expression Regulation ; Genome, Human/*genetics ; Humans ; Male ; Organ Specificity/genetics ; Phenotype ; Polymorphism, Single Nucleotide ; Sequence Analysis, RNA ; Sex Factors ; *Transcriptome
    Published by:
    http://www.aaas.org/

    Latest Papers from Table of Contents or Articles in Press
  7. 7
    Staff View
    Publication Date:
    2015-05-09
    Publisher:
    American Association for the Advancement of Science (AAAS)
    Print ISSN:
    0036-8075
    Electronic ISSN:
    1095-9203
    Topics:
    Biology
    Chemistry and Pharmacology
    Computer Science
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Alternative Splicing ; Gene Expression Profiling ; *Gene Expression Regulation ; Gene Silencing ; *Genetic Variation ; Genome, Human/*genetics ; Heterozygote ; Humans ; Nonsense Mediated mRNA Decay ; Phenotype ; Proteins/*genetics ; *Transcriptome
    Published by:
    http://www.aaas.org/

    Latest Papers from Table of Contents or Articles in Press
  8. 8
    R. Guigo ; J. Valcarcel
    American Association for the Advancement of Science (AAAS)
    Published 2015
    Staff View
    Publication Date:
    2015-01-13
    Publisher:
    American Association for the Advancement of Science (AAAS)
    Print ISSN:
    0036-8075
    Electronic ISSN:
    1095-9203
    Topics:
    Biology
    Chemistry and Pharmacology
    Computer Science
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    *Artificial Intelligence ; Child Development Disorders, Pervasive/*genetics ; Colorectal Neoplasms, Hereditary Nonpolyposis/*genetics ; Genome-Wide Association Study/*methods ; Humans ; Molecular Sequence Annotation/*methods ; Muscular Atrophy, Spinal/*genetics ; RNA Splicing/*genetics
    Published by:
    http://www.aaas.org/

    Latest Papers from Table of Contents or Articles in Press
  9. 9
    L. Chen ; M. Kostadima ; J. H. Martens ; G. Canu ; S. P. Garcia ; E. Turro ; K. Downes ; I. C. Macaulay ; E. Bielczyk-Maczynska ; S. Coe ; S. Farrow ; P. Poudel ; F. Burden ; S. B. Jansen ; W. J. Astle ; A. Attwood ; T. Bariana ; B. de Bono ; A. Breschi ; J. C. Chambers ; F. A. Choudry ; L. Clarke ; P. Coupland ; M. van der Ent ; W. N. Erber ; J. H. Jansen ; R. Favier ; M. E. Fenech ; N. Foad ; K. Freson ; C. van Geet ; K. Gomez ; R. Guigo ; D. Hampshire ; A. M. Kelly ; H. H. Kerstens ; J. S. Kooner ; M. Laffan ; C. Lentaigne ; C. Labalette ; T. Martin ; S. Meacham ; A. Mumford ; S. Nurnberg ; E. Palumbo ; B. A. van der Reijden ; D. Richardson ; S. J. Sammut ; G. Slodkowicz ; A. U. Tamuri ; L. Vasquez ; K. Voss ; S. Watt ; S. Westbury ; P. Flicek ; R. Loos ; N. Goldman ; P. Bertone ; R. J. Read ; S. Richardson ; A. Cvejic ; N. Soranzo ; W. H. Ouwehand ; H. G. Stunnenberg ; M. Frontini ; A. Rendon
    American Association for the Advancement of Science (AAAS)
    Published 2014
    Staff View
    Publication Date:
    2014-09-27
    Publisher:
    American Association for the Advancement of Science (AAAS)
    Print ISSN:
    0036-8075
    Electronic ISSN:
    1095-9203
    Topics:
    Biology
    Chemistry and Pharmacology
    Computer Science
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    *Alternative Splicing ; Cell Lineage/*genetics ; Genetic Variation ; Hematopoiesis/*genetics ; Hematopoietic Stem Cells/*cytology/metabolism ; Humans ; NFI Transcription Factors/genetics/metabolism ; RNA-Binding Proteins/metabolism ; Thrombopoiesis/genetics ; Transcriptome
    Published by:
    http://www.aaas.org/

    Latest Papers from Table of Contents or Articles in Press
  10. 10
    Staff View
    Publication Date:
    2014-04-18
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Animals ; Cells, Cultured ; Chromatin/chemistry/metabolism ; Chromosomes, Human, Pair 21/genetics ; Chromosomes, Mammalian/genetics ; DNA Replication Timing ; Down Syndrome/*genetics/pathology ; Female ; Fetus/cytology ; Fibroblasts ; Gene Expression Regulation/*genetics ; Genome/*genetics ; Histones/chemistry/metabolism ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Lysine/metabolism ; Male ; Methylation ; Mice ; Transcriptome/*genetics ; Twins, Monozygotic/genetics
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  11. 11
    M. B. Gerstein ; J. Rozowsky ; K. K. Yan ; D. Wang ; C. Cheng ; J. B. Brown ; C. A. Davis ; L. Hillier ; C. Sisu ; J. J. Li ; B. Pei ; A. O. Harmanci ; M. O. Duff ; S. Djebali ; R. P. Alexander ; B. H. Alver ; R. Auerbach ; K. Bell ; P. J. Bickel ; M. E. Boeck ; N. P. Boley ; B. W. Booth ; L. Cherbas ; P. Cherbas ; C. Di ; A. Dobin ; J. Drenkow ; B. Ewing ; G. Fang ; M. Fastuca ; E. A. Feingold ; A. Frankish ; G. Gao ; P. J. Good ; R. Guigo ; A. Hammonds ; J. Harrow ; R. A. Hoskins ; C. Howald ; L. Hu ; H. Huang ; T. J. Hubbard ; C. Huynh ; S. Jha ; D. Kasper ; M. Kato ; T. C. Kaufman ; R. R. Kitchen ; E. Ladewig ; J. Lagarde ; E. Lai ; J. Leng ; Z. Lu ; M. MacCoss ; G. May ; R. McWhirter ; G. Merrihew ; D. M. Miller ; A. Mortazavi ; R. Murad ; B. Oliver ; S. Olson ; P. J. Park ; M. J. Pazin ; N. Perrimon ; D. Pervouchine ; V. Reinke ; A. Reymond ; G. Robinson ; A. Samsonova ; G. I. Saunders ; F. Schlesinger ; A. Sethi ; F. J. Slack ; W. C. Spencer ; M. H. Stoiber ; P. Strasbourger ; A. Tanzer ; O. A. Thompson ; K. H. Wan ; G. Wang ; H. Wang ; K. L. Watkins ; J. Wen ; K. Wen ; C. Xue ; L. Yang ; K. Yip ; C. Zaleski ; Y. Zhang ; H. Zheng ; S. E. Brenner ; B. R. Graveley ; S. E. Celniker ; T. R. Gingeras ; R. Waterston
    Nature Publishing Group (NPG)
    Published 2014
    Staff View
    Publication Date:
    2014-08-29
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Animals ; Caenorhabditis elegans/embryology/*genetics/growth & development ; Chromatin/genetics ; Cluster Analysis ; Drosophila melanogaster/*genetics/growth & development ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental/genetics ; Histones/metabolism ; Humans ; Larva/genetics/growth & development ; Models, Genetic ; Molecular Sequence Annotation ; Promoter Regions, Genetic/genetics ; Pupa/genetics/growth & development ; RNA, Untranslated/genetics ; Sequence Analysis, RNA ; Transcriptome/*genetics
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  12. 12
    F. Yue ; Y. Cheng ; A. Breschi ; J. Vierstra ; W. Wu ; T. Ryba ; R. Sandstrom ; Z. Ma ; C. Davis ; B. D. Pope ; Y. Shen ; D. D. Pervouchine ; S. Djebali ; R. E. Thurman ; R. Kaul ; E. Rynes ; A. Kirilusha ; G. K. Marinov ; B. A. Williams ; D. Trout ; H. Amrhein ; K. Fisher-Aylor ; I. Antoshechkin ; G. DeSalvo ; L. H. See ; M. Fastuca ; J. Drenkow ; C. Zaleski ; A. Dobin ; P. Prieto ; J. Lagarde ; G. Bussotti ; A. Tanzer ; O. Denas ; K. Li ; M. A. Bender ; M. Zhang ; R. Byron ; M. T. Groudine ; D. McCleary ; L. Pham ; Z. Ye ; S. Kuan ; L. Edsall ; Y. C. Wu ; M. D. Rasmussen ; M. S. Bansal ; M. Kellis ; C. A. Keller ; C. S. Morrissey ; T. Mishra ; D. Jain ; N. Dogan ; R. S. Harris ; P. Cayting ; T. Kawli ; A. P. Boyle ; G. Euskirchen ; A. Kundaje ; S. Lin ; Y. Lin ; C. Jansen ; V. S. Malladi ; M. S. Cline ; D. T. Erickson ; V. M. Kirkup ; K. Learned ; C. A. Sloan ; K. R. Rosenbloom ; B. Lacerda de Sousa ; K. Beal ; M. Pignatelli ; P. Flicek ; J. Lian ; T. Kahveci ; D. Lee ; W. J. Kent ; M. Ramalho Santos ; J. Herrero ; C. Notredame ; A. Johnson ; S. Vong ; K. Lee ; D. Bates ; F. Neri ; M. Diegel ; T. Canfield ; P. J. Sabo ; M. S. Wilken ; T. A. Reh ; E. Giste ; A. Shafer ; T. Kutyavin ; E. Haugen ; D. Dunn ; A. P. Reynolds ; S. Neph ; R. Humbert ; R. S. Hansen ; M. De Bruijn ; L. Selleri ; A. Rudensky ; S. Josefowicz ; R. Samstein ; E. E. Eichler ; S. H. Orkin ; D. Levasseur ; T. Papayannopoulou ; K. H. Chang ; A. Skoultchi ; S. Gosh ; C. Disteche ; P. Treuting ; Y. Wang ; M. J. Weiss ; G. A. Blobel ; X. Cao ; S. Zhong ; T. Wang ; P. J. Good ; R. F. Lowdon ; L. B. Adams ; X. Q. Zhou ; M. J. Pazin ; E. A. Feingold ; B. Wold ; J. Taylor ; A. Mortazavi ; S. M. Weissman ; J. A. Stamatoyannopoulos ; M. P. Snyder ; R. Guigo ; T. R. Gingeras ; D. M. Gilbert ; R. C. Hardison ; M. A. Beer ; B. Ren
    Nature Publishing Group (NPG)
    Published 2014
    Staff View
    Publication Date:
    2014-11-21
    Publisher:
    Nature Publishing Group (NPG)
    Print ISSN:
    0028-0836
    Electronic ISSN:
    1476-4687
    Topics:
    Biology
    Chemistry and Pharmacology
    Medicine
    Natural Sciences in General
    Physics
    Keywords:
    Animals ; Cell Lineage/genetics ; Chromatin/genetics/metabolism ; Conserved Sequence/genetics ; DNA Replication/genetics ; Deoxyribonuclease I/metabolism ; Gene Expression Regulation/genetics ; Gene Regulatory Networks/genetics ; Genome/*genetics ; Genome-Wide Association Study ; *Genomics ; Humans ; Mice/*genetics ; *Molecular Sequence Annotation ; RNA/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Species Specificity ; Transcription Factors/metabolism ; Transcriptome/genetics
    Published by:
    http://www.nature.com/

    Latest Papers from Table of Contents or Articles in Press
  13. 13
    Staff View
    ISSN:
    1573-4951
    Keywords:
    Sequence alignment strategies ; Assessment of secondary structure prediction methods ; Solvation ; AUTODOCK ; Molecular electrostatic potential
    Source:
    Springer Online Journal Archives 1860-2000
    Topics:
    Chemistry and Pharmacology
    Notes:
    Abstract The three-dimensional modelling of proteins is a useful tool to fill the gap between the number of sequenced proteins and the number of experimentally known 3D structures. However, when the degree of homology between the protein and the available 3D templates is low, model building becomes a difficult task and the reliability of the results depends critically on the correctness of the sequence alignment. For this reason, we have undertaken the modelling of human cytochrome P450 1A2 starting by a careful analysis of several sequence alignment strategies (multiple sequence alignments and the TOPITS threading technique). The best results were obtained using TOPITS followed by a manual refinement to avoid unlikely gaps. Because TOPITS uses secondary structure predictions, several methods that are available for this purpose (Levin, Gibrat, DPM, NnPredict, PHD, SOPM and NNSP) have also been evaluated on cytochromes P450 with known 3D structures. More reliable predictions on α-helices have been obtained with PHD, which is the method implemented in TOPITS. Thus, a 3D model for human cytochrome P450 1A2 has been built using the known crystal coordinates of P450 BM3 as the template. The model was refined using molecular mechanics computations. The model obtained shows a consistent location of the substrate recognition segments previously postulated for the CYP2 family members. The interaction of caffeine and a carcinogenic aromatic amine (MeIQ), which are characteristic P450 1A2 substrates, has been investigated. The substrates were solvated taking into account their molecular electrostatic potential distributions. The docking of the solvated substrates in the active site of the model was explored with the AUTODOCK programme, followed by molecular mechanics optimisation of the most interesting complexes. Stable complexes were obtained that could explain the oxidation of the considered substrates by cytochrome P450 1A2 and could offer an insight into the role played by water molecules.
    Type of Medium:
    Electronic Resource
    URL:
    http://dx.doi.org/10.1023/A:1007947411145

    Articles: DFG German National Licenses