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Guidelines for Genome-Scale Analysis of Biological Rhythms.
Hughes, Michael E; Abruzzi, Katherine C; Allada, Ravi; Anafi, Ron; Arpat, Alaaddin Bulak; Asher, Gad; Baldi, Pierre; de Bekker, Charissa; Bell-Pedersen, Deborah; Blau, Justin; Brown, Steve; Ceriani, M Fernanda; Chen, Zheng; Chiu, Joanna C; Cox, Juergen; Crowell, Alexander M; DeBruyne, Jason P; Dijk, Derk-Jan; DiTacchio, Luciano; Doyle, Francis J; Duffield, Giles E; Dunlap, Jay C; Eckel-Mahan, Kristin; Esser, Karyn A; FitzGerald, Garret A; Forger, Daniel B; Francey, Lauren J; Fu, Ying-Hui; Gachon, Frédéric; Gatfield, David; de Goede, Paul; Golden, Susan S; Green, Carla; Harer, John; Harmer, Stacey; Haspel, Jeff; Hastings, Michael H; Herzel, Hanspeter; Herzog, Erik D; Hoffmann, Christy; Hong, Christian; Hughey, Jacob J; Hurley, Jennifer M; de la Iglesia, Horacio O; Johnson, Carl; Kay, Steve A; Koike, Nobuya; Kornacker, Karl; Kramer, Achim; Lamia, Katja.
Afiliación
  • Hughes ME; 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
  • Abruzzi KC; 2 Department of Biology and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA.
  • Allada R; 3 Department of Neurobiology, Northwestern University, Evanston, Illinois, USA.
  • Anafi R; 4 Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA.
  • Arpat AB; 5 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland.
  • Asher G; 6 Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • Baldi P; 7 Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
  • de Bekker C; 8 Institute for Genomics and Bioinformatics, University of California, Irvine, USA.
  • Bell-Pedersen D; 9 Department of Biology, University of Central Florida, Orlando, USA.
  • Blau J; 10 Department of Biology, Texas A&M University, College Station, USA.
  • Brown S; 11 Department of Biology, New York University, New York, USA.
  • Ceriani MF; 12 Institute of Pharmacology and Toxicology, University of Zürich, Switzerland.
  • Chen Z; 13 Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.
  • Chiu JC; 14 Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, USA.
  • Cox J; 15 Department of Entomology and Nematology, University of California, Davis, USA.
  • Crowell AM; 16 Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany.
  • DeBruyne JP; 17 Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
  • Dijk DJ; 18 Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, Georgia, USA.
  • DiTacchio L; 19 Surrey Sleep Research Centre, University of Surrey, Guildford, UK.
  • Doyle FJ; 20 The University of Kansas Medical Center, University of Kansas, Kansas City, USA.
  • Duffield GE; 21 John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, Massachusetts, USA.
  • Dunlap JC; 22 Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA.
  • Eckel-Mahan K; 17 Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
  • Esser KA; 23 Institute of Molecular Medicine, McGovern Medical School, UT Health Houston, Houston, Texas, USA.
  • FitzGerald GA; 24 Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, USA.
  • Forger DB; 25 Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA.
  • Francey LJ; 26 Department of Mathematics, University of Michigan, Ann Arbor, USA.
  • Fu YH; 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
  • Gachon F; 28 Kavli Institute for Fundamental Neuroscience, Weill Institute of Neuroscience, Department of Neurology, University of California, San Francisco, USA.
  • Gatfield D; 29 Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland.
  • de Goede P; 5 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland.
  • Golden SS; 30 Department of Endocrinology & Metabolism, Academic Medical Center, Amsterdam, the Netherlands.
  • Green C; 31 Center for Circadian Biology and Division of Biological Sciences, University of California, San Diego, La Jolla, USA.
  • Harer J; 32 Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, USA.
  • Harmer S; 33 Department of Mathematics, Duke University, Durham, North Carolina, USA.
  • Haspel J; 34 Department of Plant Biology, University of California, Davis, USA.
  • Hastings MH; 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
  • Herzel H; 35 Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
  • Herzog ED; 36 Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Germany.
  • Hoffmann C; 37 Department of Biology, Washington University in St. Louis, Missouri, USA.
  • Hong C; 1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
  • Hughey JJ; 27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
  • Hurley JM; 38 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
  • de la Iglesia HO; 39 Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA.
  • Johnson C; 40 Department of Biology, University of Washington, Seattle, USA.
  • Kay SA; 41 Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.
  • Koike N; 42 Department of Cell and Molecular Biology, The Scripps Research Institute, University of California, San Diego, La Jolla, USA.
  • Kornacker K; 43 Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Japan.
  • Kramer A; 44 Division of Sensory Biophysics, The Ohio State University, Columbus, USA.
  • Lamia K; 45 Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Germany.
J Biol Rhythms ; 32(5): 380-393, 2017 Oct.
Article en En | MEDLINE | ID: mdl-29098954
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding "big data" that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them.
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Estadística como Asunto / Ritmo Circadiano / Genoma / Genómica Tipo de estudio: Guideline Límite: Humans Idioma: En Revista: J Biol Rhythms Asunto de la revista: FISIOLOGIA Año: 2017 Tipo del documento: Article País de afiliación: Estados Unidos
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Estadística como Asunto / Ritmo Circadiano / Genoma / Genómica Tipo de estudio: Guideline Límite: Humans Idioma: En Revista: J Biol Rhythms Asunto de la revista: FISIOLOGIA Año: 2017 Tipo del documento: Article País de afiliación: Estados Unidos