Guidelines for Genome-Scale Analysis of Biological Rhythms
| العنوان: | Guidelines for Genome-Scale Analysis of Biological Rhythms |
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| المؤلفون: | Achim Kramer, Karl Kornacker, Justin Blau, Susan S. Golden, Samuel S. C. Rund, Michael H. Hastings, Han Wang, Joanna C. Chiu, Pierre Baldi, Andrew J. Millar, David Gatfield, Tanya L. Leise, Christy Hoffmann, María Teresa Camacho Olmedo, Scott Sherrill-Mix, Derk-Jan Dijk, Debra J. Skene, Jason P. DeBruyne, Hanspeter Herzel, Charles J. Weitz, Gad Asher, Jiajia Li, Katja A. Lamia, Francis J. Doyle, John B. Hogenesch, Tomasz Zielinski, Stacey L. Harmer, Xiaodong Li, Jacob J. Hughey, Christian I. Hong, Zheng Chen, Michael Rosbash, Jennifer J. Loros, Maria S. Robles, Jennifer M. Hurley, Jerome S. Menet, Scott A. Lewis, Karyn A. Esser, Juergen Cox, M. Fernanda Ceriani, Ying-Hui Fu, Joseph S. Takahashi, Ying Xu, Hiroki R. Ueda, Giles E. Duffield, Garret A. FitzGerald, Michael E. Hughes, Deborah Bell-Pedersen, Carl Hirschie Johnson, Marc D. Ruben, Felix Naef, Paul de Goede, Amita Sehgal, Horacio O. de la Iglesia, Akhilesh B. Reddy, Alaaddin Bulak Arpat, Todd C. Mockler, Emi Nagoshi, Dmitri A. Nusinow, Luciano DiTacchio, Gang Wu, Lauren J. Francey, John Harer, Steve A. Kay, Charissa de Bekker, Aziz Sancar, Ron C. Anafi, Katherine C. Abruzzi, Seung Hee Yoo, Kai-Florian Storch, Nobuya Koike, Daniel B. Forger, Erik D. Herzog, Andrew C. Liu, Louis J. Ptáček, Carla B. Green, Michael W. Young, Michael N. Nitabach, Eric E. Zhang, Jay C. Dunlap, Alexander M. Crowell, Tami A. Martino, Frédéric Gachon, Ravi Allada, Pål O. Westermark, Till Roenneberg, Martha Merrow, Herman Wijnen, Kristin Eckel-Mahan, Steve Brown, Jeff Haspel, Paolo Sassone-Corsi, David A. Rand |
| المساهمون: | ANS - Cellular & Molecular Mechanisms, Other departments, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism |
| المصدر: | Journal of Biological Rhythms, vol. 32, no. 5, pp. 380-393 CONICET Digital (CONICET) Consejo Nacional de Investigaciones Científicas y Técnicas instacron:CONICET Journal of biological rhythms, 32(5), 380-393. SAGE Publications Inc. Journal of Biological Rhythms Hughes, M E, Abruzzi, K C, Allada, R, Anafi, R, Arpat, A B, Asher, G, Baldi, P, de Bekker, C, Bell-Pedersen, D, Blau, J, Brown, S, Ceriani, M F, Chen, Z, Chiu, J C, Cox, J, Crowell, A M, DeBruyne, J P, Dijk, D-J, DiTacchio, L, Doyle, F J, Duffield, G E, Dunlap, J C, Eckel-Mahan, K, Esser, K A, FitzGerald, G A, Forger, D B, Francey, L J, Fu, Y-H, Gachon, F, Gatfield, D, de Goede, P, Golden, S S, Green, C, Harer, J, Harmer, S, Haspel, J, Hastings, M H, Herzel, H, Herzog, E D, Hoffmann, C, Hong, C, Hughey, J J, Hurley, J M, de la Iglesia, H O, Johnson, C, Kay, S A, Koike, N, Kornacker, K, Kramer, A, Lamia, K, Leise, T, Lewis, S A, Li, J, Li, X, Liu, A C, Loros, J J, Martino, T A, Menet, J S, Merrow, M, Millar, A J, Mockler, T, Naef, F, Nagoshi, E, Nitabach, M N, Olmedo, M, Nusinow, D A, Ptáček, L J, Rand, D, Reddy, A B, Robles, M S, Roenneberg, T, Rosbash, M, Ruben, M D, Rund, S S C, Sancar, A, Sassone-Corsi, P, Sehgal, A, Sherrill-Mix, S, Skene, D J, Storch, K-F, Takahashi, J S, Ueda, H R, Wang, H, Weitz, C, Westermark, P O, Wijnen, H, Xu, Y, Wu, G, Yoo, S-H, Young, M, Zhang, E E, Zielinski, T & Hogenesch, J B 2017, ' Guidelines for Genome-Scale Analysis of Biological Rhythms ', Journal of biological rhythms, vol. 32, no. 5, 748730417728663, pp. 380-393 . https://doi.org/10.1177/0748730417728663Test Hughes, ME; Abruzzi, KC; Allada, R; Anafi, R; Arpat, AB; Asher, G; et al.(2017). Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of Biological Rhythms, 32(5), 380-393. doi: 10.1177/0748730417728663. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/2dq117tjTest Journal of biological rhythms, 32(5): 380-393 |
| بيانات النشر: | SAGE Publications, 2017. |
| سنة النشر: | 2017 |
| مصطلحات موضوعية: | Proteomics, 0301 basic medicine, JBR Perspectives on Data Analysis, ChIP-seq, RNA-seq, biostatistics, circadian rhythms, computational biology, diurnal rhythms, functional genomics, guidelines, metabolomics, proteomics, systems biology, Physiology, Statistics as Topic, Big data, GUIDELINES, Genome, purl.org/becyt/ford/1 [https], DIURNAL RHYTHMS, RNA-SEQ, Systems Biology, CHIP-SEQ, Genomics, Circadian Rhythm, 3. Good health, SYSTEMS BIOLOGY, Benchmark (computing), PROTEOMICS, CIENCIAS NATURALES Y EXACTAS, COMPUTATIONAL BIOLOGY, Otras Ciencias Biológicas, Systems biology, Computational biology, Biology, METABOLOMICS, Ciencias Biológicas, QH301, 03 medical and health sciences, Physiology (medical), Humans, FUNCTIONAL GENOMICS, purl.org/becyt/ford/1.6 [https], Set (psychology), business.industry, Mechanism (biology), Computational Biology, BIOSTATISTICS, Data science, 030104 developmental biology, Genome Biology, CIRCADIAN RHYTHMS, business, Software |
| الوصف: | 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. Fil: Hughes, Michael E.. Washington University School Of Medicine In St. Louis; Estados Unidos Fil: Abruzzi, Katherine C.. Brandeis University; Estados Unidos Fil: Allada, Ravi. Northwestern University; Estados Unidos Fil: Anafi, Ron. University of Pennsylvania; Estados Unidos Fil: Arpat, Alaaddin Bulak. Universite de Lausanne; Suiza Fil: Asher, Gad. Weizmann Institute Of Science Israel; Israel Fil: Baldi, Pierre. University of California at Irvine; Estados Unidos Fil: de Bekker, Charissa. University Of Central Florida; Estados Unidos Fil: Bell Pedersen, Deborah. Texas A&M University; Estados Unidos Fil: Blau, Justin. University of New York; Estados Unidos Fil: Brown, Steve. Universitat Zurich; Suiza Fil: Ceriani, Maria Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Chen, Zheng. University Of Texas Health Science Center At Houston; Estados Unidos Fil: Chiu, Joanna C.. University of California at Davis; Estados Unidos Fil: Cox, Juergen. Max Planck Institute Of Biochemistry; Alemania Fil: Crowell, Alexander M.. Geisel School Of Medicine At Dartmouth; Estados Unidos Fil: DeBruyne, Jason P.. Morehouse School Of Medicine; Estados Unidos Fil: Dijk, Derk-Jan. University Of Surrey; Reino Unido Fil: DiTacchio, Luciano. University Of Kansas Medical Center; Estados Unidos Fil: Doyle, Francis J.. Harvard University; Estados Unidos Fil: Duffield, Giles E.. University of Notre Dame; Estados Unidos Fil: Dunlap, Jay C.. Geisel School Of Medicine At Dartmouth; Estados Unidos Fil: Eckel Mahan, Kristin. University Of Texas Medical School At Houston; Estados Unidos Fil: Esser, Karyn A.. University Of Florida College Of Medicine; Estados Unidos Fil: FitzGerald, Garret A.. University of Pennsylvania; Estados Unidos Fil: Forger, Daniel B.. University Of Michigan; Estados Unidos Fil: Francey, Lauren J.. Cincinnati Children's Hospital Medical Center; Estados Unidos Fil: Fu, Ying Hui. University of California; Estados Unidos Fil: Gachon, Frédéric. Nestlé Institute Of Health Sciences; Suiza Fil: Gatfield, David. Universite de Lausanne; Suiza Fil: de Goede, Paul. University Of Amsterdam; Países Bajos Fil: Golden, Susan S.. University of California at San Diego; Estados Unidos Fil: Green, Carla. University of Texas; Estados Unidos Fil: Harer, John. University of Duke; Estados Unidos Fil: Harmer, Stacey. University of California at Davis; Estados Unidos Fil: Haspel, Jeff. Washington University; Estados Unidos Fil: Hastings, Michael H.. The Medical Research Council Laboratory Of Molecular Biology; Reino Unido Fil: Herzel, Hanspeter. Charité Universitätsmedizin Berlin; Alemania Fil: Herzog, Erik D.. Washington University in St. Louis; Estados Unidos Fil: Hoffmann, Christy. Washington University in St. Louis; Estados Unidos Fil: Hong, Christian. Cincinnati Children's Hospital Medical Center; Estados Unidos Fil: Hughey, Jacob J.. Vanderbilt University School Of Medicine; Estados Unidos Fil: Hurley, Jennifer M.. Rensselaer Polytechnic Institute; Estados Unidos Fil: de la Iglesia, Daniel Horacio. University Of Washington; Estados Unidos Fil: Johnson, Carl. Vanderbilt University; Estados Unidos Fil: Kay, Steve A.. University of California at San Diego; Estados Unidos Fil: Koike, Nobuya. Kyoto Prefectural University Of Medicine; Japón Fil: Kornacker, Karl. Ohio State University; Estados Unidos Fil: Kramer, Achim. Charité Universitätsmedizin Berlin; Alemania Fil: Lamia, Katja. The Scripps Research Institute; Estados Unidos Fil: Leise, Tanya. Amherst College; Estados Unidos Fil: Lewis, Scott A.. Washington University; Estados Unidos Fil: Li, Jiajia. Washington University; Estados Unidos Fil: Li, Xiaodong. Wuhan University; China Fil: Liu, Andrew C.. The University Of Memphis; Estados Unidos Fil: Loros, Jennifer J.. Geisel School Of Medicine At Dartmouth; Estados Unidos Fil: Martino, Tami A.. University of Guelph; Canadá Fil: Menet, Jerome S.. Texas A&M University; Estados Unidos Fil: Merrow, Martha. Ludwig Maximilians Universitat; Alemania Fil: Millar, Andrew J.. University of Edinburgh; Reino Unido Fil: Mockler, Todd. Donald Danforth Plant Science Center; Estados Unidos Fil: Naef, Felix. Ecole Polytechnique Federale de Lausanne; Suiza Fil: Nagoshi, Emi. Universidad de Ginebra; Suiza Fil: Nitabach, Michael N.. University of Yale. School of Medicine; Estados Unidos Fil: Olmedo, Maria. Universidad de Sevilla; España Fil: Nusinow, Dmitri A.. Donald Danforth Plant Science Center; Estados Unidos Fil: Ptácek, Louis J.. University of California; Estados Unidos Fil: Rand, David. University of Warwick; Reino Unido Fil: Reddy, Akhilesh B.. The Francis Crick Institute; Reino Unido Fil: Robles, Maria S.. Ludwig Maximilians Universitat; Alemania Fil: Roenneberg, Till. Ludwig Maximilians Universitat; Alemania Fil: Rosbash, Michael. Brandeis University; Estados Unidos Fil: Ruben, Marc D.. Cincinnati Children's Hospital Medical Center; Estados Unidos Fil: Rund, Samuel S.C.. University of Edinburgh; Reino Unido Fil: Sancar, Aziz. University of North Carolina; Estados Unidos Fil: Sassone Corsi, Paolo. University of California at Irvine; Estados Unidos Fil: Sehgal, Amita. University of Pennsylvania; Estados Unidos Fil: Sherrill Mix, Scott. University of Pennsylvania; Estados Unidos Fil: Skene, Debra J.. University Of Surrey; Reino Unido Fil: Storch, Kai Florian. Mcgill University, Douglas Mental Health University Institute; Canadá Fil: Takahashi, Joseph S.. Ut Southwestern Medical Center; Estados Unidos Fil: Ueda, Hiroki R.. The University of Tokyo; Japón Fil: Wang, Han. Soochow University; China Fil: Weitz, Charles. Harvard Medical School; Estados Unidos Fil: Westermark, P. O.. Leibniz Institute For Farm Animal Biology; Alemania Fil: Wijnen, Herman. University of Southampton; Reino Unido Fil: Xu, Ying. Soochow University; China Fil: Wu, Gang. Cincinnati Children's Hospital Medical Center; Estados Unidos Fil: Yoo, Seung Hee. University of Texas; Estados Unidos Fil: Young, Michael. The Rockefeller University; Estados Unidos Fil: Zhang, Eric Erquan. National Institute Of Biological Sciences, Beijing; China Fil: Zielinski, Tomasz. University of Edinburgh; Reino Unido Fil: Hogenesch, John B.. Cincinnati Children's Hospital Medical Center; Estados Unidos |
| وصف الملف: | application/pdf; text |
| تدمد: | 1552-4531 0748-7304 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::98132f5b6879e2975b22c568261f17f7Test https://doi.org/10.1177/0748730417728663Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....98132f5b6879e2975b22c568261f17f7 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15524531 07487304 |
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