Guidelines for Genome-Scale Analysis of Biological Rhythms
- Autores
- 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, Maria 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, Daniel Horacio; Johnson, Carl; Kay, Steve A.; Koike, Nobuya; Kornacker, Karl; Kramer, Achim; Lamia, Katja; Leise, Tanya; Lewis, Scott A.; Li, Jiajia; Li, Xiaodong; Liu, Andrew C.; Loros, Jennifer J.; Martino, Tami A.; Menet, Jerome S.; Merrow, Martha; Millar, Andrew J.; Mockler, Todd; Naef, Felix; Nagoshi, Emi; Nitabach, Michael N.; Olmedo, Maria; Nusinow, Dmitri A.; Ptácek, Louis J.; Rand, David; Reddy, Akhilesh B.; Robles, Maria S.; Roenneberg, Till; Rosbash, Michael; Ruben, Marc D.; Rund, Samuel S.C.; Sancar, Aziz; Sassone Corsi, Paolo; Sehgal, Amita; Sherrill Mix, Scott; Skene, Debra J.; Storch, Kai Florian; Takahashi, Joseph S.; Ueda, Hiroki R.; Wang, Han; Weitz, Charles; Westermark, P. O.; Wijnen, Herman; Xu, Ying; Wu, Gang; Yoo, Seung Hee; Young, Michael; Zhang, Eric Erquan; Zielinski, Tomasz; Hogenesch, John B.
- Año de publicación
- 2017
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- 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 - Materia
-
BIOSTATISTICS
CHIP-SEQ
CIRCADIAN RHYTHMS
COMPUTATIONAL BIOLOGY
DIURNAL RHYTHMS
FUNCTIONAL GENOMICS
GUIDELINES
METABOLOMICS
PROTEOMICS
RNA-SEQ
SYSTEMS BIOLOGY - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
.jpg)
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/48680
Ver los metadatos del registro completo
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CONICET Digital (CONICET) |
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Guidelines for Genome-Scale Analysis of Biological RhythmsHughes, Michael E.Abruzzi, Katherine C.Allada, RaviAnafi, RonArpat, Alaaddin BulakAsher, GadBaldi, Pierrede Bekker, CharissaBell Pedersen, DeborahBlau, JustinBrown, SteveCeriani, Maria FernandaChen, ZhengChiu, Joanna C.Cox, JuergenCrowell, Alexander M.DeBruyne, Jason P.Dijk, Derk-JanDiTacchio, LucianoDoyle, Francis J.Duffield, Giles E.Dunlap, Jay C.Eckel Mahan, KristinEsser, Karyn A.FitzGerald, Garret A.Forger, Daniel B.Francey, Lauren J.Fu, Ying HuiGachon, FrédéricGatfield, Davidde Goede, PaulGolden, Susan S.Green, CarlaHarer, JohnHarmer, StaceyHaspel, JeffHastings, Michael H.Herzel, HanspeterHerzog, Erik D.Hoffmann, ChristyHong, ChristianHughey, Jacob J.Hurley, Jennifer M.de la Iglesia, Daniel HoracioJohnson, CarlKay, Steve A.Koike, NobuyaKornacker, KarlKramer, AchimLamia, KatjaLeise, TanyaLewis, Scott A.Li, JiajiaLi, XiaodongLiu, Andrew C.Loros, Jennifer J.Martino, Tami A.Menet, Jerome S.Merrow, MarthaMillar, Andrew J.Mockler, ToddNaef, FelixNagoshi, EmiNitabach, Michael N.Olmedo, MariaNusinow, Dmitri A.Ptácek, Louis J.Rand, DavidReddy, Akhilesh B.Robles, Maria S.Roenneberg, TillRosbash, MichaelRuben, Marc D.Rund, Samuel S.C.Sancar, AzizSassone Corsi, PaoloSehgal, AmitaSherrill Mix, ScottSkene, Debra J.Storch, Kai FlorianTakahashi, Joseph S.Ueda, Hiroki R.Wang, HanWeitz, CharlesWestermark, P. O.Wijnen, HermanXu, YingWu, GangYoo, Seung HeeYoung, MichaelZhang, Eric ErquanZielinski, TomaszHogenesch, John B.BIOSTATISTICSCHIP-SEQCIRCADIAN RHYTHMSCOMPUTATIONAL BIOLOGYDIURNAL RHYTHMSFUNCTIONAL GENOMICSGUIDELINESMETABOLOMICSPROTEOMICSRNA-SEQSYSTEMS BIOLOGYhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Genome 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 UnidosFil: Abruzzi, Katherine C.. Brandeis University; Estados UnidosFil: Allada, Ravi. Northwestern University; Estados UnidosFil: Anafi, Ron. University of Pennsylvania; Estados UnidosFil: Arpat, Alaaddin Bulak. Universite de Lausanne; SuizaFil: Asher, Gad. Weizmann Institute Of Science Israel; IsraelFil: Baldi, Pierre. University of California at Irvine; Estados UnidosFil: de Bekker, Charissa. University Of Central Florida; Estados UnidosFil: Bell Pedersen, Deborah. Texas A&M University; Estados UnidosFil: Blau, Justin. University of New York; Estados UnidosFil: Brown, Steve. Universitat Zurich; SuizaFil: 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; ArgentinaFil: Chen, Zheng. University Of Texas Health Science Center At Houston; Estados UnidosFil: Chiu, Joanna C.. University of California at Davis; Estados UnidosFil: Cox, Juergen. Max Planck Institute Of Biochemistry; AlemaniaFil: Crowell, Alexander M.. Geisel School Of Medicine At Dartmouth; Estados UnidosFil: DeBruyne, Jason P.. Morehouse School Of Medicine; Estados UnidosFil: Dijk, Derk-Jan. University Of Surrey; Reino UnidoFil: DiTacchio, Luciano. University Of Kansas Medical Center; Estados UnidosFil: Doyle, Francis J.. Harvard University; Estados UnidosFil: Duffield, Giles E.. University of Notre Dame; Estados UnidosFil: Dunlap, Jay C.. Geisel School Of Medicine At Dartmouth; Estados UnidosFil: Eckel Mahan, Kristin. University Of Texas Medical School At Houston; Estados UnidosFil: Esser, Karyn A.. University Of Florida College Of Medicine; Estados UnidosFil: FitzGerald, Garret A.. University of Pennsylvania; Estados UnidosFil: Forger, Daniel B.. University Of Michigan; Estados UnidosFil: Francey, Lauren J.. Cincinnati Children's Hospital Medical Center; Estados UnidosFil: Fu, Ying Hui. University of California; Estados UnidosFil: Gachon, Frédéric. Nestlé Institute Of Health Sciences; SuizaFil: Gatfield, David. Universite de Lausanne; SuizaFil: de Goede, Paul. University Of Amsterdam; Países BajosFil: Golden, Susan S.. University of California at San Diego; Estados UnidosFil: Green, Carla. University of Texas; Estados UnidosFil: Harer, John. University of Duke; Estados UnidosFil: Harmer, Stacey. University of California at Davis; Estados UnidosFil: Haspel, Jeff. Washington University; Estados UnidosFil: Hastings, Michael H.. The Medical Research Council Laboratory Of Molecular Biology; Reino UnidoFil: Herzel, Hanspeter. Charité Universitätsmedizin Berlin; AlemaniaFil: Herzog, Erik D.. Washington University in St. Louis; Estados UnidosFil: Hoffmann, Christy. Washington University in St. Louis; Estados UnidosFil: Hong, Christian. Cincinnati Children's Hospital Medical Center; Estados UnidosFil: Hughey, Jacob J.. Vanderbilt University School Of Medicine; Estados UnidosFil: Hurley, Jennifer M.. Rensselaer Polytechnic Institute; Estados UnidosFil: de la Iglesia, Daniel Horacio. University Of Washington; Estados UnidosFil: Johnson, Carl. Vanderbilt University; Estados UnidosFil: Kay, Steve A.. University of California at San Diego; Estados UnidosFil: Koike, Nobuya. Kyoto Prefectural University Of Medicine; JapónFil: Kornacker, Karl. Ohio State University; Estados UnidosFil: Kramer, Achim. Charité Universitätsmedizin Berlin; AlemaniaFil: Lamia, Katja. The Scripps Research Institute; Estados UnidosFil: Leise, Tanya. Amherst College; Estados UnidosFil: Lewis, Scott A.. Washington University; Estados UnidosFil: Li, Jiajia. Washington University; Estados UnidosFil: Li, Xiaodong. Wuhan University; ChinaFil: Liu, Andrew C.. The University Of Memphis; Estados UnidosFil: Loros, Jennifer J.. Geisel School Of Medicine At Dartmouth; Estados UnidosFil: Martino, Tami A.. University of Guelph; CanadáFil: Menet, Jerome S.. Texas A&M University; Estados UnidosFil: Merrow, Martha. Ludwig Maximilians Universitat; AlemaniaFil: Millar, Andrew J.. University of Edinburgh; Reino UnidoFil: Mockler, Todd. Donald Danforth Plant Science Center; Estados UnidosFil: Naef, Felix. Ecole Polytechnique Federale de Lausanne; SuizaFil: Nagoshi, Emi. Universidad de Ginebra; SuizaFil: Nitabach, Michael N.. University of Yale. School of Medicine; Estados UnidosFil: Olmedo, Maria. Universidad de Sevilla; EspañaFil: Nusinow, Dmitri A.. Donald Danforth Plant Science Center; Estados UnidosFil: Ptácek, Louis J.. University of California; Estados UnidosFil: Rand, David. University of Warwick; Reino UnidoFil: Reddy, Akhilesh B.. The Francis Crick Institute; Reino UnidoFil: Robles, Maria S.. Ludwig Maximilians Universitat; AlemaniaFil: Roenneberg, Till. Ludwig Maximilians Universitat; AlemaniaFil: Rosbash, Michael. Brandeis University; Estados UnidosFil: Ruben, Marc D.. Cincinnati Children's Hospital Medical Center; Estados UnidosFil: Rund, Samuel S.C.. University of Edinburgh; Reino UnidoFil: Sancar, Aziz. University of North Carolina; Estados UnidosFil: Sassone Corsi, Paolo. University of California at Irvine; Estados UnidosFil: Sehgal, Amita. University of Pennsylvania; Estados UnidosFil: Sherrill Mix, Scott. University of Pennsylvania; Estados UnidosFil: Skene, Debra J.. University Of Surrey; Reino UnidoFil: Storch, Kai Florian. Mcgill University, Douglas Mental Health University Institute; CanadáFil: Takahashi, Joseph S.. Ut Southwestern Medical Center; Estados UnidosFil: Ueda, Hiroki R.. The University of Tokyo; JapónFil: Wang, Han. Soochow University; ChinaFil: Weitz, Charles. Harvard Medical School; Estados UnidosFil: Westermark, P. O.. Leibniz Institute For Farm Animal Biology; AlemaniaFil: Wijnen, Herman. University of Southampton; Reino UnidoFil: Xu, Ying. Soochow University; ChinaFil: Wu, Gang. Cincinnati Children's Hospital Medical Center; Estados UnidosFil: Yoo, Seung Hee. University of Texas; Estados UnidosFil: Young, Michael. The Rockefeller University; Estados UnidosFil: Zhang, Eric Erquan. National Institute Of Biological Sciences, Beijing; ChinaFil: Zielinski, Tomasz. University of Edinburgh; Reino UnidoFil: Hogenesch, John B.. Cincinnati Children's Hospital Medical Center; Estados UnidosSAGE Publications2017-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/48680Hughes, Michael E.; Abruzzi, Katherine C.; Allada, Ravi; Anafi, Ron; Arpat, Alaaddin Bulak; et al.; Guidelines for Genome-Scale Analysis of Biological Rhythms; SAGE Publications; Journal of Biological Rhythms; 32; 5; 10-2017; 380-3930748-73041552-4531CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://journals.sagepub.com/doi/10.1177/0748730417728663info:eu-repo/semantics/altIdentifier/doi/10.1177/0748730417728663info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T15:04:13Zoai:ri.conicet.gov.ar:11336/48680instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 15:04:13.921CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
| dc.title.none.fl_str_mv |
Guidelines for Genome-Scale Analysis of Biological Rhythms |
| title |
Guidelines for Genome-Scale Analysis of Biological Rhythms |
| spellingShingle |
Guidelines for Genome-Scale Analysis of Biological Rhythms Hughes, Michael E. BIOSTATISTICS CHIP-SEQ CIRCADIAN RHYTHMS COMPUTATIONAL BIOLOGY DIURNAL RHYTHMS FUNCTIONAL GENOMICS GUIDELINES METABOLOMICS PROTEOMICS RNA-SEQ SYSTEMS BIOLOGY |
| title_short |
Guidelines for Genome-Scale Analysis of Biological Rhythms |
| title_full |
Guidelines for Genome-Scale Analysis of Biological Rhythms |
| title_fullStr |
Guidelines for Genome-Scale Analysis of Biological Rhythms |
| title_full_unstemmed |
Guidelines for Genome-Scale Analysis of Biological Rhythms |
| title_sort |
Guidelines for Genome-Scale Analysis of Biological Rhythms |
| dc.creator.none.fl_str_mv |
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, Maria 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, Daniel Horacio Johnson, Carl Kay, Steve A. Koike, Nobuya Kornacker, Karl Kramer, Achim Lamia, Katja Leise, Tanya Lewis, Scott A. Li, Jiajia Li, Xiaodong Liu, Andrew C. Loros, Jennifer J. Martino, Tami A. Menet, Jerome S. Merrow, Martha Millar, Andrew J. Mockler, Todd Naef, Felix Nagoshi, Emi Nitabach, Michael N. Olmedo, Maria Nusinow, Dmitri A. Ptácek, Louis J. Rand, David Reddy, Akhilesh B. Robles, Maria S. Roenneberg, Till Rosbash, Michael Ruben, Marc D. Rund, Samuel S.C. Sancar, Aziz Sassone Corsi, Paolo Sehgal, Amita Sherrill Mix, Scott Skene, Debra J. Storch, Kai Florian Takahashi, Joseph S. Ueda, Hiroki R. Wang, Han Weitz, Charles Westermark, P. O. Wijnen, Herman Xu, Ying Wu, Gang Yoo, Seung Hee Young, Michael Zhang, Eric Erquan Zielinski, Tomasz Hogenesch, John B. |
| author |
Hughes, Michael E. |
| author_facet |
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, Maria 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, Daniel Horacio Johnson, Carl Kay, Steve A. Koike, Nobuya Kornacker, Karl Kramer, Achim Lamia, Katja Leise, Tanya Lewis, Scott A. Li, Jiajia Li, Xiaodong Liu, Andrew C. Loros, Jennifer J. Martino, Tami A. Menet, Jerome S. Merrow, Martha Millar, Andrew J. Mockler, Todd Naef, Felix Nagoshi, Emi Nitabach, Michael N. Olmedo, Maria Nusinow, Dmitri A. Ptácek, Louis J. Rand, David Reddy, Akhilesh B. Robles, Maria S. Roenneberg, Till Rosbash, Michael Ruben, Marc D. Rund, Samuel S.C. Sancar, Aziz Sassone Corsi, Paolo Sehgal, Amita Sherrill Mix, Scott Skene, Debra J. Storch, Kai Florian Takahashi, Joseph S. Ueda, Hiroki R. Wang, Han Weitz, Charles Westermark, P. O. Wijnen, Herman Xu, Ying Wu, Gang Yoo, Seung Hee Young, Michael Zhang, Eric Erquan Zielinski, Tomasz Hogenesch, John B. |
| author_role |
author |
| author2 |
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, Maria 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, Daniel Horacio Johnson, Carl Kay, Steve A. Koike, Nobuya Kornacker, Karl Kramer, Achim Lamia, Katja Leise, Tanya Lewis, Scott A. Li, Jiajia Li, Xiaodong Liu, Andrew C. Loros, Jennifer J. Martino, Tami A. Menet, Jerome S. Merrow, Martha Millar, Andrew J. Mockler, Todd Naef, Felix Nagoshi, Emi Nitabach, Michael N. Olmedo, Maria Nusinow, Dmitri A. Ptácek, Louis J. Rand, David Reddy, Akhilesh B. Robles, Maria S. Roenneberg, Till Rosbash, Michael Ruben, Marc D. Rund, Samuel S.C. Sancar, Aziz Sassone Corsi, Paolo Sehgal, Amita Sherrill Mix, Scott Skene, Debra J. Storch, Kai Florian Takahashi, Joseph S. Ueda, Hiroki R. Wang, Han Weitz, Charles Westermark, P. O. Wijnen, Herman Xu, Ying Wu, Gang Yoo, Seung Hee Young, Michael Zhang, Eric Erquan Zielinski, Tomasz Hogenesch, John B. |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
BIOSTATISTICS CHIP-SEQ CIRCADIAN RHYTHMS COMPUTATIONAL BIOLOGY DIURNAL RHYTHMS FUNCTIONAL GENOMICS GUIDELINES METABOLOMICS PROTEOMICS RNA-SEQ SYSTEMS BIOLOGY |
| topic |
BIOSTATISTICS CHIP-SEQ CIRCADIAN RHYTHMS COMPUTATIONAL BIOLOGY DIURNAL RHYTHMS FUNCTIONAL GENOMICS GUIDELINES METABOLOMICS PROTEOMICS RNA-SEQ SYSTEMS BIOLOGY |
| purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
| dc.description.none.fl_txt_mv |
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 |
| description |
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. |
| publishDate |
2017 |
| dc.date.none.fl_str_mv |
2017-10 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/48680 Hughes, Michael E.; Abruzzi, Katherine C.; Allada, Ravi; Anafi, Ron; Arpat, Alaaddin Bulak; et al.; Guidelines for Genome-Scale Analysis of Biological Rhythms; SAGE Publications; Journal of Biological Rhythms; 32; 5; 10-2017; 380-393 0748-7304 1552-4531 CONICET Digital CONICET |
| url |
http://hdl.handle.net/11336/48680 |
| identifier_str_mv |
Hughes, Michael E.; Abruzzi, Katherine C.; Allada, Ravi; Anafi, Ron; Arpat, Alaaddin Bulak; et al.; Guidelines for Genome-Scale Analysis of Biological Rhythms; SAGE Publications; Journal of Biological Rhythms; 32; 5; 10-2017; 380-393 0748-7304 1552-4531 CONICET Digital CONICET |
| dc.language.none.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/http://journals.sagepub.com/doi/10.1177/0748730417728663 info:eu-repo/semantics/altIdentifier/doi/10.1177/0748730417728663 |
| dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
| eu_rights_str_mv |
openAccess |
| rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
| dc.format.none.fl_str_mv |
application/pdf application/pdf |
| dc.publisher.none.fl_str_mv |
SAGE Publications |
| publisher.none.fl_str_mv |
SAGE Publications |
| dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
| reponame_str |
CONICET Digital (CONICET) |
| collection |
CONICET Digital (CONICET) |
| instname_str |
Consejo Nacional de Investigaciones Científicas y Técnicas |
| repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
| repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
| _version_ |
1846083185414242304 |
| score |
13.22299 |