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
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/48680

id CONICETDig_b85fef4874db95063a6ad243ece8c439
oai_identifier_str oai:ri.conicet.gov.ar:11336/48680
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling 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.
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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
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