GuidelineJournal of biological rhythms2017
Guidelines for Genome-Scale Analysis of Biological Rhythms.
Abstract readGuideline
In one paragraph
Guideline in Journal of biological rhythms, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 156 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
156citing papers in PubMed, 1 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
156 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of Diurnal Transcriptomics in Mouse Liver Reveals Low Repeatability of Rhythm Analyses.Journal of biological rhythms · 2023Pooled it
- BMAL1 in cardiovascular diseases: Molecular mechanisms, circadian regulation and translational perspectives (Review).Molecular medicine reports · 2026Review
- Rev-erb-α in Skeletal Muscle Adaptation: Integrating Circadian Control Mechanisms and Exercise Dynamic Responses.Journal of cellular physiology · 2026Review
- Remodeling of the hepatic circadian transcriptome across the estrous cycle.bioRxiv : the preprint server for biology · 2026Article
- Cell-type-specific circadian and light-responsive transcriptional dynamics in adultProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Cyanobacterial Circadian Clock: Molecular Mechanisms and Physiological Outputs.Plants (Basel, Switzerland) · 2026Review
- Unlocking the potential of circadian biology for cardiovascular health.Physiological reviews · 2026Review
- D-Box Binding Protein (DBP) as a Circadian Output Regulator: Molecular Mechanisms, Tissue-Specific Functions, and Disease Relevance.International journal of molecular sciences · 2026Review
- Circadian timing of the dystrophin associated complex across the brain and body.Fluids and barriers of the CNS · 2026Review
- Feeding-regulated glycogen metabolism drives rhythmic liver protein secretion.Nature metabolism · 2026Article
- The sleep-wake history contributes to rhythmic BMAL1 chromatin binding in the cerebral cortex but not in the liver.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Diurnal variation of wearable device-based heart rate variability in the Chronic Renal Insufficiency Cohort study.NPJ digital medicine · 2025Article
- Time-Series RNA Sequencing Reveals Temperature-Specific and Temperature-Compensated Circadian Genes inbioRxiv : the preprint server for biology · 2025Article
- A glial circadian gene expression atlas reveals cell-type and disease-specific reprogramming in response to amyloid pathology or aging.Nature neuroscience · 2025Article
- Optimization of experimental designs for biological rhythm discovery.PLoS computational biology · 2025Article
- The circadian regulator PER1 inhibits osteoclastogenesis by activating inflammatory genes.bioRxiv : the preprint server for biology · 2025Article
- Article
- A Bayesian framework for genome-wide circadian rhythmicity biomarker detection.Briefings in bioinformatics · 2025Article
- Site- and cell-type-specific miRNA and mRNA genes and networks across the cortex, striatum, and hypothalamus.Communications biology · 2025Article
- Identification and correction of time-series transcriptomic anomalies.Nucleic acids research · 2025Article
96 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
93 authors.
Michael E Hughes1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
Katherine C Abruzzi2 Department of Biology and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA.
Ravi Allada3 Department of Neurobiology, Northwestern University, Evanston, Illinois, USA.
Ron Anafi4 Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA.
Alaaddin Bulak Arpat5 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland.
Gad Asher7 Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
Pierre Baldi8 Institute for Genomics and Bioinformatics, University of California, Irvine, USA.
Charissa de Bekker9 Department of Biology, University of Central Florida, Orlando, USA.
Deborah Bell-Pedersen10 Department of Biology, Texas A&M University, College Station, USA.
Justin Blau11 Department of Biology, New York University, New York, USA.
Steve Brown12 Institute of Pharmacology and Toxicology, University of Zürich, Switzerland.
M Fernanda Ceriani13 Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.
Zheng Chen14 Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, USA.
Joanna C Chiu15 Department of Entomology and Nematology, University of California, Davis, USA.
Juergen Cox16 Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany.
Alexander M Crowell17 Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
Jason P DeBruyne18 Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, Georgia, USA.
Derk-Jan Dijk19 Surrey Sleep Research Centre, University of Surrey, Guildford, UK.
Luciano DiTacchio20 The University of Kansas Medical Center, University of Kansas, Kansas City, USA.
Francis J Doyle21 John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, Massachusetts, USA.
Giles E Duffield22 Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA.
Jay C Dunlap17 Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
Kristin Eckel-Mahan23 Institute of Molecular Medicine, McGovern Medical School, UT Health Houston, Houston, Texas, USA.
Karyn A Esser24 Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, USA.
Garret A FitzGerald25 Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA.
Daniel B Forger26 Department of Mathematics, University of Michigan, Ann Arbor, USA.
Lauren J Francey27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
Ying-Hui Fu28 Kavli Institute for Fundamental Neuroscience, Weill Institute of Neuroscience, Department of Neurology, University of California, San Francisco, USA.
Frédéric Gachon29 Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland.
David Gatfield5 Center for Integrative Genomics, Génopode, University of Lausanne, Lausanne, Switzerland.
Paul de Goede30 Department of Endocrinology & Metabolism, Academic Medical Center, Amsterdam, the Netherlands.
Susan S Golden31 Center for Circadian Biology and Division of Biological Sciences, University of California, San Diego, La Jolla, USA.
Carla Green32 Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, USA.
John Harer33 Department of Mathematics, Duke University, Durham, North Carolina, USA.
Stacey Harmer34 Department of Plant Biology, University of California, Davis, USA.
Jeff Haspel1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
Michael H Hastings35 Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
Hanspeter Herzel36 Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Germany.
Erik D Herzog37 Department of Biology, Washington University in St. Louis, Missouri, USA.
Christy Hoffmann1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
Christian Hong27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
Jacob J Hughey38 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
Jennifer M Hurley39 Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA.
Horacio O de la Iglesia40 Department of Biology, University of Washington, Seattle, USA.
Carl Johnson41 Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.
Steve A Kay42 Department of Cell and Molecular Biology, The Scripps Research Institute, University of California, San Diego, La Jolla, USA.
Nobuya Koike43 Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Japan.
Karl Kornacker44 Division of Sensory Biophysics, The Ohio State University, Columbus, USA.
Achim Kramer45 Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Germany.
Katja Lamia46 Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA.
Tanya Leise47 Department of Mathematics and Statistics, Amherst College, Amherst, Massachusetts, USA.
Scott A Lewis1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
Jiajia Li1 Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.
Xiaodong Li49 Department of Cell Biology, College of Life Sciences at Wuhan University, China.
Andrew C Liu50 Department of Biological Sciences, University of Memphis, Tennessee, USA.
Jennifer J Loros51 Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
Tami A Martino52 Centre for Cardiovascular Investigations, Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada.
Jerome S Menet10 Department of Biology, Texas A&M University, College Station, USA.
Martha Merrow53 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany.
Andrew J Millar54 SynthSys and School of Biological Sciences, University of Edinburgh, UK.
Todd Mockler55 Donald Danforth Plant Science Center, St. Louis, Missouri, USA.
Felix Naef56 The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland.
Emi Nagoshi57 Department of Genetics and Evolution, University of Geneva, Switzerland.
Michael N Nitabach58 Department of Cellular and Molecular Physiology, Department of Genetics, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut, USA.
Maria Olmedo59 Department of Genetics, University of Seville, Spain.
Dmitri A Nusinow55 Donald Danforth Plant Science Center, St. Louis, Missouri, USA.
Louis J Ptáček60 Department of Neurology, University of California, San Francisco, USA.
David Rand61 Warwick Systems Biology and Mathematics Institute, University of Warwick, Conventry, UK.
Akhilesh B Reddy62 The Francis Crick Institute, London, UK, and UCL Institute of Neurology, Queen Square, London, UK.
Maria S Robles53 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany.
Till Roenneberg53 Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Germany.
Michael Rosbash2 Department of Biology and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts, USA.
Marc D Ruben27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
Samuel S C Rund63 Centre for Immunity, Infection and Evolution, University of Edinburgh, UK.
Aziz Sancar64 Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, USA.
Paolo Sassone-Corsi65 Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, USA.
Amita Sehgal66 Howard Hughes Medical Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA.
Scott Sherrill-Mix67 Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA.
Debra J Skene68 Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.
Kai-Florian Storch69 Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, Canada.
Joseph S Takahashi70 Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, USA.
Hiroki R Ueda71 Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Osaka, Japan.
Han Wang72 Center for Circadian Clocks, Soochow University, Suzhou, Jiangsu, China.
Charles Weitz73 Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA.
Pål O Westermark74 Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
Herman Wijnen75 Biological Sciences and Institute for Life Sciences, University of Southampton, UK.
Ying Xu76 Cam-Su GRC, Soochow University, Suzhou, China.
Gang Wu27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
Seung-Hee Yoo14 Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, USA.
Michael Young77 Laboratory of Genetics, Rockefeller University, New York, New York, USA.
Eric Erquan Zhang78 National Institute of Biological Sciences, Beijing, China.
Tomasz Zielinski54 SynthSys and School of Biological Sciences, University of Edinburgh, UK.
John B Hogenesch27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
Funding
Translational Research Support CoreP30ES013508 · NIEHS · UNIVERSITY OF PENNSYLVANIA · PI Trevor M Penning · 2006 to 2026
$35.3MUniversity of Florida Older Americans Independence Center (OAIC)P30AG028740 · NIA · UNIVERSITY OF FLORIDA · PI Peihua Qiu · 2007 to 2026
$22.8MMolecular, Cellular and Physiological Mechanisms of the Mammalian Circadian ClockR01NS054794 · NINDS · UNIVERSITY OF PENNSYLVANIA · PI HOGENESCH, JOHN B, LIU, ANDREW C. · 2007 to 2022
$8.1MProgram Evaluation - Internal & External U54NS083932 · NINDS · MOREHOUSE SCHOOL OF MEDICINE · PI MACLEISH, PETER RAYMOND · 2013 to 2017
$7.7MGenetic and Molecular Dissection of the Neurospora ClockR35GM118021 · NIGMS · DARTMOUTH COLLEGE · PI Jay C. Dunlap · 2016 to 2026
$7.3MResearch Project: Sensory and Multisensory Contributions to AutismU54HD083211 · NICHD · VANDERBILT UNIVERSITY MEDICAL CENTER · PI DYKENS, ELISABETH MAY · 2015 to 2019
$7.1MUndergraduate Summer Research Experience: Molecular and cellular mechanisms of circadian timekeeping in a prokaryote modelR35GM118290 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GOLDEN, SUSAN S · 2016 to 2025
$6.7MRegulation of pacemaker neuronsR01GM063911 · NIGMS · NEW YORK UNIVERSITY · PI BLAU, JUSTIN · 2002 to 2019
$5.6MMolecular Genetic Analysis of Fungal Circadian RythmsR01GM058529 · NIGMS · TEXAS A&M UNIVERSITY SYSTEM · PI BELL-PEDERSEN, DEBORAH · 1999 to 2017
$4.6MOrganoids as a Model System for Studying Gastrointestinal DiseaseU19AI116491 · NIAID · UNIVERSITY OF CINCINNATI · PI WEISS, ALISON A., WELLS, JAMES M · 2015 to 2019
$4.6MCircadian Programs in BacteriaR37GM067152 · NIGMS · VANDERBILT UNIVERSITY · PI JOHNSON, CARL HIRSCHIE · 2015 to 2024
$4.1MSynaptic Microcircuits Underlying Associative LearningR01NS091070 · NINDS · YALE UNIVERSITY · PI NITABACH, MICHAEL · 2014 to 2024
$4.0MBiotechnology and Biological Sciences Research Council BB/F022883/1Medical Research Council MC_U105170643Medical Research Council MR/N006321/1NIAID NIH HHS U19 AI116491NIAMS NIH HHS R21 AR069266NIA NIH HHS R01 AG045795NIA NIH HHS R01 AG045828NIBIB NIH HHS U01 EB021956NIBIB NIH HHS U01 EB022546NIDDK NIH HHS R01 DK097164NIGMS NIH HHS R01 GM063911NIGMS NIH HHS R01 GM069418NIGMS NIH HHS R01 GM087508NIGMS NIH HHS R01 GM098931NIGMS NIH HHS R01 GM102225NIGMS NIH HHS R01 GM104991NIGMS NIH HHS R01 GM111387NIGMS NIH HHS R01 GM112991NIGMS NIH HHS R01 GM114424NIGMS NIH HHS R35 GM118021NIGMS NIH HHS R35 GM118022NIGMS NIH HHS R35 GM118290NIGMS NIH HHS SC1 GM109861NINDS NIH HHS R01 NS054794NINDS NIH HHS R01 NS091070NINDS NIH HHS R01 NS094211NINDS NIH HHS R01 NS095367NINDS NIH HHS U54 NS083932Wellcome Trust
Abstract
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.
Indexed as
GenomeGenomicsBiostatisticsCircadian RhythmComputational BiologyHumansMetabolomicsProteomicsSoftwareStatistics as TopicSystems BiologybiostatisticsChIP-seqcircadian rhythmscomputational biologydiurnal rhythmsfunctional genomicsguidelinesmetabolomicsproteomicsRNA-seqsystems biology
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