cran: MetaCycle | Projects | Ecosyste.ms: Papers

10.15252/msb.20209498

Developmental function and state transitions of a gene expression oscillator in <i>Caenorhabditis elegans</i>
Cited by: 43
Author(s): Milou W.M. Meeuse, Yannick P Hauser, Lucas J Morales Moya, Gert‐Jan Hendriks, Jan Eglinger, Guy Bogaarts, Charisios D. Tsiairis, Helge Großhans
Software Mentions: 14
Published: over 4 years ago

10.3390/genes12030352

Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data
Cited by: 10
Author(s): Vera-Khlara S. Oh, Robert W. Li
Software Mentions: 12
Published: over 3 years ago

10.3390/cells8080920

The Snapdragon LATE ELONGATED HYPOCOTYL Plays A Dual Role in Activating Floral Growth and Scent Emission
Cited by: 9
Author(s): Marta I. Terry, Fernando Pérez-Sánz, Pedro J. Navarro, Julia Weiß, Marcos Egea‐Cortines
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1007666

Methods detecting rhythmic gene expression are biologically relevant only for strong signal
Cited by: 22
Author(s): David Laloum, Marc Robinson‐Rechavi
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pbio.3000792

Heritable gene expression variability and stochasticity govern clonal heterogeneity in circadian period
Cited by: 12
Author(s): K. L. Nikhil, Sandra Korge, Achim Kramer
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pgen.1008265

Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain
Cited by: 23
Author(s): Aldrin B. Lugena, Ying Zhang, Jérôme S. Menet, Christine Merlin
Software Mentions: 7
Published: over 5 years ago

10.1016/j.dib.2019.103909

RNA-sequencing data highlighting the time-of-day-dependent transcriptome of the central circadian pacemaker in Sox2-deficient mice
Cited by: 4
Author(s): Arthur H. Cheng, Pascale Bouchard-Cannon, Rob W. Ness, Hai-Ying Mary Cheng
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.65574

KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism
Cited by: 16
Author(s): Anthony A Ruberto, Aline Gréchez-Cassiau, Sabrina Guérin, Luc Martin, Johana S. Revel, Mohamed Mehiri, Malayannan Subramaniam, Franck Delaunay, Michèle Teboul
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-47343-w

A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line
Cited by: 9
Author(s): Nikolaï Genov, Alireza Basti, Marconi Abreu, Rosario Astaburuaga, Angela Relógio
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pbio.3000435

Single-cell in vivo imaging of cellular circadian oscillators in zebrafish
Cited by: 13
Author(s): Haifang Wang, Zeyong Yang, Xingxing Li, Di Huang, Shuguang Yu, Jie He, Yuanhai Li, Jun Yan
Software Mentions: 5
Published: over 4 years ago

10.3390/cells8040343

The Petunia CHANEL Gene is a ZEITLUPE Ortholog Coordinating Growth and Scent Profiles
Cited by: 18
Author(s): Marta I. Terry, Fernando Pérez-Sánz, María Victoria Díaz-Galián, Felipe Pérez de los Cobos, Pedro J. Navarro, Marcos Egea‐Cortines, Julia Weiß
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-018-2257-4

MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data
Cited by: 8
Author(s): Hitoshi Iuchi, Masahiro Sugimoto, Masaru Tomita
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2021.664334

Disruption of Circadian Transcriptome in Lung by Acute Sleep Deprivation
Cited by: 6
Author(s): Yuntao Lu, Bing Liu, Junjie Ma, Shuo Yang, Ju Huang
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2019.00917

Nuclear Lamin B1 Interactions With Chromatin During the Circadian Cycle Are Uncoupled From Periodic Gene Expression
Cited by: 19
Author(s): Annaël Brunet, Frida Forsberg, Qiong Fan, Thomas Sæther, Philippe Collas
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-78851-9

Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output
Cited by: 7
Author(s): Evan S. Littleton, Madison L. Childress, Michaela L. Gosting, Ayana N. Jackson, Shihoko Kojima
Software Mentions: 4
Published: almost 4 years ago

10.1093/treephys/tpaa130

Photoperiod-dependent transcriptional modifications in key metabolic pathways in <i>Coffea arabica</i>
Cited by: 3
Author(s): Doâa Djerrab, Benoît Bertrand, Jean‐Christophe Breitler, Sophie Léran, Eveline Déchamp, Claudine Campa, Célia Barrachina, Geneviève Conéjéro, Hervé Etienne, Ronan Sulpice
Software Mentions: 4
Published: about 4 years ago

10.1128/mSystems.00116-21

Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome
Cited by: 25
Author(s): Celeste Allaband, Amulya Lingaraju, Cameron Martino, Baylee J. Russell, Anupriya Tripathi, Orit Poulsen, Ana Carolina Dantas Machado, Dan Zhou, Jin Xue, Emmanuel O. Elijah, Atul Malhotra, Pieter C. Dorrestein, Rob Knight, Gabriel G. Haddad, Amir Zarrinpar
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms22157810

Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis
Cited by: 4
Author(s): Shital Kumar Mishra, Taole Liu, Han Wang
Software Mentions: 4
Published: over 3 years ago

10.3390/biology10040266

PER2 Circadian Oscillation Sensitizes Esophageal Cancer Cells to Chemotherapy
Cited by: 6
Author(s): Juan Alfonso Redondo, Romain Bibes, Alizée Vercauteren Drubbel, Benjamin Dassy, Xavier Bisteau, Eléonore Maury, Benjamin Beck
Software Mentions: 3
Published: over 3 years ago

10.5334/jcr.213

Genes Relevant to Tissue Response to Cancer Therapy Display Diurnal Variation in mRNA Expression in Human Oral Mucosa
Cited by: 3
Author(s): Fangyi Gu, Eduardo Cortes Gomez, Jianhong Chen, Matthew F. Buas, Nicolas F. Schlecht, Karen Hulme, Shweta Vishwas Kulkarni, Prashant Singh, Richard J. O’Connor, Christine B. Ambrosone, Anurag Singh, Jianmin Wang
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-017-03797-4

Remodeling of the cycling transcriptome of the oyster Crassostrea gigas by the harmful algae Alexandrium minutum
Cited by: 20
Author(s): Laura Payton, Mickael Perrigault, Claire Hoede, Jean‐Charles Massabuau, Mohamedou Sow, Arnaud Huvet, Floriane Boullot, Caroline Fabioux, Hélène Hégaret, Damien Tran
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.13552

Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue
Cited by: 58
Author(s): Renske Erion, Anna N. King, Gang Wu, John B. Hogenesch, Amita Sehgal
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.63056

A transcriptomic taxonomy of Drosophila circadian neurons around the clock
Cited by: 62
Author(s): Dingbang Ma, Dariusz Przybylski, Katharine C. Abruzzi, Matthias Schlichting, Qunlong Li, Xi Long, Michael Rosbash
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.44642

Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila
Cited by: 51
Author(s): Ane Martín Anduaga, Naveh Evantal, Inés Lucía Patop, Osnat Bartok, Ron Weiss, Sebastián Kadener
Software Mentions: 3
Published: about 5 years ago

10.1534/g3.118.200559

Identification and Characterization of Transcripts Regulated by Circadian Alternative Polyadenylation in Mouse Liver
Cited by: 17
Author(s): Kerry L. Gendreau, Benjamin A Unruh, Chuanli Zhou, Shihoko Kojima
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pbio.3000228

G1/S cell cycle regulators mediate effects of circadian dysregulation on tumor growth and provide targets for timed anticancer treatment
Cited by: 64
Author(s): Yool Lee, Nicholas F. Lahens, Shirley Zhang, Joseph L. Bedont, Jeffrey Field, Amita Sehgal
Software Mentions: 3
Published: over 5 years ago

10.1523/JNEUROSCI.0921-20.2020

The mRNA-Binding Protein RBM3 Regulates Activity Patterns and Local Synaptic Translation in Cultured Hippocampal Neurons
Cited by: 14
Author(s): Sinem M. Sertel, Malena S. von Elling-Tammen, Silvio O. Rizzoli
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-019-46656-0

REV-ERBα and REV-ERBβ function as key factors regulating Mammalian Circadian Output
Cited by: 57
Author(s): Ryosuke Ikeda, Yoshiki Tsuchiya, Nobuya Koike, Yasuhiro Umemura, Hitoshi Inokawa, Ryutaro Ono, Maho Inoue, Yuh Sasawaki, Tess Grieten, Naoki Okubo, Kazuya Ikoma, Hiroyoshi Fujiwara, Toshikazu Kubo, Kazuhiro Yagita
Software Mentions: 2
Published: over 5 years ago

10.1111/ejn.14411

Effect of acute total sleep deprivation on plasma melatonin, cortisol and metabolite rhythms in females
Cited by: 42
Author(s): Aya Honma, Victoria L. Revell, Pippa J. Gunn, Sarah K. Davies, Benita Middleton, Florence I. Raynaud, Debra J. Skene
Software Mentions: 2
Published: over 5 years ago

10.1186/s12870-018-1244-2

Diel pattern of circadian clock and storage protein gene expression in leaves and during seed filling in cowpea (Vigna unguiculata)
Cited by: 13
Author(s): Julia Weiß, Marta I. Terry, Marina Martos-Fuentes, Lisa Letourneux, Victoria Ruiz-Hernández, Juan Antonio Fernández Hernández, Marcos Egea‐Cortines
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12870-020-2238-4

Full moonlight-induced circadian clock entrainment in Coffea arabica
Cited by: 15
Author(s): Jean‐Christophe Breitler, Doâa Djerrab, Sophie Léran, Lucile Toniutti, Charlie Guittin, Dany Séverac, Marine Pratlong, Alexis Dereeper, Hervé Etienne, Benoît Bertrand
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.joca.2021.02.008

Circadian time series proteomics reveals daily dynamics in cartilage physiology
Cited by: 15
Author(s): Michal Dudek, Constanza Angelucci, Dharshika Pathiranage, Ping Wang, Venkatesh Mallikarjun, Craig Lawless, Joe Swift, Karl E. Kadler, Ray Boot-Handford, Judith A. Hoyland, Shireen R. Lamandé, John F. Bateman, Qing‐Jun Meng
Software Mentions: 2
Published: over 3 years ago

10.1016/j.isci.2021.102335

A multi-tissue multi-omics analysis reveals distinct kineztics in entrainment of diurnal transcriptomes by inverted feeding
Cited by: 27
Author(s): Haoran Xin, Fang Deng, Mingxia Zhou, Rongfeng Huang, Xiaogen Ma, He Tian, Yan Tan, Xinghua Chen, Dan Deng, Guanghou Shui, Zhihui Zhang, Min‐Dian Li
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-020-6639-4

Endogenous circadian time genes expressions in the liver of mice under constant darkness
Cited by: 23
Author(s): Huan Li, Shiyao Zhang, Wenxiang Zhang, Siyu Chen, Anjara Rabearivony, Yujie Shi, Jie Liu, Christopher J. Corton, Chang Liu
Software Mentions: 2
Published: over 4 years ago

10.1016/j.molmet.2019.11.004

The core clock gene, Bmal1, and its downstream target, the SNARE regulatory protein secretagogin, are necessary for circadian secretion of glucagon-like peptide-1
Cited by: 32
Author(s): Andrew D. Biancolin, Alexandre Martchenko, Emilia Mitova, Patrick Gurges, Everan Michalchyshyn, J. P. Chalmers, Alessandro Doria, Josyf C. Mychaleckyj, Alice E. Adriaenssens, Frank Reimann, Fiona M. Gribble, Manuel Gil‐Lozano, Brian Cox, Patricia L. Brubaker
Software Mentions: 2
Published: almost 5 years ago

10.3390/cancers12113103

An Optimal Time for Treatment—Predicting Circadian Time by Machine Learning and Mathematical Modelling
Cited by: 20
Author(s): Janina Hesse, Deeksha Malhan, Müge Yalҫin, Ouda Aboumanify, Alireza Basti, Angela Relógio
Software Mentions: 2
Published: about 4 years ago

10.3390/cells9092070

Dynamic High-Sensitivity Quantitation of Procollagen-I by Endogenous CRISPR-Cas9 NanoLuciferase Tagging
Cited by: 7
Author(s): Ben Calverley, Karl E. Kadler, Adam Pickard
Software Mentions: 2
Published: about 4 years ago

10.3390/metabo11050328

Tick-Tock Consider the Clock: The Influence of Circadian and External Cycles on Time of Day Variation in the Human Metabolome—A Review
Cited by: 12
Author(s): Thomas P M Hancox, Debra J. Skene, Robert Dallmann, Warwick B. Dunn
Software Mentions: 2
Published: over 3 years ago

10.1038/s41377-021-00542-5

In vivo flow cytometry reveals a circadian rhythm of circulating tumor cells
Cited by: 31
Author(s): Xi Zhu, Yuanzhen Suo, Yuting Fu, Fuli Zhang, Nan Ding, K. Sandy Pang, Conghua Xie, Xiaofu Weng, Meilu Tian, Hao He, Xunbin Wei
Software Mentions: 1
Published: over 3 years ago

10.1016/j.xpro.2021.100701

Protocol for setup and circadian analysis of inverted feeding in mice
Cited by: 8
Author(s): Haoran Xin, Rongfeng Huang, Mingxia Zhou, Xinyu Bao, Jianghui Chen, Fan Zhou, Xiao‐Qin Wan, Shifei Tong, Fang Deng, Min‐Dian Li, Zhihui Zhang
Software Mentions: 1
Published: about 3 years ago

10.1016/j.xpro.2021.100539

Collecting mouse livers for transcriptome analysis of daily rhythms
Cited by: 2
Author(s): Thomas Mortimer, Patrick-Simon Welz, Salvador Aznar Benitah, Kevin B. Koronowski
Software Mentions: 1
Published: over 3 years ago

10.1177/0748730417728663

Guidelines for Genome-Scale Analysis of Biological Rhythms
Cited by: 193
Author(s): Michael Hughes, Katherine C. Abruzzi, Ravi Allada, Ron C. Anafi, Alaaddin Bulak Arpat, Gad Asher, Pierre Baldi, Charissa de Bekker, Deborah Bell-Pedersen, Justin Blau, Steve Brown, M. Fernanda Ceriani, Jake Y. Chen, Joanna C. Chiu, Juergen Cox, Alexander M. Crowell, Jason P. DeBruyne, Derk Jan Dijk, Luciano DiTacchio, Francis J. Doyle, Giles E. Duffield, Jay C. Dunlap, Kristin Eckel‐Mahan, Karyn A. Esser, Garret A. FitzGerald, Daniel B. Forger, Lauren J. Francey, Ying Hui Fu, Frédéric Gachon, David Gatfield, Paul de Goede, Susan S. Golden, Carla B. Green, John Harer, Stacey L. Harmer, Jeff Haspel, Michael H. Hastings, Hanspeter Herzel, Erik D. Herzog, Christy Hoffmann, Christian I. Hong, Jacob J. Hughey, Jennifer M. Hurley, Horacio O. de la Iglesia, Carl Hirschie Johnson, Steve A. Kay, Nobuya Koike, Karl Kornacker, Achim Kramer, Katja Lamia, Tanya Leise, Scott A. Lewis, Jiajia Li, Xiaodong Li, Andrew C. Liu, Jennifer J. Loros, Tami A. Martino, Jérôme S. Menet, Martha Merrow, Andrew J. Millar, Todd C. Mockler, Félix Naef, Emi Nagoshi, Michael N. Nitabach, María Olmedo, Dmitri A. Nusinow, Louis J. Ptáček, D.A.J. Rand, Akhilesh B. Reddy, María S. Robles, Till Roenneberg, Michael Rosbash, Marc D. Ruben, Samuel S. C. Rund, Aziz Sancar, Paolo Sassone‐Corsi, Amita Sehgal, Scott Sherrill-Mix, Debra J. Skene, Kai Florian Storch, Joseph S. Takahashi, Hiroki R. Ueda, Han Wang, Charles J. Weitz, Pål O. Westermark, Herman Wijnen, Ying Xu, Gang Wu, Seung Hee Yoo, Michael W. Young, Eric Erquan Zhang, Tomasz Zieliński, John B. Hogenesch
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms18071499

Entrainment of Breast Cell Lines Results in Rhythmic Fluctuations of MicroRNAs
Cited by: 13
Author(s): Rafael Chacolla-Huaringa, Jorge E. Moreno-Cuevas, Víctor Treviño, Sean-Patrick Scott
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-69294-3

Circadian clock-controlled gene expression in co-cultured, mat-forming cyanobacteria
Cited by: 7
Author(s): Christine Hörnlein, Veronique Confurius-Guns, Michele Grego, Lucas J. Stal, Henk Bolhuis
Software Mentions: 1
Published: about 4 years ago

10.3389/fncel.2019.00487

Processing Bodies Oscillate in Neuro 2A Cells
Cited by: 4
Author(s): Melisa Malcolm, Lucía Saad, Laura Gabriela Penazzi, Eduardo Garbarino-Pico
Software Mentions: 1
Published: about 5 years ago

10.1186/s13073-020-00768-9

A population-based gene expression signature of molecular clock phase from a single epidermal sample
Cited by: 25
Author(s): Gang Wu, Marc D. Ruben, Lauren J. Francey, Smith Dl, Joseph D. Sherrill, John E. Oblong, Kevin J. Mills, John B. Hogenesch
Software Mentions: 1
Published: over 4 years ago

10.3390/diagnostics11061082

Circadian Biology in Obstructive Sleep Apnea
Cited by: 13
Author(s): Bala S. C. Koritala, Zachary Conroy, Smith Dl
Software Mentions: 1
Published: over 3 years ago

Projects: cran: MetaCycle

Papers Mentioning MetaCycle 47