Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: MetaCycle
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/MetaCycle
Evaluate Periodicity in Large Scale Data
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Latest release: over 5 years ago
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Papers Mentioning MetaCycle 47
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 DataCited 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 EmissionCited by: 9
Author(s): Marta I. Terry, Fernando Pérez-Sánz, Pedro J. Navarro, Julia Weiß, Marcos Egea‐Cortines
Software Mentions: 8
Published: about 5 years ago
10.1371/journal.pcbi.1007666
Methods detecting rhythmic gene expression are biologically relevant only for strong signalCited 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 periodCited 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 brainCited 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 miceCited 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 metabolismCited 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: about 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 lineCited 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 zebrafishCited 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 ProfilesCited 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 dataCited 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 DeprivationCited 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 ExpressionCited 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 outputCited 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 MetabolomeCited 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 TestisCited 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 ChemotherapyCited 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 MucosaCited 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 minutumCited 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 tissueCited 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 clockCited 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 DrosophilaCited by: 51
Author(s): Ane Martín Anduaga, Naveh Evantal, Inés Lucía Patop, Osnat Bartok, Ron Weiss, Sebastián Kadener
Software Mentions: 3
Published: almost 5 years ago
10.1534/g3.118.200559
Identification and Characterization of Transcripts Regulated by Circadian Alternative Polyadenylation in Mouse LiverCited 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 treatmentCited 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 NeuronsCited 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 OutputCited 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 femalesCited 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: over 6 years ago
10.1186/s12870-020-2238-4
Full moonlight-induced circadian clock entrainment in Coffea arabicaCited 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 physiologyCited 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 feedingCited 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 darknessCited 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-1Cited 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 ModellingCited 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 TaggingCited 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 ReviewCited 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 cellsCited 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 miceCited 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 rhythmsCited 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 RhythmsCited 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 MicroRNAsCited 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 cyanobacteriaCited 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 CellsCited 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 sampleCited 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: about 4 years ago
10.3390/diagnostics11061082
Circadian Biology in Obstructive Sleep ApneaCited by: 13
Author(s): Bala S. C. Koritala, Zachary Conroy, Smith Dl
Software Mentions: 1
Published: over 3 years ago