CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics

By Diego Darriba, Guillermo L. Taboada, Ramón Doallo, David Posada. Nature Methods, 2012

11,475 citations recorded by the source corpus.

Subfields: Endocrine and Autonomic Systems, Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/65deebcc4e04585c08c2c349eb28091a5da4b573

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In Endocrine and Autonomic Systems

In Genetics

In Plant Science

Citations in the corpus

The effects of light pollution on biological rhythms of birds: an integrated, mechanistic perspective (2015, neutral): “Such effects are mirrored by the circadian nature of many biochemical, physiological and behavioral processes, demonstrated in humans and model rodent species (Panda et al. 2002; Dallmann et al. 2012; Patel et al. 2012; Azzi et al. 2014).”
Systematics of the Gracilariales (Rhodophyta) including new subfamilies, tribes, subgenera, and two new genera, Agarophyton gen. nov. and Crassa gen. nov. (2018, background): “, Gracilaria sensu Gargiulo et al. (1992) or sensu Abbott (1995), while others recognize only Gracilariopsis as a distinct taxon from a Gracilaria-Hydropuntia complex.”
Reprogramming of the Circadian Clock by Nutritional Challenge (2013, positive): “Each metabolite and transcript identified in the livers of animals fed NC or HFD were integrated within the computational resource, CircadiOmics (Eckel-Mahan et al., 2012; Patel et al., 2012).”
Resurrection and emendation of the Hypoxylaceae, recognised from a multigene phylogeny of the Xylariales (2017, methodology): “The best fitting substitution model for each single gene alignment and the MGAwas determined using jModeltest 2.1.7 (Darriba et al. 2012; Guindon and Gascuel 2003).”
Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence (2016, neutral): “1.7 (Darriba et al. 2012; Guindon and Gascuel 2003) (Table 3).”
The 2019‐new coronavirus epidemic: Evidence for virus evolution (2020, methodology): “The best‐fitting nucleotide substitution model was chosen by jModeltest software.(11) ML tree was reconstructed using generalized time‐reversible plus gamma distribution and invariant sites (+G+I) as an evolutionary model using MEGA‐X.”
Polypores and genus concepts in Phanerochaetaceae (Polyporales, Basidiomycota) (2016, methodology): “Models were chosen based on AIC scoring produced in jmodeltest (Darriba et al. 2012).”
Transmission dynamics and evolutionary history of 2019‐nCoV (2020, methodology): “10.(24) To evaluate the phylogenetic signals of the datasets, we performed likelihood‐mapping analysis(25) using TREE‐ PUZZLE v5.”
Unravelling the global invasion routes of a worldwide invader, the red swamp crayfish (Procambarus clarkii) (2019, methodology): “A 185 hierarchical series of tests based on the Bayesian Information Criterion (BIC) was applied to 186 identify the most appropriate nucleotide substitution model among 88 models tested, as 187 implemented in jModelTest 2 (Darriba et al., 2012).”
The polyphasic analysis of two native Raphidiopsis isolates supports the unification of the genera Raphidiopsis and Cylindrospermopsis (Nostocales, Cyanobacteria) (2018, methodology): “The ML tree was conducted by applying an evolutionary model chosen by jModelTest v2 software (Darriba et al. 2012) using the Akaike information criterion: general time reversible þ invariant þ gamma (GTR þ I þ G).”
Roholtiella , gen. nov. (Nostocales, Cyanobacteria)—a tapering and branching cyanobacteria of the family Nostocaceae (2015, methodology): “The ML tree was constructed applying the GTR+I+Γ model chosen according to akaike Information Criterion provided by jModeltest 2 software (darriba et al. 2012).”
Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, methodology): “This model of sequence evolution was the best fit for the concatenated ddRADseq data (using matrix s50), determined using jModelTest (Darriba et al. 2012).”
The floating Sargassum (Phaeophyceae) of the South Atlantic Ocean – likely scenarios (2017, neutral): “Model evolution for the alignment was performed in jModelTest v2 (Darriba et al. 2012), and the selected model was GTRþG, G ¼ 0.5809 [nucleotide frequency (0.1614 0.2455 0.3538 0.2394), rate matrix (3.3349 5.9266 1.7475 0.6499 5.9118 1.0000)].”
Out‐of‐Tibet: the spatio‐temporal evolution of Gentiana (Gentianaceae) (2016, methodology): “Based upon the AIC and BIC criterion in jModeltest 2.1.3 (Darriba et al., 2012), the best-fitting models of sequence evolution were GTR+G+I (ITS) and GTR+G (cpDNA, combined dataset).”