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Citations per year

Number of citations per year for the bioinformatics software tool GeneCycle

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This map represents all the scientific publications referring to GeneCycle per scientific context
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GeneCycle specifications


Unique identifier OMICS_13332
Name GeneCycle
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.2
Stability Stable
MASS, R(≥2.7.0), longitudinal(≥1.1.3), fdrtool(≥ 1.2.5)
Maintained Yes




No version available



  • person_outline Miika Ahdesmaki

Publications for GeneCycle

GeneCycle citations


High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci

Sci Rep
PMCID: 5532269
PMID: 28751729
DOI: 10.1038/s41598-017-06110-5

[…] plot and Cytoscape (v3.1.0), location of related clusters was visualized by Circos. Gene expression periodicity was measured on 120 interpolated expression values for each replicate time series using GeneCycle, candidate periodically expressed genes were identified as having the same calculated dominant cycling frequency between biological replicates. Time-dependent expression signatures were esta […]


Domestic chickens activate a piRNA defense against avian leukosis virus

PMCID: 5383398
PMID: 28384097
DOI: 10.7554/eLife.24695.029

[…] a prerequisite for this analysis. The distance spectrum of RPFs from mRNAs already showed a 3-nt periodicity pattern. We then transformed the distance spectrum using the ‘periodogram’ function of the GeneCycle package () with the ‘clone’ method. The relative spectral density was calculated by normalizing to the value at the third position. […]


Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity

PLoS One
PMCID: 4709092
PMID: 26751389
DOI: 10.1371/journal.pone.0146643

[…] rding was separated and analyzed for periods of 24 hours (Circwave and periods between 19 and 28 hours (Circwave Batch, p<0.02). Periodogram analysis was performed using R statistical program and the GeneCycle package [] followed by Fisher's exact g Test to obtain p-values of each culture. Spread/motility measures, periods, amplitudes, and damping coefficients were compared by 1- or 2-way ANOVA, w […]


Transcriptome Analysis of Plant Hormone Related Tomato (Solanum lycopersicum) Genes in a Sunlight Type Plant Factory

PLoS One
PMCID: 4666670
PMID: 26624004
DOI: 10.1371/journal.pone.0143412
call_split See protocol

[…] sion numbers; DRA003530, DRA003529 and DRA003528). Histogram analyses with RPKM values of <0.1 were set to 0.1, and RPKM values were log (2) transformed. Statistical analyses were performed using the GeneCycle and samr packages of R software. p-values were calculated using Fisher’s exact g test, and sorting data for heatmaps were as follows: 24-h cycle; maximum value, 7 (time, 6:00); minimum value […]


Ability to Generate Patient Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes

PLoS One
PMCID: 4556673
PMID: 26325287
DOI: 10.1371/journal.pone.0136851

[…] corresponding false discovery rate (FDR) [–]. FDR <0.2 was considered significant []. To compare protein expression levels across multiple generations, a g-statistic was used []. R packages including GeneCycle, q value and ClassComparison were employed []. […]


New approaches for the standardization and validation of a real time qPCR assay using TaqMan probes for quantification of yellow fever virus on clinical samples with high quality parameters

PMCID: 4514303
PMID: 26011746
DOI: 10.4161/21645515.2014.990854

[…] ope proteinnonstructural proteinenzyme-linked immunosorbent assaydeoxyribonucleic aciddetection limitquantification limitBrazilian Health Surveillance Agencycoefficient of variationhuman constitutive genecycle thresholdexogenous internal positive controlplaque former unitfood and drug administration agencyjapanese encephalitis virusdengue virusmumps virusmeasles virusmultiplicity of infectionWest […]

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GeneCycle institution(s)
Institute of Signal Processing, Tampere University of Technology, Tampere, Finland; Institute for Systems Biology, WA, USA; Marine Environmental Biology, University of Southern California, CA, USA; ProSanos Corporation, Harrisburg, PA, USA; Department of Statistics, University of Munich, Munich, Germany; Department of Mathematics and Statistics, University of Cyprus, Nicosia, Cyprus
GeneCycle funding source(s)
This work was supported by an Emmy Noether research grant (STR 624/1-2) from the Deutsche Forschungsgemeinschaft, Tampere Graduate School in Information Science and Engineering and the Academy of Finland, project No. 213462 (Finnish Centre of Excellence program (2006 – 2011)), and R01 GM072855 grant from NIH.

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