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Items: 1 to 20 of 103

1.

Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data.

Deckard A, Anafi RC, Hogenesch JB, Haase SB, Harer J.

Bioinformatics. 2013 Dec 15;29(24):3174-80. doi: 10.1093/bioinformatics/btt541. Epub 2013 Sep 20.

2.

SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data.

Perea JA, Deckard A, Haase SB, Harer J.

BMC Bioinformatics. 2015 Aug 16;16:257. doi: 10.1186/s12859-015-0645-6.

3.

Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation.

Yang R, Su Z.

Bioinformatics. 2010 Jun 15;26(12):i168-74. doi: 10.1093/bioinformatics/btq189.

4.

A maximum entropy algorithm for rhythmic analysis of genome-wide expression patterns.

Langmead CJ, McClung CR, Donald BR.

Proc IEEE Comput Soc Bioinform Conf. 2002;1:237-45.

PMID:
15838140
5.
6.

Evolution and regulation of cellular periodic processes: a role for paralogues.

Trachana K, Jensen LJ, Bork P.

EMBO Rep. 2010 Mar;11(3):233-8. doi: 10.1038/embor.2010.9. Epub 2010 Feb 19.

7.

Frequency-based time-series gene expression recomposition using PRIISM.

Rosa BA, Jiao Y, Oh S, Montgomery BL, Qin W, Chen J.

BMC Syst Biol. 2012 Jun 15;6:69. doi: 10.1186/1752-0509-6-69.

8.

The circadian clock and cell cycle: interconnected biological circuits.

Masri S, Cervantes M, Sassone-Corsi P.

Curr Opin Cell Biol. 2013 Dec;25(6):730-4. doi: 10.1016/j.ceb.2013.07.013. Epub 2013 Aug 19. Review.

9.

Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms.

Glynn EF, Chen J, Mushegian AR.

Bioinformatics. 2006 Feb 1;22(3):310-6. Epub 2005 Nov 22.

PMID:
16303799
10.

LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data.

Yang R, Zhang C, Su Z.

Bioinformatics. 2011 Apr 1;27(7):1023-5. doi: 10.1093/bioinformatics/btr041. Epub 2011 Feb 3.

PMID:
21296749
11.

Identifying periodically expressed transcripts in microarray time series data.

Wichert S, Fokianos K, Strimmer K.

Bioinformatics. 2004 Jan 1;20(1):5-20.

PMID:
14693803
12.

Merging microarray cell synchronization experiments through curve alignment.

Hermans F, Tsiporkova E.

Bioinformatics. 2007 Jan 15;23(2):e64-70.

PMID:
17237107
13.

RNA profiling in circadian biology.

Walker JR, Hogenesch JB.

Methods Enzymol. 2005;393:366-76.

PMID:
15817299
14.

Aberrant temporal growth pattern and morphology of root and shoot caused by a defective circadian clock in Arabidopsis thaliana.

Ruts T, Matsubara S, Wiese-Klinkenberg A, Walter A.

Plant J. 2012 Oct;72(1):154-61. doi: 10.1111/j.1365-313X.2012.05073.x. Epub 2012 Jul 24.

15.

Detecting biological associations between genes based on the theory of phase synchronization.

Kim CS, Riikonen P, Salakoski T.

Biosystems. 2008 May;92(2):99-113. doi: 10.1016/j.biosystems.2007.12.006. Epub 2008 Jan 11.

PMID:
18289772
16.

Permutation test for periodicity in short time series data.

Ptitsyn AA, Zvonic S, Gimble JM.

BMC Bioinformatics. 2006 Sep 6;7 Suppl 2:S10.

17.

A methyl transferase links the circadian clock to the regulation of alternative splicing.

Sanchez SE, Petrillo E, Beckwith EJ, Zhang X, Rugnone ML, Hernando CE, Cuevas JC, Godoy Herz MA, Depetris-Chauvin A, Simpson CG, Brown JW, Cerdán PD, Borevitz JO, Mas P, Ceriani MF, Kornblihtt AR, Yanovsky MJ.

Nature. 2010 Nov 4;468(7320):112-6. doi: 10.1038/nature09470. Epub 2010 Oct 20.

PMID:
20962777
18.

Quantitative inference of dynamic regulatory pathways via microarray data.

Chang WC, Li CW, Chen BS.

BMC Bioinformatics. 2005 Mar 7;6:44.

19.

Transcriptome network component analysis with limited microarray data.

Galbraith SJ, Tran LM, Liao JC.

Bioinformatics. 2006 Aug 1;22(15):1886-94. Epub 2006 Jun 9.

PMID:
16766556
20.

Comprehensive analysis of circadian periodic pattern in plant transcriptome.

Ptitsyn A.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S18. doi: 10.1186/1471-2105-9-S9-S18.

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