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Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators.

Levati E, Sartini S, Ottonello S, Montanini B.

Comput Struct Biotechnol J. 2016 Jun 29;14:262-70. doi: 10.1016/j.csbj.2016.06.004. eCollection 2016. Review.


YCRD: Yeast Combinatorial Regulation Database.

Wu WS, Hsieh YC, Lai FJ.

PLoS One. 2016 Jul 8;11(7):e0159213. doi: 10.1371/journal.pone.0159213. eCollection 2016.


The CDK-APC/C Oscillator Predominantly Entrains Periodic Cell-Cycle Transcription.

Rahi SJ, Pecani K, Ondracka A, Oikonomou C, Cross FR.

Cell. 2016 Apr 7;165(2):475-87. doi: 10.1016/j.cell.2016.02.060.


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.


Regulation of Ace2-dependent genes requires components of the PBF complex in Schizosaccharomyces pombe.

Suárez MB, Alonso-Nuñez ML, del Rey F, McInerny CJ, Vázquez de Aldana CR.

Cell Cycle. 2015;14(19):3124-37. doi: 10.1080/15384101.2015.1078035. Epub 2015 Aug 3.


Semiparametric Bayes local additive models for longitudinal data.

Hua Z, Zhu H, Dunson DB.

Stat Biosci. 2015 May 1;7(1):90-107.


A new transcription factor for mitosis: in Schizosaccharomyces pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression.

Garg A, Futcher B, Leatherwood J.

Nucleic Acids Res. 2015 Aug 18;43(14):6874-88. doi: 10.1093/nar/gkv274. Epub 2015 Apr 23.


A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae.

Wu WS, Wei ML, Yeh CM, Chang DT.

BMC Syst Biol. 2014;8 Suppl 5:S9. doi: 10.1186/1752-0509-8-S5-S9. Epub 2014 Dec 12.


A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms.

Lai FJ, Chang HT, Huang YM, Wu WS.

BMC Syst Biol. 2014;8 Suppl 4:S9. doi: 10.1186/1752-0509-8-S4-S9. Epub 2014 Dec 8.


Highly sensitive inference of time-delayed gene regulation by network deconvolution.

Chen H, Mundra PA, Zhao LN, Lin F, Zheng J.

BMC Syst Biol. 2014;8 Suppl 4:S6. doi: 10.1186/1752-0509-8-S4-S6. Epub 2014 Dec 8.


A novel role for lncRNAs in cell cycle control during stress adaptation.

Solé C, Nadal-Ribelles M, de Nadal E, Posas F.

Curr Genet. 2015 Aug;61(3):299-308. doi: 10.1007/s00294-014-0453-y. Epub 2014 Sep 28. Review.


Checkpoints couple transcription network oscillator dynamics to cell-cycle progression.

Bristow SL, Leman AR, Simmons Kovacs LA, Deckard A, Harer J, Haase SB.

Genome Biol. 2014 Sep 5;15(9):446. doi: 10.1186/s13059-014-0446-7.


TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information.

Kim Y, Jang JH, Choi S, Hwang D.

Bioinformatics. 2014 Sep 1;30(17):i453-60. doi: 10.1093/bioinformatics/btu454.


Identifying transcription factor complexes and their roles.

Will T, Helms V.

Bioinformatics. 2014 Sep 1;30(17):i415-21. doi: 10.1093/bioinformatics/btu448.


Phenotypic robustness and the assortativity signature of human transcription factor networks.

Pechenick DA, Payne JL, Moore JH.

PLoS Comput Biol. 2014 Aug 14;10(8):e1003780. doi: 10.1371/journal.pcbi.1003780. eCollection 2014 Aug.


Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics.

Ostrow AZ, Nellimoottil T, Knott SR, Fox CA, Tavaré S, Aparicio OM.

PLoS One. 2014 Feb 4;9(2):e87647. doi: 10.1371/journal.pone.0087647. eCollection 2014.


Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression.

Eser P, Demel C, Maier KC, Schwalb B, Pirkl N, Martin DE, Cramer P, Tresch A.

Mol Syst Biol. 2014 Jan 30;10:717. doi: 10.1002/msb.134886. Print 2014. Erratum in: Mol Syst Biol. 2014;10:726.


Topology and control of the cell-cycle-regulated transcriptional circuitry.

Haase SB, Wittenberg C.

Genetics. 2014 Jan;196(1):65-90. doi: 10.1534/genetics.113.152595. Review.

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