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Items: 1 to 20 of 83

1.

A primer on thermodynamic-based models for deciphering transcriptional regulatory logic.

Dresch JM, Richards M, Ay A.

Biochim Biophys Acta. 2013 Sep;1829(9):946-53. doi: 10.1016/j.bbagrm.2013.04.011. Epub 2013 May 1. Review.

PMID:
23643643
2.

Global parameter estimation for thermodynamic models of transcriptional regulation.

Suleimenov Y, Ay A, Samee MA, Dresch JM, Sinha S, Arnosti DN.

Methods. 2013 Jul 15;62(1):99-108. doi: 10.1016/j.ymeth.2013.05.012. Epub 2013 May 30.

PMID:
23726942
3.

Thermodynamic state ensemble models of cis-regulation.

Sherman MS, Cohen BA.

PLoS Comput Biol. 2012;8(3):e1002407. doi: 10.1371/journal.pcbi.1002407. Epub 2012 Mar 29.

4.

Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects.

Dresch JM, Liu X, Arnosti DN, Ay A.

BMC Syst Biol. 2010 Oct 24;4:142. doi: 10.1186/1752-0509-4-142.

5.

Inferring gene regulatory networks by thermodynamic modeling.

Chen CC, Zhong S.

BMC Genomics. 2008 Sep 16;9 Suppl 2:S19. doi: 10.1186/1471-2164-9-S2-S19.

6.

Optimizing static thermodynamic models of transcriptional regulation.

Bauer DC, Bailey TL.

Bioinformatics. 2009 Jul 1;25(13):1640-6. doi: 10.1093/bioinformatics/btp283. Epub 2009 Apr 27.

7.

Thermodynamics-based models of transcriptional regulation with gene sequence.

Wang S, Shen Y, Hu J.

Bioprocess Biosyst Eng. 2015 Dec;38(12):2469-76. doi: 10.1007/s00449-015-1484-6. Epub 2015 Oct 12.

PMID:
26458822
8.

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression.

He X, Samee MA, Blatti C, Sinha S.

PLoS Comput Biol. 2010 Sep 16;6(9). pii: e1000935. doi: 10.1371/journal.pcbi.1000935.

9.

STREAM: Static Thermodynamic REgulAtory Model of transcription.

Bauer DC, Bailey TL.

Bioinformatics. 2008 Nov 1;24(21):2544-5. doi: 10.1093/bioinformatics/btn467. Epub 2008 Sep 6.

10.

Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data.

Samee AH, Sinha S.

Methods. 2013 Jul 15;62(1):79-90. doi: 10.1016/j.ymeth.2013.03.005. Epub 2013 Apr 26.

PMID:
23624421
11.

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo.

Fakhouri WD, Ay A, Sayal R, Dresch J, Dayringer E, Arnosti DN.

Mol Syst Biol. 2010;6:341. doi: 10.1038/msb.2009.97. Epub 2010 Jan 19.

12.

Foundations for modeling the dynamics of gene regulatory networks: a multilevel-perspective review.

Sanchez-Osorio I, Ramos F, Mayorga P, Dantan E.

J Bioinform Comput Biol. 2014 Feb;12(1):1330003. doi: 10.1142/S0219720013300037. Epub 2013 Dec 20. Review.

PMID:
24467752
13.

Energetic methods to study bifunctional biotin operon repressor.

Beckett D.

Methods Enzymol. 1998;295:424-50.

PMID:
9750231
14.

Thermodynamic models of combinatorial gene regulation by distant enhancers.

Narula J, Igoshin OA.

IET Syst Biol. 2010 Nov;4(6):393-408. doi: 10.1049/iet-syb.2010.0010.

PMID:
21073238
15.

Modeling regulatory networks with weight matrices.

Weaver DC, Workman CT, Stormo GD.

Pac Symp Biocomput. 1999:112-23.

16.

A mathematical model for synergistic eukaryotic gene activation.

Wang J, Ellwood K, Lehman A, Carey MF, She ZS.

J Mol Biol. 1999 Feb 19;286(2):315-25.

PMID:
9973553
17.

tCal: transcriptional probability calculator using thermodynamic model.

Zhou X, Su Z.

Bioinformatics. 2008 Nov 15;24(22):2639-40. doi: 10.1093/bioinformatics/btn494. Epub 2008 Sep 16.

PMID:
18796477
18.

Ab initio thermodynamic modeling of distal multisite transcription regulation.

Saiz L, Vilar JM.

Nucleic Acids Res. 2008 Feb;36(3):726-31. Epub 2007 Dec 1.

19.

Transcriptional regulation by the numbers: models.

Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R.

Curr Opin Genet Dev. 2005 Apr;15(2):116-24. Review.

20.

An equilibrium partitioning model connecting gene expression and cis-motif content.

Mellor J, DeLisi C.

Bioinformatics. 2006 Jul 15;22(14):e368-74.

PMID:
16873495

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