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Items: 1 to 20 of 71

1.

Stochastic modeling of the relationship between copy number and gene expression based on transcriptional logic.

Hsu FH, Serpedin E, Chen Y, Dougherty ER.

IEEE Trans Biomed Eng. 2012 Jan;59(1):272-80. doi: 10.1109/TBME.2011.2173341. Epub 2011 Oct 24.

PMID:
22042124
2.

Evaluating dynamic effects of copy number alterations on gene expression using a single transcription model.

Hsu FH, Serpedin E, Chen Y, Dougherty ER.

IEEE Trans Biomed Eng. 2012 Oct;59(10):2726-36.

PMID:
22996722
3.

Stochastic model of transcription factor-regulated gene expression.

Karmakar R, Bose I.

Phys Biol. 2006 Sep 28;3(3):200-8.

PMID:
17021384
4.

Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.

Yuan Y, Rueda OM, Curtis C, Markowetz F.

Bioinformatics. 2011 Oct 1;27(19):2679-85. doi: 10.1093/bioinformatics/btr450. Epub 2011 Jul 30.

PMID:
21804112
5.

Transcriptional stochasticity in gene expression.

Lipniacki T, Paszek P, Marciniak-Czochra A, Brasier AR, Kimmel M.

J Theor Biol. 2006 Jan 21;238(2):348-67. Epub 2005 Jul 21.

PMID:
16039671
6.

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Bioinformatics. 2008 Apr 21;9:203. doi: 10.1186/1471-2105-9-203.

7.

Catching transcriptional regulation by thermostatistical modeling.

Frank TD, Cheong A, Okada-Hatakeyama M, Kholodenko BN.

Phys Biol. 2012 Aug;9(4):045007. doi: 10.1088/1478-3975/9/4/045007. Epub 2012 Aug 7.

PMID:
22871947
8.

Signal propagation in nonlinear stochastic gene regulatory networks.

Achimescu S, Lipan O.

Syst Biol (Stevenage). 2006 May;153(3):120-34.

PMID:
16984086
9.

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
10.

Identification of transcription factor cooperativity via stochastic system model.

Chang YH, Wang YC, Chen BS.

Bioinformatics. 2006 Sep 15;22(18):2276-82. Epub 2006 Jul 14.

PMID:
16844711
11.

MicroRNAs preferentially target the genes with high transcriptional regulation complexity.

Cui Q, Yu Z, Pan Y, Purisima EO, Wang E.

Biochem Biophys Res Commun. 2007 Jan 19;352(3):733-8. Epub 2006 Nov 27.

PMID:
17141185
12.

Inter- and intra-combinatorial regulation by transcription factors and microRNAs.

Zhou Y, Ferguson J, Chang JT, Kluger Y.

BMC Genomics. 2007 Oct 30;8:396.

13.

Estimating conditional probabilities for the detection of unfavorable copy number alterations in a targeted therapy.

Hsu FH, Dougherty ER, Chen Y, Serpedin E.

IEEE Trans Biomed Eng. 2013 Oct;60(10):2933-42. doi: 10.1109/TBME.2013.2266356. Epub 2013 Jun 5.

PMID:
23744663
14.

Nonspecific transcription factor binding can reduce noise in the expression of downstream proteins.

Soltani M, Bokes P, Fox Z, Singh A.

Phys Biol. 2015 Aug 12;12(5):055002. doi: 10.1088/1478-3975/12/5/055002.

PMID:
26267711
15.

Stochastic dynamic modeling of short gene expression time-series data.

Wang Z, Yang F, Ho DW, Swift S, Tucker A, Liu X.

IEEE Trans Nanobioscience. 2008 Mar;7(1):44-55. doi: 10.1109/TNB.2008.2000149.

PMID:
18334455
16.

Stochastically driven genetic circuits.

Tsimring LS, Volfson D, Hasty J.

Chaos. 2006 Jun;16(2):026103.

PMID:
16822035
17.

Detection of eQTL modules mediated by activity levels of transcription factors.

Sun W, Yu T, Li KC.

Bioinformatics. 2007 Sep 1;23(17):2290-7. Epub 2007 Jun 28.

PMID:
17599927
18.

Model-based analysis of matrix metalloproteinase expression under mechanical shear.

Sun HB, Liu Y, Qian L, Yokota H.

Ann Biomed Eng. 2003 Feb;31(2):171-80.

PMID:
12627825
19.

Predicting genetic regulatory response using classification.

Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i232-40.

PMID:
15262804
20.

Effect of feedback regulation on stochastic gene expression.

Tao Y, Zheng X, Sun Y.

J Theor Biol. 2007 Aug 21;247(4):827-36. Epub 2007 Mar 24.

PMID:
17507034

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