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Items: 15

1.

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist.

Drawert B, Hellander A, Bales B, Banerjee D, Bellesia G, Daigle BJ Jr, Douglas G, Gu M, Gupta A, Hellander S, Horuk C, Nath D, Takkar A, Wu S, Lötstedt P, Krintz C, Petzold LR.

PLoS Comput Biol. 2016 Dec 8;12(12):e1005220. doi: 10.1371/journal.pcbi.1005220. eCollection 2016 Dec.

2.

SParSE++: improved event-based stochastic parameter search.

Roh MK, Daigle BJ Jr.

BMC Syst Biol. 2016 Nov 25;10(1):109.

3.

Identification of disease states associated with coagulopathy in trauma.

Zhang Y, Wu TB, Daigle BJ Jr, Cohen M, Petzold L.

BMC Med Inform Decis Mak. 2016 Sep 22;16(1):124.

4.

Systems biology approach to understanding post-traumatic stress disorder.

Thakur GS, Daigle BJ Jr, Dean KR, Zhang Y, Rodriguez-Fernandez M, Hammamieh R, Yang R, Jett M, Palma J, Petzold LR, Doyle FJ 3rd.

Mol Biosyst. 2015 Apr;11(4):980-93. doi: 10.1039/c4mb00404c. Review.

PMID:
25627823
5.

Inferring single-cell gene expression mechanisms using stochastic simulation.

Daigle BJ Jr, Soltani M, Petzold LR, Singh A.

Bioinformatics. 2015 May 1;31(9):1428-35. doi: 10.1093/bioinformatics/btv007. Epub 2015 Jan 7.

6.

Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder.

Yang R, Daigle BJ Jr, Muhie SY, Hammamieh R, Jett M, Petzold L, Doyle FJ 3rd.

BMC Syst Biol. 2013 Aug 20;7:80. doi: 10.1186/1752-0509-7-80.

7.

Mice lacking the β2 adrenergic receptor have a unique genetic profile before and after focal brain ischaemia.

White RE, Palm C, Xu L, Ling E, Ginsburg M, Daigle BJ, Han R, Patterson A, Altman RB, Giffard RG.

ASN Neuro. 2012 Sep 7;4(5). pii: e00096. doi: 10.1042/AN20110020.

8.

Accelerated maximum likelihood parameter estimation for stochastic biochemical systems.

Daigle BJ Jr, Roh MK, Petzold LR, Niemi J.

BMC Bioinformatics. 2012 May 1;13:68. doi: 10.1186/1471-2105-13-68.

9.

Core module biomarker identification with network exploration for breast cancer metastasis.

Yang R, Daigle BJ Jr, Petzold LR, Doyle FJ 3rd.

BMC Bioinformatics. 2012 Jan 18;13:12. doi: 10.1186/1471-2105-13-12.

10.

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events.

Roh MK, Daigle BJ Jr, Gillespie DT, Petzold LR.

J Chem Phys. 2011 Dec 21;135(23):234108. doi: 10.1063/1.3668100.

11.

Automated estimation of rare event probabilities in biochemical systems.

Daigle BJ Jr, Roh MK, Gillespie DT, Petzold LR.

J Chem Phys. 2011 Jan 28;134(4):044110. doi: 10.1063/1.3522769.

12.

Independent component analysis: mining microarray data for fundamental human gene expression modules.

Engreitz JM, Daigle BJ Jr, Marshall JJ, Altman RB.

J Biomed Inform. 2010 Dec;43(6):932-44. doi: 10.1016/j.jbi.2010.07.001. Epub 2010 Jul 7.

13.

Using pre-existing microarray datasets to increase experimental power: application to insulin resistance.

Daigle BJ Jr, Deng A, McLaughlin T, Cushman SW, Cam MC, Reaven G, Tsao PS, Altman RB.

PLoS Comput Biol. 2010 Mar 26;6(3):e1000718. doi: 10.1371/journal.pcbi.1000718.

14.

M-BISON: microarray-based integration of data sources using networks.

Daigle BJ Jr, Altman RB.

BMC Bioinformatics. 2008 Apr 25;9:214. doi: 10.1186/1471-2105-9-214.

15.

Mucosal biofilm formation on middle-ear mucosa in the chinchilla model of otitis media.

Ehrlich GD, Veeh R, Wang X, Costerton JW, Hayes JD, Hu FZ, Daigle BJ, Ehrlich MD, Post JC.

JAMA. 2002 Apr 3;287(13):1710-5.

PMID:
11926896

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