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Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles.

Kim M, Zorraquino V, Tagkopoulos I.

PLoS Comput Biol. 2015 Mar 16;11(3):e1004127. doi: 10.1371/journal.pcbi.1004127. eCollection 2015 Mar.


From data to optimal decision making: a data-driven, probabilistic machine learning approach to decision support for patients with sepsis.

Tsoukalas A, Albertson T, Tagkopoulos I.

JMIR Med Inform. 2015 Feb 24;3(1):e11. doi: 10.2196/medinform.3445.


An Arabidopsis gene regulatory network for secondary cell wall synthesis.

Taylor-Teeples M, Lin L, de Lucas M, Turco G, Toal TW, Gaudinier A, Young NF, Trabucco GM, Veling MT, Lamothe R, Handakumbura PP, Xiong G, Wang C, Corwin J, Tsoukalas A, Zhang L, Ware D, Pauly M, Kliebenstein DJ, Dehesh K, Tagkopoulos I, Breton G, Pruneda-Paz JL, Ahnert SE, Kay SA, Hazen SP, Brady SM.

Nature. 2015 Jan 29;517(7536):571-5. doi: 10.1038/nature14099. Epub 2014 Dec 24.


A systems biology analysis of brain microvascular endothelial cell lipotoxicity.

Aung HH, Tsoukalas A, Rutledge JC, Tagkopoulos I.

BMC Syst Biol. 2014 Jul 4;8:80. doi: 10.1186/1752-0509-8-80.


An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli.

Carrera J, Estrela R, Luo J, Rai N, Tsoukalas A, Tagkopoulos I.

Mol Syst Biol. 2014 Jul 1;10:735. doi: 10.15252/msb.20145108.


Optimal part and module selection for synthetic gene circuit design automation.

Huynh L, Tagkopoulos I.

ACS Synth Biol. 2014 Aug 15;3(8):556-64. doi: 10.1021/sb400139h. Epub 2014 Feb 27.


From vital signs to clinical outcomes for patients with sepsis: a machine learning basis for a clinical decision support system.

Gultepe E, Green JP, Nguyen H, Adams J, Albertson T, Tagkopoulos I.

J Am Med Inform Assoc. 2014 Mar-Apr;21(2):315-25. doi: 10.1136/amiajnl-2013-001815. Epub 2013 Aug 19.


Promoter element arising from the fusion of standard BioBrick parts.

Yao AI, Fenton TA, Owsley K, Seitzer P, Larsen DJ, Sit H, Lau J, Nair A, Tantiongloc J, Tagkopoulos I, Facciotti MT.

ACS Synth Biol. 2013 Feb 15;2(2):111-20. doi: 10.1021/sb300114d. Epub 2013 Jan 11. Erratum in: ACS Synth Biol. 2013 Jun 21;2(6):351.


SBROME: a scalable optimization and module matching framework for automated biosystems design.

Huynh L, Tsoukalas A, Köppe M, Tagkopoulos I.

ACS Synth Biol. 2013 May 17;2(5):263-73. doi: 10.1021/sb300095m. Epub 2013 Mar 11.


A flood-based information flow analysis and network minimization method for gene regulatory networks.

Pavlogiannis A, Mozhayskiy V, Tagkopoulos I.

BMC Bioinformatics. 2013 Apr 24;14:137. doi: 10.1186/1471-2105-14-137.


Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli.

Dragosits M, Mozhayskiy V, Quinones-Soto S, Park J, Tagkopoulos I.

Mol Syst Biol. 2013;9:643. doi: 10.1038/msb.2012.76.


Microbial evolution in vivo and in silico: methods and applications.

Mozhayskiy V, Tagkopoulos I.

Integr Biol (Camb). 2013 Feb;5(2):262-77. doi: 10.1039/c2ib20095c. Review.


Microbial factories under control: auto-regulatory control through engineered stress-induced feedback.

Tagkopoulos I.

Bioengineered. 2013 Jan-Feb;4(1):5-8. doi: 10.4161/bioe.21935. Epub 2012 Aug 24.


Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis.

Liang Y, Wu H, Lei R, Chong RA, Wei Y, Lu X, Tagkopoulos I, Kung SY, Yang Q, Hu G, Kang Y.

J Biol Chem. 2012 Sep 28;287(40):33533-44. Epub 2012 Aug 8.


Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution.

Mozhayskiy V, Tagkopoulos I.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S13. doi: 10.1186/1471-2105-13-S10-S13.


Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation.

Mozhayskiy V, Tagkopoulos I.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S10. doi: 10.1186/1471-2105-13-S10-S10.


Automatic design of synthetic gene circuits through mixed integer non-linear programming.

Huynh L, Kececioglu J, Köppe M, Tagkopoulos I.

PLoS One. 2012;7(4):e35529. doi: 10.1371/journal.pone.0035529. Epub 2012 Apr 20.


A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli.

Dragosits M, Nicklas D, Tagkopoulos I.

J Biol Eng. 2012 Mar 30;6(1):2. doi: 10.1186/1754-1611-6-2.


Predictive behavior within microbial genetic networks.

Tagkopoulos I, Liu YC, Tavazoie S.

Science. 2008 Jun 6;320(5881):1313-7. doi: 10.1126/science.1154456. Epub 2008 May 8.


Symmetric and asymmetric multi-modality biclustering analysis for microarray data matrix.

Kung SY, Mak MW, Tagkopoulos I.

J Bioinform Comput Biol. 2006 Apr;4(2):275-98.

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