{"id":17,"date":"2013-02-26T20:32:40","date_gmt":"2013-02-26T20:32:40","guid":{"rendered":"http:\/\/faculty.engineering.ucdavis.edu\/template\/?page_id=17"},"modified":"2020-12-07T23:49:06","modified_gmt":"2020-12-07T23:49:06","slug":"publications","status":"publish","type":"page","link":"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<div id=\"Journals\">\n<h4><strong>Warning: This page is outdated. Please check the laboratory website for more recent information!<\/strong><\/h4>\n<p><a href=\"http:\/\/tagkopouloslab.ucdavis.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Lab webpage: <\/a><a href=\"http:\/\/tagkopouloslab.ucdavis.edu\/\" target=\"_blank\" rel=\"noopener noreferrer\">Tagkopoulos&#8217; lab web page<\/a><\/p>\n<h4><strong><span style=\"text-decoration: underline\">Journals:<\/span><\/strong><\/h4>\n<p>[J24] M. Meisner, J.A. Rosenheim, I. Tagkopoulos, &#8220;A data-driven, machine learning framework for optimal pest management in cotton&#8221;, <em>Ecosphere<\/em>, 2015 (in press)<\/p>\n<p>[J23] N. Rai, A. Ferreiro, A. Neckelmann, A. Soon, A. Yao, J. Siegel, M. Facciotti, I. Tagkopoulos, &#8220;RiboTALE: A modular, inducible system for accurate gene expression control&#8221;, <abbr title=\"Digital Object Identifier\">doi<\/abbr>:10.1038\/srep10658, <b><i>Scientific Reports<\/i><\/b>, 5: 10658, 2015 <a href=\"http:\/\/www.nature.com\/articles\/srep10658\" target=\"_blank\" rel=\"noopener noreferrer\">(link)<\/a><\/p>\n<p>[J22] L. Huynh, I. Tagkopoulos, &#8220;Fast and Accurate Circuit Design Automation through Hierarchical Model Switching&#8221;, doi:10.1021\/sb400139h, <b><i>ACS Synthetic Biology<\/i><\/b>, <span class=\"citation_volume\">4<\/span> (8), pp 890\u2013897, 2015 <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb500339k\" target=\"_blank\" rel=\"noopener noreferrer\">(link)<\/a><\/p>\n<p>[J21] M. Kim, V. Zorraquino, I. Tagkopoulos, &#8220;Microbial Forensics: Predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles&#8221;, <b><i>PLoS Computational Biology<\/i><\/b>, 2015 Mar;11 (3):e1004127<\/p>\n<p>[J20] A. Tsoukalas, T. Albertson, I. Tagkopoulos, &#8220;From data to optimal decision making: A data-driven, probabilistic machine learning approach to decision support for patients with Sepsis&#8221;, <b><i>JMIR Medical Informatics<\/i><\/b>, 3(1), 2015 <a href=\"http:\/\/medinform.jmir.org\/2015\/1\/e11\/#Introduction\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2015_JMIR.pdf\">(pdf)<\/a><\/p>\n<p>[J19] TM. Taylor-Teeples, L. Lin, M. de Lucas, G. Turco, T. W. Toal, A. Gaudinier, N. F. Young, G. M. Trabucco, M. T. Veling, R. Lamothe, P. P. Handakumbura, G. Xiong, C. Wang, J. Corwin, A. Tsoukalas, L. Zhang, D. Ware, M. Pauly, D. J. Kliebenstein, K. Dehesh, I. Tagkopoulos, G. Breton, J. L. Pruneda-Paz, S. E. Ahnert, S. A. Kay, S. P. Hazen, S. M. Brady, &#8220;An <i>Arabidopsis<\/i> gene regulatory network for secondary cell wall biosynthesis&#8221;, doi:10.1038\/nature14099, 517, 571\u2013575, <b><b><i>Nature<\/i><\/b><\/b>, 2015 <a href=\"http:\/\/www.nature.com\/nature\/journal\/v517\/n7536\/full\/nature14099.html\">(link)<\/a><\/p>\n<p>[J18] V. Zorraquino, S. Quinones, M. Kim, N. Rai, I. Tagkopoulos, &#8220;Deciphering cross-stress responses in Escherichia coli under complex evolutionary scenarios&#8221;, <b><i>bioRxiv<\/i><\/b>, doi: http:\/\/dx.doi.org\/10.1101\/010595 <a href=\"http:\/\/biorxiv.org\/content\/early\/2014\/10\/22\/010595\">(link)<\/a><\/p>\n<p>[J17] J. Carrera, R. Estrela, J. Luo, N. Rai, A. Tsoukalas, I. Tagkopoulos, &#8220;An integrative, multi-layer, genome-scale model reveals the phenotypic landscape of Escherichia coli&#8221;, <b><i>Molecular Systems Biology<\/i><\/b>, 10(7):735, 2014 <a href=\"http:\/\/msb.embopress.org\/cgi\/pmidlookup?view=long&amp;pmid=24987114\">(link)<\/a><\/p>\n<p>[J16] H.H. Aung, A. Tsoukalas, J. Rutledge, I. Tagkopoulos, &#8220;A Systems Biology Analysis of Brain Microvascular Endothelial Cell Lipotoxicity&#8221;, <b><i>BMC Systems Biology<\/i><\/b>, 8:80, 2014 <a href=\"http:\/\/www.biomedcentral.com\/1752-0509\/8\/80\">(link)<\/a><\/p>\n<p>[J15] L. Huynh, I. Tagkopoulos, &#8220;Optimal part and module selection for synthetic gene circuit design automation&#8221;, doi:10.1021\/sb400139h, <b><i>ACS Synthetic Biology<\/i><\/b>, 2014 <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb400139h\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2014_ACS_sb400139h.pdf\">(pdf)<\/a><\/p>\n<p>[J14] E. Gultepe, J. Green, H. Nguyen, J. Adams, T. Albertson, I. Tagkopoulos, &#8220;From vital signs to clinical outcomes for sepsis patients: A clinical decision support system based on discriminative classification&#8221;, doi:10.1136\/amiajnl-2013-001815, <b><i>Journal of the American Medical Informatics Association (JAMIA)<\/i><\/b>, 21(2):315-25, 2014 <a href=\"http:\/\/jamia.bmj.com\/content\/21\/2\/315.long\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_JAMIA_amiajnl-2013-001815.pdf\">(pdf)<\/a><\/p>\n<p>[J13] M. Dragosits, V. Mozhayskiy, S. Quinones-Soto, J. Park, I.Tagkopoulos, &#8220;Evolutionary potential,cross-stress behavior, and the genetic basis of acquired stress resistance in <b><i>Escherichia coli<\/i><\/b>&#8220;, doi:10.1038\/msb.2012.76, 9:643, <b><i>Molecular Systems Biology<\/i><\/b>, 2013 <a href=\"http:\/\/www.nature.com\/msb\/journal\/v9\/n1\/full\/msb201276.html\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_MSB_CrossStress.pdf\">(pdf)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_MSB_CrossStress_SOM.pdf\">(Suppl. Mat. pdf)<\/a><\/p>\n<p>[J12] A. Yao, T. Fenton, K. Owsley, P. Seitzer, D. Larsen, H. Lam, J. Lau, A. Nair, J. Tantiongloc, I. Tagkopoulos, M. Facciotti, &#8220;Promoter activity arising from the fusion of standard BioBrick parts&#8221;, 2 (2), pp 111\u2013120, DOI: 10.1021\/sb300114d, <b><i>ACS Synthetic Biology<\/i><\/b>, 2013 <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb300114d\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_ACS_Parts.pdf\">(pdf)<\/a><\/p>\n<p>[J11] A. Pavlogiannis, V. Mozhayskiy, I. Tagkopoulos, &#8220;A flood-based information flow analysis and network minimization method for bacterial systems&#8221;, 14:137 DOI:10.1186\/1471-2105-14-137, <b><i>BMC Bioinformatics<\/i><\/b>, 2013 <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/14\/137\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_BMC_1471-2105-14-137.pdf\">(pdf)<\/a><\/p>\n<p>[J10] L. Huynh, A. Tsoukalas, M. K\u00f6ppe, I.Tagkopoulos, &#8220;SBROME: A scalable optimization and module matching framework for automated biosystem design&#8221;, DOI: 10.1021\/sb300095m, pp 263-273, <b><i>ACS Synthetic Biology<\/i><\/b>, 2013 <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb300095m\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_ACS_sb300095m.pdf\">(pdf)<\/a><\/p>\n<p>[J9] V. Mozhayskiy, I. Tagkopoulos, &#8220;Microbial evolution <b><i>in vivo<\/i><\/b> and <b><i>in silico<\/i><\/b>: methods and applications&#8221;, DOI:10.1039\/C2IB20095C, 5(2):262-77, <b><i>Integrative Biology<\/i><\/b>, 2012 <a href=\"http:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2013\/IB\/C2IB20095C\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2012_IB_MicroEvo.pdf\">(pdf)<\/a><\/p>\n<p>[J8] Y. Liang, H. Wu, R. Lei, RA. Chong, Y. Wei, X. Lu, I. Tagkopoulos, SY. Kung, Q. Yang, G. Hu, Y. Kang, &#8220;Transcriptional Network Analysis Identififies BACH1 as a Master Regulator of Breast Cancer Bone Metastasis&#8221;, 287(40):33533-44, <b><i>Journal of Biological Chemistry<\/i><\/b>, 2012 <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22875853\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_JBC_33533.full.pdf\">(pdf)<\/a><\/p>\n<p>[J7] I. Tagkopoulos, &#8220;Microbial factories under control: Auto-regulatory control through engineered stress-induced feedback&#8221;, 4:1, 1-4, <b><i>Bioengineered<\/i><\/b>, 2013 <a href=\"http:\/\/www.landesbioscience.com\/journals\/bioe\/article\/21935\/\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2012_BUGS_RPP.pdf\">(pdf)<\/a><\/p>\n<p>[J6] L. Huynh, J. Kececioglu, M. K\u00f6ppe, I.Tagkopoulos, &#8220;Automated Design of Synthetic Gene Circuits through Linear Approximation and Mixed Integer Optimization&#8221;, 7(4):e35529, <b><i>PLoS ONE<\/i><\/b>, 2012 <a href=\"http:\/\/www.plosone.org\/article\/info:doi\/10.1371\/journal.pone.0035529\">(link)<\/a><\/p>\n<p>[J5] M. Dragosits, D. Nicklas, I.Tagkopoulos, &#8220;A synthetic biology approach to self-regulatory recombinant protein production in <b><i>Escherichia coli<\/i><\/b>&#8220;, 6:2, <b><i>Journal of Biological Engineering<\/i><\/b>, 2012 <a href=\"http:\/\/www.jbioleng.org\/content\/6\/1\/2\">(link)<\/a><\/p>\n<p>[J4] V.Mozhayskiy, I.Tagkopoulos, &#8220;Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation&#8221;, doi: 10.1186\/1471-2105-13-S10-S10, 13:S10, <b><i>BMC Bioinformatics<\/i><\/b>, 2012 <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/13\/S10\/S10\">(link)<\/a><\/p>\n<p>[J3] V.Mozhayskiy, I.Tagkopoulos, &#8220;Horizontal gene transfer dynamics and distribution of fitness effects during microbial In silico Evolution&#8221;, doi: 10.1186\/1471-2105-13-S10-S13, 13:S13, <b><i>BMC Bioinformatics<\/i><\/b>, 2012 <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/13\/S10\/S13\">(link)<\/a><\/p>\n<p>[J2] I.Tagkopoulos, Y.Liu, S. Tavazoie, &#8220;Predictive Behavior Within Microbial Genetic Networks&#8221;, <b><i>Science<\/i><\/b>, 320:1313-7, 2008 <a href=\"http:\/\/www.sciencemag.org\/content\/320\/5881\/1313.long\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2008_Science_1313.full.pdf\">(pdf)<\/a><\/p>\n<p>[J1] S.Y.Kung, M.W. Mak, and I.Tagkopoulos, &#8220;Symmetric and Asymmetric Multi-modality Biclustering Analysis for Microarray Data Matrix&#8221;, <b><i>Journal of Bioinformatics and Computational Biology<\/i><\/b>, vol 4(2), pp. 275-298, 2006 <a href=\"http:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720006002065\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2006_JBCB_jbcb06.pdf\">(pdf)<\/a><br \/>\n[J23] N. Rai, A. Ferreiro, A. Neckelmann, A. Soon, A. Yao, J. Siegel, M. Facciotti, I. Tagkopoulos, &#8220;RiboTALE: A modular, inducible system for accurate gene expression control&#8221;, <b><i>Scientific Reports<\/i><\/b>, 2015 (in press)<\/p>\n<p>[J22] L. Huynh, I. Tagkopoulos, &#8220;Fast and Accurate Circuit Design Automation through Hierarchical Model Switching&#8221;, doi:10.1021\/sb400139h, <b><i>ACS Synthetic Biology<\/i><\/b>, 2015 (in press)<a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb500339k\">(link)<\/a>, <a href=\"http:\/\/web.cs.ucdavis.edu\/%7Eiliast\/papers\/2015_ACS_sb500339k.pdf\">(pdf)<\/a><\/p>\n<p>[J21] M. Kim, V. Zorraquino, I. Tagkopoulos, &#8220;Microbial Forensics: Predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles&#8221;, <b><i>PLoS Computational Biology<\/i><\/b>, 2015 Mar;11 (3):e1004127<\/p>\n<p>[J20] A. Tsoukalas, T. Albertson, I. Tagkopoulos, &#8220;From data to optimal decision making: A data-driven, probabilistic machine learning approach to decision support for patients with Sepsis&#8221;, <b><i>JMIR Medical Informatics<\/i><\/b>, 3(1), 2015<\/p>\n<p>[J20] V. Zorraquino, S. Quinones, M. Kim, N. Rai, I. Tagkopoulos, &#8220;Deciphering cross-stress responses in Escherichia coli under complex evolutionary scenarios&#8221;, under review, ISME Journal, 2014<\/p>\n<p>[J19] M. Kim, V. Zorraquino, I. Tagkopoulos, &#8220;Microbial Forensics: Predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles&#8221;, under revision, PLoS Computational Biology, 2014<\/p>\n<p>[J18] A. Tsoukalas, T. Albertson, I. Tagkopoulos, &#8220;From data to optimal decision making: A data-driven, probabilistic machine learning approach to decision support for patients with Sepsis&#8221;, under revision, JMIR, 2014<\/p>\n<p>[J17] J. Carrera, R. Estrela, J. Luo, N. Rai, A. Tsoukalas, I. Tagkopoulos, &#8220;An integrative, multi-layer, genome-scale model reveals the phenotypic landscape of Escherichia coli&#8221;, <i>Molecular Systems Biology<\/i>, 10(7):735, 2014 <a href=\"http:\/\/msb.embopress.org\/cgi\/pmidlookup?view=long&amp;pmid=24987114\">(link)<\/a><\/p>\n<p>[J16] H.H. Aung, A. Tsoukalas, J. Rutledge, I. Tagkopoulos, &#8220;A Systems Biology Analysis of Brain Microvascular Endothelial Cell Lipotoxicity&#8221;, <i>BMC Systems Biology<\/i>, 8:80, 2014 <a href=\"http:\/\/www.biomedcentral.com\/1752-0509\/8\/80\">(link)<\/a><\/p>\n<p>[J15] L. Huynh, I. Tagkopoulos, &#8220;Optimal part and module selection for synthetic gene circuit design automation&#8221;, doi:10.1021\/sb400139h, ACS Synthetic Biology, 2014 <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb400139h\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2014_ACS_sb400139h.pdf\">(pdf)<\/a><\/p>\n<p>[J14] E. Gultepe, J. Green, H. Nguyen, J. Adams, T. Albertson, I. Tagkopoulos, &#8220;From vital signs to clinical outcomes for sepsis patients: A clinical decision support system based on discriminative classification&#8221;, doi:10.1136\/amiajnl-2013-001815, <i>Journal of the American Medical Informatics Association (JAMIA)<\/i>, 21(2):315-25, 2014 <a href=\"http:\/\/jamia.bmj.com\/content\/21\/2\/315.long\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_JAMIA_amiajnl-2013-001815.pdf\">(pdf)<\/a><\/p>\n<p>[J13] M. Dragosits, V. Mozhayskiy, S. Quinones-Soto, J. Park, I.Tagkopoulos, &#8220;Evolutionary potential,cross-stress behavior, and the genetic basis of acquired stress resistance in <i>Escherichia coli<\/i>&#8220;, doi:10.1038\/msb.2012.76, 9:643, <i>Nature\/EMBO Molecular Systems Biology<\/i>, 2013 <a href=\"http:\/\/www.nature.com\/msb\/journal\/v9\/n1\/full\/msb201276.html\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_MSB_CrossStress.pdf\">(pdf)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_MSB_CrossStress_SOM.pdf\">(Suppl. Mat. pdf)<\/a><\/p>\n<p>[J12] A. Yao, T. Fenton, K. Owsley, P. Seitzer, D. Larsen, H. Lam, J. Lau, A. Nair, J. Tantiongloc, I. Tagkopoulos, M. Facciotti, &#8220;Promoter activity arising from the fusion of standard BioBrick parts&#8221;, 2 (2), pp 111\u2013120, DOI: 10.1021\/sb300114d, ACS Synthetic Biology, 2013 <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb300114d\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_ACS_Parts.pdf\">(pdf)<\/a><\/p>\n<p>[J11] A. Pavlogiannis, V. Mozhayskiy, I. Tagkopoulos, &#8220;A flood-based information flow analysis and network minimization method for bacterial systems&#8221;, 14:137 DOI:10.1186\/1471-2105-14-137, BMC Bioinformatics, 2013 <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/14\/137\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_BMC_1471-2105-14-137.pdf\">(pdf)<\/a><\/p>\n<p>[J10] L. Huynh, A. Tsoukalas, M. K\u00f6ppe, I.Tagkopoulos, &#8220;SBROME: A scalable optimization and module matching framework for automated biosystem design&#8221;, DOI: 10.1021\/sb300095m, pp 263-273, ACS Synthetic Biology, 2013 <a href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb300095m\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_ACS_sb300095m.pdf\">(pdf)<\/a><\/p>\n<p>[J9] V. Mozhayskiy, I. Tagkopoulos, &#8220;Microbial evolution <i>in vivo<\/i> and <i>in silico<\/i>: methods and applications&#8221;, DOI:10.1039\/C2IB20095C, 5(2):262-77, Integrative Biology, 2012 <a href=\"http:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2013\/IB\/C2IB20095C\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2012_IB_MicroEvo.pdf\">(pdf)<\/a><\/p>\n<p>[J8] Y. Liang, H. Wu, R. Lei, RA. Chong, Y. Wei, X. Lu, I. Tagkopoulos, SY. Kung, Q. Yang, G. Hu, Y. Kang, &#8220;Transcriptional Network Analysis Identififies BACH1 as a Master Regulator of Breast Cancer Bone Metastasis&#8221;, 287(40):33533-44, Journal of Biological Chemistry, 2012 <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22875853\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2013_JBC_33533.full.pdf\">(pdf)<\/a><\/p>\n<p>[J7] I. Tagkopoulos, &#8220;Microbial factories under control: Auto-regulatory control through engineered stress-induced feedback&#8221;, 4:1, 1-4, Bioengineered, 2013 <a href=\"http:\/\/www.landesbioscience.com\/journals\/bioe\/article\/21935\/\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2012_BUGS_RPP.pdf\">(pdf)<\/a><\/p>\n<p>[J6] L. Huynh, J. Kececioglu, M. K\u00f6ppe, I.Tagkopoulos, &#8220;Automated Design of Synthetic Gene Circuits through Linear Approximation and Mixed Integer Optimization&#8221;, 7(4):e35529, PLoS ONE, 2012 <a href=\"http:\/\/www.plosone.org\/article\/info:doi\/10.1371\/journal.pone.0035529\">(link)<\/a><\/p>\n<p>[J5] M. Dragosits, D. Nicklas, I.Tagkopoulos, &#8220;A synthetic biology approach to self-regulatory recombinant protein production in <i>Escherichia coli<\/i>&#8220;, 6:2, Journal of Biological Engineering, 2012 <a href=\"http:\/\/www.jbioleng.org\/content\/6\/1\/2\">(link)<\/a><\/p>\n<p>[J4] V.Mozhayskiy, I.Tagkopoulos, &#8220;Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation&#8221;, doi: 10.1186\/1471-2105-13-S10-S10, 13:S10, BMC Bioinformatics, 2012 <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/13\/S10\/S10\">(link)<\/a><\/p>\n<p>[J3] V.Mozhayskiy, I.Tagkopoulos, &#8220;Horizontal gene transfer dynamics and distribution of fitness effects during microbial In silico Evolution&#8221;, doi: 10.1186\/1471-2105-13-S10-S13, 13:S13, BMC Bioinformatics, 2012 <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/13\/S10\/S13\">(link)<\/a><\/p>\n<p>[J2] I.Tagkopoulos, Y.Liu, S. Tavazoie, &#8220;Predictive Behavior Within Microbial Genetic Networks&#8221;, Science, 320:1313-7, 2008 <a href=\"http:\/\/www.sciencemag.org\/content\/320\/5881\/1313.long\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2008_Science_1313.full.pdf\">(pdf)<\/a><\/p>\n<p>[J1] S.Y.Kung, M.W. Mak, and I.Tagkopoulos, &#8220;Symmetric and Asymmetric Multi-modality Biclustering Analysis for Microarray Data Matrix&#8221;, Journal of Bioinformatics and Computational Biology, vol 4(2), pp. 275-298, 2006 <a href=\"http:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720006002065\">(link)<\/a>, <a href=\"http:\/\/www.cs.ucdavis.edu\/%7Eiliast\/papers\/2006_JBCB_jbcb06.pdf\">(pdf)<\/a><\/p>\n<\/div>\n<div id=\"Conferences\">\n<h4><span style=\"text-decoration: underline\">Peer-reviewed Conference Publications:<\/span><\/h4>\n<p>[C13] E. Gultepe, Hien Nguyen, Tim Albertson, I.Tagkopoulos, &#8220;A Bayesian network for early diagnosis of sepsis patients: a basis for a clinical decision support system&#8221;, 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Las Vegas, NV, pp.1-5, 23-25, 2012<\/p>\n<p>[C12] L. Huynh, I.Tagkopoulos, &#8220;A robust, library-based, optimization-driven method for automatic gene circuit design&#8221;, 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Las Vegas, NV, pp.1-6, 24-26, 2012<\/p>\n<p>[C11] L.Huynh, J.Kececioglu, I.Tagkopoulos, &#8220;Scaling responsibly, Towards a reusable, modular, automated gene circuit design&#8221;, Proceedings of the 3rd International Workshop on Bio-design Automation, IWBDA&#8217;12, San Diego, 2012.<\/p>\n<p>[C10] R. Miller, V.Mozhayskiy, I.Tagkopoulos, KL. Ma, &#8220;EVEVis: A Multi-Scale Visualization System for Dense Evolutionary Data&#8221;, 1st IEEE Symposium on Biological Data Visualization, pp. 143-150, Providence, Rhode Island, 2011<\/p>\n<p>[C9] V.Mozhayskiy, R. Miller, KL. Ma, I.Tagkopoulos, &#8220;A Scalable Multi-scale Framework for Parallel Simulation and Visualization of Microbial Evolution&#8221;, TeraGrid2011; Salt Lake City, Utah, 2011, DOI:10.1145\/2016741.2016749 (Best Paper Award)<\/p>\n<p>[C8] V.Mozhayskiy, I.Tagkopoulos, &#8220;In silico Evolution of Multi-scale Microbial Systems in the Presence of Mobile Genetic Elements and Horizontal Gene Transfer&#8221;, ISBRA2011, Lecture Notes in Bioinformatics, LNBI 6674, pp.262-273, Springer, 2011<\/p>\n<p>[C7] L.Huynh, J.Kececioglu, I.Tagkopoulos, &#8220;Automated Design of Synthetic Gene Circuits through Linear Approximation and Mixed Integer Optimization&#8221;, Proceedings of the 3rd International Workshop on Bio-design Automation, IWBDA2011, San Diego, 2011.<\/p>\n<p>[C6] I.Tagkopoulos, D. Serpanos, &#8220;Gene Classification and Regulatory Prediction Based on Transcriptional Modeling.&#8221; Proceedings of the IEEE Symposium on Signal Processing and Information Technology, ISSPIT2005, pp. 29-34, Proceedings of the Firth IEEE International Symposium on Signal Processing and Information Technology, Athens, Greece, 2005.<\/p>\n<p>[C5] I.Tagkopoulos, &#8220;A Transcriptional Approach to Gene Clustering&#8221;, CIBCB2005, Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp.1-7, San Diego, California, 2005. (student paper award)<\/p>\n<p>[C4] I.Tagkopoulos, N. Slavov, S.Y. Kung, &#8220;Multi-class Biclustering and Classification Based on Modeling of Gene Regulatory Networks&#8221;, BIBE2005, Proceedings of the 5th IEEE Symposium on Bioengineering and Bioinformatics, pp. 89-96, Minneapolis, Minnesota, 2005.<\/p>\n<p>[C3] S.Y.Kung, M.W. Mak, and I.Tagkopoulos, &#8220;Multi-Metric and Multi-Substructure Biclustering Analysis for Gene Expression Data&#8221;, CSB2005, Proceedings of the IEEE Computational Systems Bioinformatics Conference, pp.123-134, Stanford, California, 2005.<\/p>\n<p>[C2] I.Tagkopoulos, C.Zukowski, G.Cavelier, D.Anastassiou, &#8220;A Custom FPGA for the Simulation of Gene Regulatory Networks&#8221;, GLSVLSI2003, Proceedings of the 13th ACM Great Lakes Symposium on VLSI, pp. 135-141, Washington D.C., 2003.<\/p>\n<p>[C1] N.D.Zervas, I.Tagkopoulos, V. Spiliotopoulos, D.Soudris, C.E.Goutis, &#8220;Comparison of DWT Scheduling Algorithms Alternatives on Programmable Platforms&#8221;, ISCAS2001, Proceedings of the International Symposium on Circuits and Systems, , pp. 761-764, vol. 2, Sidney, Australia, 2001.<\/p>\n<\/div>\n<h4><span style=\"text-decoration: underline\">Other means (book chapters, extended abstracts, articles)<\/span><\/h4>\n<p>[O12] T.Evitts, K.Gabric, I.Tagkopoulos, &#8220;Quorum Sensing in Bacteria&#8221;, NSF BioMath Module, COMAP, pp. 1-42 (in press).<\/p>\n<p>[O11] M. Dragosits, V. Mozhayskiy, D. Nicklas, I. Tagkopoulos: &#8216;Synthetic biology and evolutionary aspects of internal and external stress for industrial microbiology &#8216;, 4th \u00d6GMBT annual meeting, September 17-19, 2012, Graz, Austria.<\/p>\n<p>[O10] L. Huynh, I. Tagkopoulos, &#8220;Scaling responsively: towards a reusable, modular, automated gene circuit design&#8221;,Proceedings of the 4rth International Workshop on Bio-design Automation, IWBDA&#8217;12, San Francisco, 2012.<\/p>\n<p>[O9] A.Pavlogiannis, V.Mozhayskiy, I.Tagkopoulos, &#8220;Network floods reveal regulatory control flows and minimal networks in synthetic and bacterial datasets&#8221;, 20th Annual Conference on Intelegent Systems for Molecular Biology, ISMB2012, Long Beach, CA. 2012.<\/p>\n<p>[O8] V. Mozhayskiy, M. Dragosits, I. Tagkopoulos, &#8220;Guided step-wise adaptation of microbial populations&#8221;, 7th Annual Systems-to-Synthesis Symposium, San Diego, CA, 2012.<\/p>\n<p>[O7] I.Tagkopoulos, &#8220;Self-regulatory circuits for recombinant protein production&#8221;, Poster, 11th Conference on Microbial Genetics and Ecology, BAGECO&#8217;11, Corfu, Greece, 2011.<\/p>\n<p>[O6] I.Tagkopoulos, &#8220;Microbial Evolution in Stressful Environments: Theory and Experiments&#8221;, Poster, 11th Conference on Microbial Genetics and Ecology, BAGECO&#8217;11, Corfu, Greece, 2011.<\/p>\n<p>[O5] L.Huynh, J.Kececioglu, I.Tagkopoulos, &#8220;Automated Design of Synthetic Gene Circuits through Linear Approximation and Mixed Integer Optimization&#8221;, Proceedings of the 3rd International Workshop on Bio-design Automation, IWBDA&#8217;11, San Diego, 2011.<\/p>\n<p>[O4] V.Mozhayskiy, I.Tagkopoulos, &#8220;Facilitated Variation of <i>in silico<\/i> Microbial Populations Affects Evolutionary Rates&#8221;, Poster and Talk, 7th International Symposium on Bioinformatics Research and Applications, Changsha, China, May 2011.<\/p>\n<p>[O3] V.Mozhayskiy, I.Tagkopoulos, &#8220;Large-scale Evolutionary Simulations of Complex Microbial Behaviors in Dynamic Environments&#8221;, Poster, 9th Annual International Conference on Computational Systems Bioinformatics, CSB&#8217;10, Stanford, 2010.<\/p>\n<p>[O2] V.Mozhayskiy, I.Tagkopoulos, &#8220;Emergence of Robust Biological Networks in Petascale Simulations of Bacterial Evolution&#8221;, Abstract, Extreme Scale I\/O and Data Analysis Workshop, NSF\/NCSA\/TACC, Austin, TX, 2010.<\/p>\n<p>[O1] V.Mozhayskiy, I.Tagkopoulos, &#8220;Simulations of Microbial Evolution in Fluctuating Environments&#8221;, Poster, 18th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB&#8217;10, Boston, 2010.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Warning: This page is outdated. Please check the laboratory website for more recent information! Lab webpage: Tagkopoulos&#8217; lab web page Journals: [J24] M. Meisner, J.A. Rosenheim, I. Tagkopoulos, &#8220;A data-driven, machine learning framework for optimal pest management in cotton&#8221;, Ecosphere, 2015 (in press) [J23] N. Rai, A. Ferreiro, A. Neckelmann, \u2026 <a class=\"continue-reading-link\" href=\"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/publications\/\"> Continue reading <span class=\"meta-nav\">&rarr; <\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"inline_featured_image":false,"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-17","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/wp-json\/wp\/v2\/pages\/17","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/wp-json\/wp\/v2\/comments?post=17"}],"version-history":[{"count":8,"href":"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/wp-json\/wp\/v2\/pages\/17\/revisions"}],"predecessor-version":[{"id":254,"href":"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/wp-json\/wp\/v2\/pages\/17\/revisions\/254"}],"wp:attachment":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/tagkopoulos\/wp-json\/wp\/v2\/media?parent=17"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}