Publications

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Lab website: http://tagkopouloslab.ucdavis.edu/

Journals:

[J24] M. Meisner, J.A. Rosenheim, I. Tagkopoulos, “A data-driven, machine learning framework for optimal pest management in cotton”, Ecosphere, 2015 (in press)

[J23] N. Rai, A. Ferreiro, A. Neckelmann, A. Soon, A. Yao, J. Siegel, M. Facciotti, I. Tagkopoulos, “RiboTALE: A modular, inducible system for accurate gene expression control”, doi:10.1038/srep10658, Scientific Reports, 5: 10658, 2015 (link)

[J22] L. Huynh, I. Tagkopoulos, “Fast and Accurate Circuit Design Automation through Hierarchical Model Switching”, doi:10.1021/sb400139h, ACS Synthetic Biology, 4 (8), pp 890–897, 2015 (link)

[J21] M. Kim, V. Zorraquino, I. Tagkopoulos, “Microbial Forensics: Predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles”, PLoS Computational Biology, 2015 Mar;11 (3):e1004127

[J20] A. Tsoukalas, T. Albertson, I. Tagkopoulos, “From data to optimal decision making: A data-driven, probabilistic machine learning approach to decision support for patients with Sepsis”, JMIR Medical Informatics, 3(1), 2015 (link), (pdf)

[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, “An Arabidopsis gene regulatory network for secondary cell wall biosynthesis”, doi:10.1038/nature14099, 517, 571–575, Nature, 2015 (link)

[J18] V. Zorraquino, S. Quinones, M. Kim, N. Rai, I. Tagkopoulos, “Deciphering cross-stress responses in Escherichia coli under complex evolutionary scenarios”, bioRxiv, doi: http://dx.doi.org/10.1101/010595 (link)

[J17] J. Carrera, R. Estrela, J. Luo, N. Rai, A. Tsoukalas, I. Tagkopoulos, “An integrative, multi-layer, genome-scale model reveals the phenotypic landscape of Escherichia coli”, Molecular Systems Biology, 10(7):735, 2014 (link)

[J16] H.H. Aung, A. Tsoukalas, J. Rutledge, I. Tagkopoulos, “A Systems Biology Analysis of Brain Microvascular Endothelial Cell Lipotoxicity”, BMC Systems Biology, 8:80, 2014 (link)

[J15] L. Huynh, I. Tagkopoulos, “Optimal part and module selection for synthetic gene circuit design automation”, doi:10.1021/sb400139h, ACS Synthetic Biology, 2014 (link), (pdf)

[J14] E. Gultepe, J. Green, H. Nguyen, J. Adams, T. Albertson, I. Tagkopoulos, “From vital signs to clinical outcomes for sepsis patients: A clinical decision support system based on discriminative classification”, doi:10.1136/amiajnl-2013-001815, Journal of the American Medical Informatics Association (JAMIA), 21(2):315-25, 2014 (link), (pdf)

[J13] M. Dragosits, V. Mozhayskiy, S. Quinones-Soto, J. Park, I.Tagkopoulos, “Evolutionary potential,cross-stress behavior, and the genetic basis of acquired stress resistance in Escherichia coli“, doi:10.1038/msb.2012.76, 9:643, Molecular Systems Biology, 2013 (link), (pdf), (Suppl. Mat. pdf)

[J12] A. Yao, T. Fenton, K. Owsley, P. Seitzer, D. Larsen, H. Lam, J. Lau, A. Nair, J. Tantiongloc, I. Tagkopoulos, M. Facciotti, “Promoter activity arising from the fusion of standard BioBrick parts”, 2 (2), pp 111–120, DOI: 10.1021/sb300114d, ACS Synthetic Biology, 2013 (link), (pdf)

[J11] A. Pavlogiannis, V. Mozhayskiy, I. Tagkopoulos, “A flood-based information flow analysis and network minimization method for bacterial systems”, 14:137 DOI:10.1186/1471-2105-14-137, BMC Bioinformatics, 2013 (link), (pdf)

[J10] L. Huynh, A. Tsoukalas, M. Köppe, I.Tagkopoulos, “SBROME: A scalable optimization and module matching framework for automated biosystem design”, DOI: 10.1021/sb300095m, pp 263-273, ACS Synthetic Biology, 2013 (link), (pdf)

[J9] V. Mozhayskiy, I. Tagkopoulos, “Microbial evolution in vivo and in silico: methods and applications”, DOI:10.1039/C2IB20095C, 5(2):262-77, Integrative Biology, 2012 (link), (pdf)

[J8] Y. Liang, H. Wu, R. Lei, RA. Chong, Y. Wei, X. Lu, I. Tagkopoulos, SY. Kung, Q. Yang, G. Hu, Y. Kang, “Transcriptional Network Analysis Identififies BACH1 as a Master Regulator of Breast Cancer Bone Metastasis”, 287(40):33533-44, Journal of Biological Chemistry, 2012 (link), (pdf)

[J7] I. Tagkopoulos, “Microbial factories under control: Auto-regulatory control through engineered stress-induced feedback”, 4:1, 1-4, Bioengineered, 2013 (link), (pdf)

[J6] L. Huynh, J. Kececioglu, M. Köppe, I.Tagkopoulos, “Automated Design of Synthetic Gene Circuits through Linear Approximation and Mixed Integer Optimization”, 7(4):e35529, PLoS ONE, 2012 (link)

[J5] M. Dragosits, D. Nicklas, I.Tagkopoulos, “A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli“, 6:2, Journal of Biological Engineering, 2012 (link)

[J4] V.Mozhayskiy, I.Tagkopoulos, “Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation”, doi: 10.1186/1471-2105-13-S10-S10, 13:S10, BMC Bioinformatics, 2012 (link)

[J3] V.Mozhayskiy, I.Tagkopoulos, “Horizontal gene transfer dynamics and distribution of fitness effects during microbial In silico Evolution”, doi: 10.1186/1471-2105-13-S10-S13, 13:S13, BMC Bioinformatics, 2012 (link)

[J2] I.Tagkopoulos, Y.Liu, S. Tavazoie, “Predictive Behavior Within Microbial Genetic Networks”, Science, 320:1313-7, 2008 (link), (pdf)

[J1] S.Y.Kung, M.W. Mak, and I.Tagkopoulos, “Symmetric and Asymmetric Multi-modality Biclustering Analysis for Microarray Data Matrix”, Journal of Bioinformatics and Computational Biology, vol 4(2), pp. 275-298, 2006 (link), (pdf)
[J23] N. Rai, A. Ferreiro, A. Neckelmann, A. Soon, A. Yao, J. Siegel, M. Facciotti, I. Tagkopoulos, “RiboTALE: A modular, inducible system for accurate gene expression control”, Scientific Reports, 2015 (in press)

[J22] L. Huynh, I. Tagkopoulos, “Fast and Accurate Circuit Design Automation through Hierarchical Model Switching”, doi:10.1021/sb400139h, ACS Synthetic Biology, 2015 (in press)(link), (pdf)

[J21] M. Kim, V. Zorraquino, I. Tagkopoulos, “Microbial Forensics: Predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles”, PLoS Computational Biology, 2015 Mar;11 (3):e1004127

[J20] A. Tsoukalas, T. Albertson, I. Tagkopoulos, “From data to optimal decision making: A data-driven, probabilistic machine learning approach to decision support for patients with Sepsis”, JMIR Medical Informatics, 3(1), 2015

[J20] V. Zorraquino, S. Quinones, M. Kim, N. Rai, I. Tagkopoulos, “Deciphering cross-stress responses in Escherichia coli under complex evolutionary scenarios”, under review, ISME Journal, 2014

[J19] M. Kim, V. Zorraquino, I. Tagkopoulos, “Microbial Forensics: Predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles”, under revision, PLoS Computational Biology, 2014

[J18] A. Tsoukalas, T. Albertson, I. Tagkopoulos, “From data to optimal decision making: A data-driven, probabilistic machine learning approach to decision support for patients with Sepsis”, under revision, JMIR, 2014

[J17] J. Carrera, R. Estrela, J. Luo, N. Rai, A. Tsoukalas, I. Tagkopoulos, “An integrative, multi-layer, genome-scale model reveals the phenotypic landscape of Escherichia coli”, Molecular Systems Biology, 10(7):735, 2014 (link)

[J16] H.H. Aung, A. Tsoukalas, J. Rutledge, I. Tagkopoulos, “A Systems Biology Analysis of Brain Microvascular Endothelial Cell Lipotoxicity”, BMC Systems Biology, 8:80, 2014 (link)

[J15] L. Huynh, I. Tagkopoulos, “Optimal part and module selection for synthetic gene circuit design automation”, doi:10.1021/sb400139h, ACS Synthetic Biology, 2014 (link), (pdf)

[J14] E. Gultepe, J. Green, H. Nguyen, J. Adams, T. Albertson, I. Tagkopoulos, “From vital signs to clinical outcomes for sepsis patients: A clinical decision support system based on discriminative classification”, doi:10.1136/amiajnl-2013-001815, Journal of the American Medical Informatics Association (JAMIA), 21(2):315-25, 2014 (link), (pdf)

[J13] M. Dragosits, V. Mozhayskiy, S. Quinones-Soto, J. Park, I.Tagkopoulos, “Evolutionary potential,cross-stress behavior, and the genetic basis of acquired stress resistance in Escherichia coli“, doi:10.1038/msb.2012.76, 9:643, Nature/EMBO Molecular Systems Biology, 2013 (link), (pdf), (Suppl. Mat. pdf)

[J12] A. Yao, T. Fenton, K. Owsley, P. Seitzer, D. Larsen, H. Lam, J. Lau, A. Nair, J. Tantiongloc, I. Tagkopoulos, M. Facciotti, “Promoter activity arising from the fusion of standard BioBrick parts”, 2 (2), pp 111–120, DOI: 10.1021/sb300114d, ACS Synthetic Biology, 2013 (link), (pdf)

[J11] A. Pavlogiannis, V. Mozhayskiy, I. Tagkopoulos, “A flood-based information flow analysis and network minimization method for bacterial systems”, 14:137 DOI:10.1186/1471-2105-14-137, BMC Bioinformatics, 2013 (link), (pdf)

[J10] L. Huynh, A. Tsoukalas, M. Köppe, I.Tagkopoulos, “SBROME: A scalable optimization and module matching framework for automated biosystem design”, DOI: 10.1021/sb300095m, pp 263-273, ACS Synthetic Biology, 2013 (link), (pdf)

[J9] V. Mozhayskiy, I. Tagkopoulos, “Microbial evolution in vivo and in silico: methods and applications”, DOI:10.1039/C2IB20095C, 5(2):262-77, Integrative Biology, 2012 (link), (pdf)

[J8] Y. Liang, H. Wu, R. Lei, RA. Chong, Y. Wei, X. Lu, I. Tagkopoulos, SY. Kung, Q. Yang, G. Hu, Y. Kang, “Transcriptional Network Analysis Identififies BACH1 as a Master Regulator of Breast Cancer Bone Metastasis”, 287(40):33533-44, Journal of Biological Chemistry, 2012 (link), (pdf)

[J7] I. Tagkopoulos, “Microbial factories under control: Auto-regulatory control through engineered stress-induced feedback”, 4:1, 1-4, Bioengineered, 2013 (link), (pdf)

[J6] L. Huynh, J. Kececioglu, M. Köppe, I.Tagkopoulos, “Automated Design of Synthetic Gene Circuits through Linear Approximation and Mixed Integer Optimization”, 7(4):e35529, PLoS ONE, 2012 (link)

[J5] M. Dragosits, D. Nicklas, I.Tagkopoulos, “A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli“, 6:2, Journal of Biological Engineering, 2012 (link)

[J4] V.Mozhayskiy, I.Tagkopoulos, “Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation”, doi: 10.1186/1471-2105-13-S10-S10, 13:S10, BMC Bioinformatics, 2012 (link)

[J3] V.Mozhayskiy, I.Tagkopoulos, “Horizontal gene transfer dynamics and distribution of fitness effects during microbial In silico Evolution”, doi: 10.1186/1471-2105-13-S10-S13, 13:S13, BMC Bioinformatics, 2012 (link)

[J2] I.Tagkopoulos, Y.Liu, S. Tavazoie, “Predictive Behavior Within Microbial Genetic Networks”, Science, 320:1313-7, 2008 (link), (pdf)

[J1] S.Y.Kung, M.W. Mak, and I.Tagkopoulos, “Symmetric and Asymmetric Multi-modality Biclustering Analysis for Microarray Data Matrix”, Journal of Bioinformatics and Computational Biology, vol 4(2), pp. 275-298, 2006 (link), (pdf)

Peer-reviewed Conference Publications:

[C13] E. Gultepe, Hien Nguyen, Tim Albertson, I.Tagkopoulos, “A Bayesian network for early diagnosis of sepsis patients: a basis for a clinical decision support system”, 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Las Vegas, NV, pp.1-5, 23-25, 2012

[C12] L. Huynh, I.Tagkopoulos, “A robust, library-based, optimization-driven method for automatic gene circuit design”, 2nd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Las Vegas, NV, pp.1-6, 24-26, 2012

[C11] L.Huynh, J.Kececioglu, I.Tagkopoulos, “Scaling responsibly, Towards a reusable, modular, automated gene circuit design”, Proceedings of the 3rd International Workshop on Bio-design Automation, IWBDA’12, San Diego, 2012.

[C10] R. Miller, V.Mozhayskiy, I.Tagkopoulos, KL. Ma, “EVEVis: A Multi-Scale Visualization System for Dense Evolutionary Data”, 1st IEEE Symposium on Biological Data Visualization, pp. 143-150, Providence, Rhode Island, 2011

[C9] V.Mozhayskiy, R. Miller, KL. Ma, I.Tagkopoulos, “A Scalable Multi-scale Framework for Parallel Simulation and Visualization of Microbial Evolution”, TeraGrid2011; Salt Lake City, Utah, 2011, DOI:10.1145/2016741.2016749 (Best Paper Award)

[C8] V.Mozhayskiy, I.Tagkopoulos, “In silico Evolution of Multi-scale Microbial Systems in the Presence of Mobile Genetic Elements and Horizontal Gene Transfer”, ISBRA2011, Lecture Notes in Bioinformatics, LNBI 6674, pp.262-273, Springer, 2011

[C7] L.Huynh, J.Kececioglu, I.Tagkopoulos, “Automated Design of Synthetic Gene Circuits through Linear Approximation and Mixed Integer Optimization”, Proceedings of the 3rd International Workshop on Bio-design Automation, IWBDA2011, San Diego, 2011.

[C6] I.Tagkopoulos, D. Serpanos, “Gene Classification and Regulatory Prediction Based on Transcriptional Modeling.” 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.

[C5] I.Tagkopoulos, “A Transcriptional Approach to Gene Clustering”, CIBCB2005, Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp.1-7, San Diego, California, 2005. (student paper award)

[C4] I.Tagkopoulos, N. Slavov, S.Y. Kung, “Multi-class Biclustering and Classification Based on Modeling of Gene Regulatory Networks”, BIBE2005, Proceedings of the 5th IEEE Symposium on Bioengineering and Bioinformatics, pp. 89-96, Minneapolis, Minnesota, 2005.

[C3] S.Y.Kung, M.W. Mak, and I.Tagkopoulos, “Multi-Metric and Multi-Substructure Biclustering Analysis for Gene Expression Data”, CSB2005, Proceedings of the IEEE Computational Systems Bioinformatics Conference, pp.123-134, Stanford, California, 2005.

[C2] I.Tagkopoulos, C.Zukowski, G.Cavelier, D.Anastassiou, “A Custom FPGA for the Simulation of Gene Regulatory Networks”, GLSVLSI2003, Proceedings of the 13th ACM Great Lakes Symposium on VLSI, pp. 135-141, Washington D.C., 2003.

[C1] N.D.Zervas, I.Tagkopoulos, V. Spiliotopoulos, D.Soudris, C.E.Goutis, “Comparison of DWT Scheduling Algorithms Alternatives on Programmable Platforms”, ISCAS2001, Proceedings of the International Symposium on Circuits and Systems, , pp. 761-764, vol. 2, Sidney, Australia, 2001.

Other means (book chapters, extended abstracts, articles)

[O12] T.Evitts, K.Gabric, I.Tagkopoulos, “Quorum Sensing in Bacteria”, NSF BioMath Module, COMAP, pp. 1-42 (in press).

[O11] M. Dragosits, V. Mozhayskiy, D. Nicklas, I. Tagkopoulos: ‘Synthetic biology and evolutionary aspects of internal and external stress for industrial microbiology ‘, 4th ÖGMBT annual meeting, September 17-19, 2012, Graz, Austria.

[O10] L. Huynh, I. Tagkopoulos, “Scaling responsively: towards a reusable, modular, automated gene circuit design”,Proceedings of the 4rth International Workshop on Bio-design Automation, IWBDA’12, San Francisco, 2012.

[O9] A.Pavlogiannis, V.Mozhayskiy, I.Tagkopoulos, “Network floods reveal regulatory control flows and minimal networks in synthetic and bacterial datasets”, 20th Annual Conference on Intelegent Systems for Molecular Biology, ISMB2012, Long Beach, CA. 2012.

[O8] V. Mozhayskiy, M. Dragosits, I. Tagkopoulos, “Guided step-wise adaptation of microbial populations”, 7th Annual Systems-to-Synthesis Symposium, San Diego, CA, 2012.

[O7] I.Tagkopoulos, “Self-regulatory circuits for recombinant protein production”, Poster, 11th Conference on Microbial Genetics and Ecology, BAGECO’11, Corfu, Greece, 2011.

[O6] I.Tagkopoulos, “Microbial Evolution in Stressful Environments: Theory and Experiments”, Poster, 11th Conference on Microbial Genetics and Ecology, BAGECO’11, Corfu, Greece, 2011.

[O5] L.Huynh, J.Kececioglu, I.Tagkopoulos, “Automated Design of Synthetic Gene Circuits through Linear Approximation and Mixed Integer Optimization”, Proceedings of the 3rd International Workshop on Bio-design Automation, IWBDA’11, San Diego, 2011.

[O4] V.Mozhayskiy, I.Tagkopoulos, “Facilitated Variation of in silico Microbial Populations Affects Evolutionary Rates”, Poster and Talk, 7th International Symposium on Bioinformatics Research and Applications, Changsha, China, May 2011.

[O3] V.Mozhayskiy, I.Tagkopoulos, “Large-scale Evolutionary Simulations of Complex Microbial Behaviors in Dynamic Environments”, Poster, 9th Annual International Conference on Computational Systems Bioinformatics, CSB’10, Stanford, 2010.

[O2] V.Mozhayskiy, I.Tagkopoulos, “Emergence of Robust Biological Networks in Petascale Simulations of Bacterial Evolution”, Abstract, Extreme Scale I/O and Data Analysis Workshop, NSF/NCSA/TACC, Austin, TX, 2010.

[O1] V.Mozhayskiy, I.Tagkopoulos, “Simulations of Microbial Evolution in Fluctuating Environments”, Poster, 18th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB’10, Boston, 2010.

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