Journals:
[J13] 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", under revision, ACS Synthetic Biology, 2013
[J12] 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", accepted, Nature/EMBO Molecular Systems Biology, 2013
[J11] A. Pavlogiannis, V. Mozhayskiy, I. Tagkopoulos, "A flood-based information flow analysis and network minimization method for bacterial systems", under revision, BMC Bioinformatics, 2012
[J10] L. Huynh, A. Tsoukalas, M. Köppe, I.Tagkopoulos, "SBROME: A scalable optimization and module matching framework for automated biosystem design", under revision, ACS Synthetic Biology, 2012
[J9] V. Mozhayskiy, I. Tagkopoulos, "Microbial evolution in vivo and in silico: methods and applications", in press, DOI:10.1039/C2IB20095C, 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", in press, Journal of Biological Chemistry, 2012
[J7] I. Tagkopoulos, "Microbial factories under control: Auto-regulatory control through engineered stress-induced feedback", 4:1, 1-4, Bioengineered, 2012
[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
[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
[J4] V.Mozhayskiy, I.Tagkopoulos, "Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation", 13:S10, BMC Bioinformatics, 2012
[J3] V.Mozhayskiy, I.Tagkopoulos, "Horizontal gene transfer dynamics and distribution of fitness effects during microbial In silico Evolution", 13:S13, BMC Bioinformatics, 2012
[J2] I.Tagkopoulos, Y.Liu, S. Tavazoie, "Predictive Behavior Within Microbial Genetic Networks", Science, 320:1313-7, 2008
[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
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.
