[J30] Kim M, Eetemadi A, Tagkopoulos I. DeepPep: Deep proteome inference from peptide profiles. PLoS Comput Biol. 2017 (under revision)

[J29] Bjornson, M, Balcke, G, Xiao, Y, de Souza, A, Wang, J, Zhabinskaya, D, Tagkopoulos, I, Tissier, A, Dehesh, K. Integrated omics analyses of retrograde signaling mutant delineate interrelated stress response strata. Plant J. 2017 (accepted)


[J28] Zorraquino V, Kim M, Rai N, Tagkopoulos I. The genetic and transcriptional basis of short and long term adaptation across multiple stresses in Escherichia coli. Mol Biol Evol. 2016 Dec 21. pii: msw269. doi: 10.1093/molbev/msw269. [Epub ahead of print] PubMed PMID: 28007978. (link), (pdf)

[J27] Huynh L, Tagkopoulos I. A Parts Database with Consensus Parameter Estimation for Synthetic Circuit Design. ACS Synth Biol. 2016 Dec 16;5(12):1412-1420. PubMed PMID: 27454439. (link), (pdf)

[J26] Kim M, Rai N, Zorraquino V, Tagkopoulos I. Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. Nat Commun. 2016 Oct 7;7:13090. doi: 10.1038/ncomms13090. PubMed PMID: 27713404; PubMed Central PMCID: PMC5059772. (link), (pdf)

[J25] Meisner MH, Jay RA, Tagkopoulos I. A data-driven, machine learning framework for optimal pest management in cotton. Ecosphere. 2016 March 31; 7(3):e01263. (link), (pdf)

[J24] Carlin DA, Caster RW, Wang X, Betzenderfer SA, Chen CX, Duong VM, Ryklansky CV, Alpekin A, Beaumont N, Kapoor H, Kim N, Mohabbot H, Pang B, Teel R, Whithaus L, Tagkopoulos I, Siegel JB. Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants. PLoS One. 2016 Jan 27;11(1):e0147596. doi: 10.1371/journal.pone.0147596. PubMed PMID: 26815142; PubMed Central PMCID: PMC4729467. (link)


[J23] Huynh L, Tagkopoulos I. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching. ACS Synth Biol. 2015 Aug 21;4(8):890-7. doi: 10.1021/sb500339k. PubMed PMID: 25916918. (link), (pdf)

[J22] Rai N, Ferreiro A, Neckelmann A, Soon A, Yao A, Siegel J, Facciotti MT, Tagkopoulos I. RiboTALE: A modular, inducible system for accurate gene expression control. Sci Rep. 2015 May 29;5:10658. doi: 10.1038/srep10658. PubMed PMID: 26023068; PubMed Central PMCID: PMC4650599. (link), (pdf)

[J21] Kim M, Zorraquino V, Tagkopoulos I. Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles. PLoS Comput Biol. 2015 Mar 16;11(3):e1004127. doi: 10.1371/journal.pcbi.1004127. Erratum in: PLoS Comput Biol. 2015 Nov;11(11):e1004617. PubMed PMID: 25774498; PubMed Central PMCID: PMC4361189. (link)

[J20] Tsoukalas A, Albertson T, Tagkopoulos I. From data to optimal decision making: a data-driven, probabilistic machine learning approach to decision support for patients with sepsis. JMIR Med Inform. 2015 Feb 24;3(1):e11. doi: 10.2196/medinform.3445. PubMed PMID: 25710907; PubMed Central PMCID: PMC4376114. (link), (pdf)

[J19] 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. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature. 2015 Jan 29;517(7536):571-5. doi: 10.1038/nature14099. PubMed PMID: 25533953; PubMed Central PMCID: PMC4333722. (link)


[J18] Huynh L, Tagkopoulos I. Optimal part and module selection for synthetic gene circuit design automation. ACS Synth Biol. 2014 Aug 15;3(8):556-64. doi: 10.1021/sb400139h. PubMed PMID: 24933033. (link), (pdf)

[J17] Aung HH, Tsoukalas A, Rutledge JC, Tagkopoulos I. A systems biology analysis of brain microvascular endothelial cell lipotoxicity. BMC Syst Biol. 2014 Jul 4;8:80. doi: 10.1186/1752-0509-8-80. PubMed PMID: 24993133; PubMed Central PMCID: PMC4112729. (link)

[J16] Carrera J, Estrela R, Luo J, Rai N, Tsoukalas A, Tagkopoulos I. An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli. Mol Syst Biol. 2014 Jul 1;10:735. doi: 10.15252/msb.20145108. PubMed PMID: 24987114; PubMed Central PMCID: PMC4299492. (link)

[J15] V. Zorraquino, S. Quinones, M. Kim, N. Rai, I. Tagkopoulos, "Deciphering cross-stress responses in Escherichia coli under complex evolutionary scenarios", bioRxiv, doi:

[J14] Gultepe E, Green JP, Nguyen H, Adams J, Albertson T, Tagkopoulos I. From vital signs to clinical outcomes for patients with sepsis: a machine learning basis for a clinical decision support system. J Am Med Inform Assoc. 2014 Mar-Apr;21(2):315-25. doi: 10.1136/amiajnl-2013-001815. PubMed PMID: 23959843; PubMed Central PMCID: PMC3932455. (link), (pdf)


[J13] Huynh L, Tsoukalas A, Köppe M, Tagkopoulos I. SBROME: a scalable optimization and module matching framework for automated biosystems design. ACS Synth Biol. 2013 May 17;2(5):263-73. doi: 10.1021/sb300095m. PubMed PMID: 23654271. (link), (pdf)

[J12] Pavlogiannis A, Mozhayskiy V, Tagkopoulos I. A flood-based information flow analysis and network minimization method for gene regulatory networks. BMC Bioinformatics. 2013 Apr 24;14:137. doi: 10.1186/1471-2105-14-137. PubMed PMID: 23617932; PubMed Central PMCID: PMC3672003. (link), (pdf)

[J11] Yao AI, Fenton TA, Owsley K, Seitzer P, Larsen DJ, Sit H, Lau J, Nair A, Tantiongloc J, Tagkopoulos I, Facciotti MT. Promoter element arising from the fusion of standard BioBrick parts. ACS Synth Biol. 2013 Feb 15;2(2):111-20. doi: 10.1021/sb300114d. Erratum in: ACS Synth Biol. 2013 Jun 21;2(6):351. PubMed PMID: 23656374. (link), (pdf)

[J10] Mozhayskiy V, Tagkopoulos I. Microbial evolution in vivo and in silico: methods and applications. RSC Integr Biol. 2013 Feb;5(2):262-77. doi: 10.1039/c2ib20095c. Review. PubMed PMID: 23096365. (link), (pdf)

[J9] Tagkopoulos I. Microbial factories under control: auto-regulatory control through engineered stress-induced feedback. Bioengineered. 2013 Jan-Feb;4(1):5-8. doi: 10.4161/bioe.21935. PubMed PMID: 22922761; PubMed Central PMCID: PMC3566021. (link), (pdf)

[J8] Dragosits M, Mozhayskiy V, Quinones-Soto S, Park J, Tagkopoulos I. Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli. Mol Syst Biol. 2013;9:643. doi: 10.1038/msb.2012.76. PubMed PMID: 23385483; PubMed Central PMCID: PMC3588905. (link), (pdf), (Suppl. Mat. pdf)


[J7] Liang Y, Wu H, Lei R, Chong RA, Wei Y, Lu X, Tagkopoulos I, Kung SY, Yang Q, Hu G, Kang Y. Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis. J Biol Chem. 2012 Sep 28;287(40):33533-44. PubMed PMID: 22875853; PubMed Central PMCID: PMC3460454(link), (pdf)

[J6] Mozhayskiy V, Tagkopoulos I. Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation. BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S10. doi: 10.1186/1471-2105-13-S10-S10. PubMed PMID: 22759415; PubMed Central PMCID: PMC3382439. (link)

[J5] Mozhayskiy V, Tagkopoulos I. Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution. BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S13. doi: 10.1186/1471-2105-13-S10-S13. PubMed PMID: 22759418; PubMed Central PMCID: PMC3382434. (link)

[J4] Dragosits M, Nicklas D, Tagkopoulos I. A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli. J Biol Eng. 2012 Mar 30;6(1):2. doi: 10.1186/1754-1611-6-2. PubMed PMID: 22463687; PubMed Central PMCID: PMC3384244. (link)

[J3] Huynh L, Kececioglu J, Köppe M, Tagkopoulos I. Automatic design of synthetic gene circuits through mixed integer non-linear programming. PLoS One. 2012;7(4):e35529. doi: 10.1371/journal.pone.0035529. PubMed PMID: 22536398; PubMed Central PMCID: PMC3334995. (link)


[J2] Tagkopoulos I, Liu YC, Tavazoie S. Predictive behavior within microbial genetic networks. Science. 2008 Jun 6;320(5881):1313-7. doi: 10.1126/science.1154456. PubMed PMID: 18467556; PubMed Central PMCID: PMC2931280. (link), (pdf)

[J1]Kung SY, Mak MW, Tagkopoulos I. Symmetric and asymmetric multi-modality biclustering analysis for microarray data matrix. J Bioinform Comput Biol. 2006 Apr;4(2):275-98. PubMed PMID: 16819784. (link), (pdf)

Peer-reviewed Conference Publications:

[C14] L.Huynh, I.Tagkopoulos, "Optimizing module matching for synthetic gene circuit design automation", Proceedings of the 5rd International Workshop on Bio-design Automation, IWBDA'13, London, 2013. (pdf)

[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 Francisco, 2012. (pdf)

[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. (pdf)

[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) (pdf)

[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. (pdf)

[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. (pdf)

[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)

[O16] I. Tagkopoulos, "Petascale Simulations of Complex Biological Behavior in Fluctuating Environments", 2nd NCSA Blue Waters Symposium for Petascale Science and Beyond, Champaign, IL, May, 2014 .

[O15] M. Kim, J. Carrera, L. Huynh, R. Estrela, N. Rai, A. Tsoukalas, I.Tagkopoulos, "An integrative genome-scale E. coli model and targeted experimentation methodology for systems and synthetic biology", 2nd Conference on Quantitative Biology, q-bio'14, Hawaii, 2014.

[O14] J. Carrera, L. Huynh, I.Tagkopoulos, "A automated synthetic gene circuit design tool based on mathematical optimization", 1st Conference on Quantitative Biology, q-bio'13, Honolulu, Hawaii, 2013.

[O13] T.Evitts, K.Gabric, I.Tagkopoulos, "Quorum Sensing in Bacteria", NSF BioMath Module, COMAP, pp. 1-42.

[O12] V. Mozhayskiy, M. Dragosits, I.Tagkopoulos, "Guided step-wise adaptation of microbial populations in silico and in vivo", 7th Annual Systems-to-Synthesis Symposium, San Diego, CA, 2012 [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] I. Tagkopoulos, `Cross-stress protection in bacteria: an evolutionary perspective", Department of Microbiology and Environmental Toxicology, UCSC, 2013.

[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.