[RV2] Wang, Xiaokang, Navneet Rai, Beatriz Merchel Piovesan Pereira, Ameen Eetemadi, and Ilias Tagkopoulos. Accelerated knowledge discovery from omics data by optimal experimental design.

[RV1] Wai Shun Mak, Steve Bertolani, XiaoKang Wang, Wen Qiao Tang, I. Tagkopoulos, David K. Wilson, and Justin B. Siegel. Genomic mining of aldehyde deformylating oxygenases defines structural features that enable engineering of function.

[J45] Pereira, Beatriz Merchel Piovesan, Xiaokang Wang, and Ilias Tagkopoulos. “A systems analysis of E. coli short and long-term transcriptomic response to biocides.” Applied and Environmental Microbiology (2020): AEM.00708-20. doi: 10.1128/AEM.00708-20 (link)

[J44] Eetemadi, Ameen, Navneet Rai, Beatriz Merchel Piovesan Pereira, Minseung Kim, Harold Schmitz, and Ilias Tagkopoulos. “The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health.” Frontiers in Microbiology (2020). doi:10.3389/fmicb.2020.00393 (link), (pdf)

[J43] Elizabeth Chin, Gabriel Simmons, Yasmine Bouzid, Annie Kan, Dustin Burnett, Ilias Tagkopoulos, and Danielle G. Lemay. “Nutrient Estimation from 24-Hour Food Recalls Using Machine Learning and Database Mapping: A Case Study with Lactose.” Nutrients (2019). doi:10.3390/nu11123045 (link)

[J42] Pereira, Beatriz Merchel Piovesan, and Ilias Tagkopoulos. “Benzalkonium chlorides: Uses, regulatory status, and microbial resistance.” Applied and Environmental Microbiology (2019): AEM-00377. doi:10.1128/AEM.00377-19 (link), (pdf)

[J41] Moon, Su-Jin, Jung Min Bae, Kyung-Su Park, Ilias Tagkopoulos, and Ki-Jo Kim. “Compendium of skin molecular signatures identifies key pathological features associated with fibrosis in systemic sclerosis.” Annals of the Rheumatic Diseases (2019): annrheumdis-2018. doi:10.1136/annrheumdis-2018-214778 (link)

[J40] Kim, Ki-Jo, Minseung Kim, Iannis Adamopoulos, and Ilias Tagkopoulos. “Compendium of synovial signatures identifies pathologic characteristics for predicting treatment response in rheumatoid arthritis patients.” Clinical Immunology (2019). doi:10.1016/j.clim.2019.03.002 (link), (pdf)

[J39] Rai, Navneet, Linh Huynh, Minseung Kim, and Ilias Tagkopoulos. “Population collapse and adaptive rescue during long‐term chemostat fermentation.” Biotechnology and bioengineering 116, no. 3 (2019): 693-703. doi:10.1002/bit.26898 (link), (pdf)

[J38] Kim, Ki-Jo, and Ilias Tagkopoulos. “Application of machine learning in rheumatic disease research.” The Korean journal of internal medicine (2018). doi:10.3904/kjim.2018.349 (link)

[J37] Eetemadi, Ameen, and Ilias Tagkopoulos. “Genetic Neural Networks: an artificial neural network architecture for capturing gene expression relationships.” Bioinformatics (2018). doi:10.1093/bioinformatics/bty945 (link), (GitHub), (pdf)

[J36] Wang, Xiaokang, Violeta Zorraquino, Minseung Kim, Athanasios Tsoukalas, and Ilias Tagkopoulos. “Predicting the evolution of Escherichia coli by a data-driven approach.” Nature communications 9, no. 1 (2018): 3562. doi:10.1038/s41467-018-05807-z (link), (Github(MutationDB portal)

[J35] Kim, Minseung, and Ilias Tagkopoulos. “Data integration and predictive modeling methods for multi-omics datasets.” Molecular omics 14, no. 1 (2018): 8-25. doi:10.1039/C7MO00051K (link),(pdf)

[J34] Kim, Ki-Jo, Navneet Rai, Minseung Kim, and Ilias Tagkopoulos. “A network-based model for drug repurposing in Rheumatoid Arthritis.” BioRxiv (2018): 335679. doi:10.1101/335679 (link)

[J33] Kim, Minseung, Ameen Eetemadi, and Ilias Tagkopoulos. “DeepPep: Deep proteome inference from peptide profiles.” PLoS computational biology 13, no. 9 (2017): e1005661. doi:10.1371/journal.pcbi.1005661 (link), (GitHub)

[J32] Freund, Gabriel S., Terrence E. O’Brien, Logan Vinson, Dylan Alexander Carlin, Andrew Yao, Wai Shun Mak, Ilias Tagkopoulos, Marc T. Facciotti, Dean J. Tantillo, and Justin B. Siegel. “Elucidating Substrate Promiscuity within the FabI Enzyme Family.” ACS chemical biology 12, no. 9 (2017): 2465-2473. doi:10.1021/acschembio.7b00400 (link), (pdf)

[J31] Bjornson, Marta, Gerd Ulrich Balcke, Yanmei Xiao, Amancio de Souza, Jin‐Zheng Wang, Dina Zhabinskaya, Ilias Tagkopoulos, Alain Tissier, and Katayoon Dehesh. “Integrated omics analyses of retrograde signaling mutant delineate interrelated stress‐response strata.” The Plant Journal 91, no. 1 (2017): 70-84. doi:10.1111/tpj.13547 (link)

[J30] Zorraquino, Violeta, Minseung Kim, Navneet Rai, and Ilias Tagkopoulos. “The genetic and transcriptional basis of short and long term adaptation across multiple stresses in Escherichia coli.” Molecular biology and evolution 34, no. 3 (2016): 707-717. doi:10.1093/molbev/msw269 (link)

[J29] Huynh, Linh, and Ilias Tagkopoulos. “A parts database with consensus parameter estimation for synthetic circuit design.” ACS synthetic biology 5, no. 12 (2016): 1412-1420. doi:10.1021/acssynbio.5b00205 (link)(pdf), (PAMDB portal)

[J28] Kim, Minseung, Navneet Rai, Violeta Zorraquino, and Ilias Tagkopoulos. “Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli.” Nature communications 7 (2016): 13090. doi:10.1038/ncomms13090 (link), (Ecomics portal), (GitHub)

[J27] Meisner, Matthew H., Jay A. Rosenheim, and Ilias Tagkopoulos. “A data‐driven, machine learning framework for optimal pest management in cotton.” Ecosphere 7, no. 3 (2016): e01263. doi:10.1002/ecs2.1263 (link)

[J26] Carlin, Dylan Alexander, Ryan W. Caster, Xiaokang Wang, Stephanie A. Betzenderfer, Claire X. Chen, Veasna M. Duong, Carolina V. Ryklansky et al. “Kinetic characterization of 100 glycoside hydrolase mutants enables the discovery of structural features correlated with kinetic constants.” PloS one11, no. 1 (2016): e0147596. doi:10.1371/journal.pone.0147596 (link)

[J25] Eetemadi, Ameen, and Ilias Tagkopoulos. “A Distribution Adaptive Framework for Prediction Interval Estimation Using Nominal Variables.” arXiv preprint arXiv:1511.05688 (2015). (link)

[J24] Huynh, Linh, and Ilias Tagkopoulos. “Fast and accurate circuit design automation through hierarchical model switching.” ACS synthetic biology 4, no. 8 (2015): 890-897. doi:10.1021/sb500339k (link)(pdf)

[J23] Rai, Navneet, Aura Ferreiro, Alexander Neckelmann, Amy Soon, Andrew Yao, Justin Siegel, Marc T. Facciotti, and Ilias Tagkopoulos. “RiboTALE: A modular, inducible system for accurate gene expression control.” Scientific reports 5 (2015): 10658. doi:10.1038/srep10658. (link)

[J22] Taylor-Teeples, Mallory, L. Lin, M. De Lucas, G. Turco, T. W. Toal, A. Gaudinier, N. F. Young et al. “An Arabidopsis gene regulatory network for secondary cell wall synthesis.” Nature517, no. 7536 (2015): 571. doi:10.1038/nature14099. (link), (pdf)

[J21] Kim, Minseung, Violeta Zorraquino, and Ilias Tagkopoulos. “Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles.” PLoS computational biology 11, no. 3 (2015): e1004127. doi:10.1371/journal.pcbi.1004127
Erratum in: PLoS computational biology (2015): e1004617. (link)

[J20] Tsoukalas, Athanasios, Timothy Albertson, and Ilias 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, no. 1 (2015): e11. doi:10.2196/medinform.3445 (link)

[J19] Huynh, Linh, and Ilias Tagkopoulos. “Optimal part and module selection for synthetic gene circuit design automation.” ACS synthetic biology 3, no. 8 (2014): 556-564. doi:10.1021/sb400139h (link)(pdf)

[J18] Aung, Hnin H., Athanasios Tsoukalas, John C. Rutledge, and Ilias Tagkopoulos. “A systems biology analysis of brain microvascular endothelial cell lipotoxicity.” BMC systems biology 8, no. 1 (2014): 80. doi:10.1186/1752-0509-8-80 (link)

[J17] Cohen, Aaron, James Lucas, Lucas Murray, Sarah Ritz, Simon Staley, Brian Tamsut, Marc Facciotti, Justin Siegel, Ilias Tagkopoulos, and Selena Wang. “Implications of an Enzymatic Biosensor for the Detection of Rancid Olive Oil.” (2014). (pdf)

[J16] Carrera, Javier, Raissa Estrela, Jing Luo, Navneet Rai, Athanasios Tsoukalas, and Ilias Tagkopoulos. “An integrative, multi‐scale, genome‐wide model reveals the phenotypic landscape of Escherichia coli.” Molecular systems biology 10, no. 7 (2014): 735. doi:10.15252/msb.20145108 (link)

[J15] Zorraquino-Salvo, Violeta, Semarhy Quinones-Soto, Minseung Kim, Navneet Rai, and Ilias Tagkopoulos. “Deciphering the genetic and transcriptional basis of cross-stress responses in Escherichia coli under complex evolutionary scenarios.” bioRxiv (2014): 010595. doi:10.1101/010595. (link)

[J14] Pavlogiannis, Andreas, Vadim Mozhayskiy, and Ilias Tagkopoulos. “A flood-based information flow analysis and network minimization method for gene regulatory networks.” BMC bioinformatics 14, no. 1 (2013): 137. doi:10.1186/1471-2105-14-137 (link)

[J13] Gultepe, Eren, Jeffrey P. Green, Hien Nguyen, Jason Adams, Timothy Albertson, and Ilias Tagkopoulos. “From vital signs to clinical outcomes for patients with sepsis: a machine learning basis for a clinical decision support system.” Journal of the American Medical Informatics Association 21, no. 2 (2013): 315-325. doi:10.1136/amiajnl-2013-001815 (link)

[J12] Huynh, Linh, Athanasios Tsoukalas, Matthias Köppe, and Ilias Tagkopoulos. “SBROME: a scalable optimization and module matching framework for automated biosystems design.” ACS synthetic biology 2, no. 5 (2013): 263-273. doi:10.1021/sb300095m (link)(pdf)

[J11] Yao, Andrew I., Timothy A. Fenton, Keegan Owsley, Phillip Seitzer, David J. Larsen, Holly Sit, Jennifer Lau et al. “Promoter element arising from the fusion of standard BioBrick parts.” ACS synthetic biology 2, no. 2 (2013): 111-120. doi:10.1021/sb300114d
Erratum in: ACS synthetic biology (2013):351. (link)(pdf)

[J10] Tagkopoulos, Ilias. “Microbial factories under control: auto-regulatory control through engineered stress-induced feedback.” Bioengineered 4, no. 1 (2013): 5-8. doi:10.4161/bioe.21935 (link)

[J9] Dragosits, Martin, Vadim Mozhayskiy, Semarhy Quinones‐Soto, Jiyeon Park, and Ilias Tagkopoulos. “Evolutionary potential, cross‐stress behavior and the genetic basis of acquired stress resistance in Escherichia coli.” Molecular systems biology 9, no. 1 (2013): 643. doi:10.1038/msb.2012.76 (link)

[J8] Mozhayskiy, Vadim, and Ilias Tagkopoulos. “Microbial evolution in vivo and in silico: methods and applications.” Integrative Biology 5, no. 2 (2012): 262-277. doi:10.1039/c2ib20095c (link)(pdf)

[J7] Liang, Yajun, Heng Wu, Rong Lei, Robert A. Chong, Yong Wei, Xin Lu, Ilias Tagkopoulos et al. “Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis.” Journal of Biological Chemistry 287, no. 40 (2012): 33533-33544. doi:10.1074/jbc.M112.392332 (link)

[J6] Mozhayskiy, Vadim, and Ilias Tagkopoulos. “Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation.” In BMC bioinformatics, vol. 13, no. 10, p. S10. BioMed Central, 2012. doi:10.1186/1471-2105-13-S10-S10 (link)

[J5] Mozhayskiy, Vadim, and Ilias Tagkopoulos. “Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution.” In BMC bioinformatics, vol. 13, no. 10, p. S13. BioMed Central, 2012. doi:10.1186/1471-2105-13-S10-S13 (link)

[J4] Dragosits, Martin, Daniel Nicklas, and Ilias Tagkopoulos. “A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli.” Journal of biological engineering 6, no. 1 (2012): 2. doi:10.1186/1754-1611-6-2 (link)

[J3] Huynh, Linh, John Kececioglu, Matthias Köppe, and Ilias Tagkopoulos. “Automatic design of synthetic gene circuits through mixed integer non-linear programming.” PloS one 7, no. 4 (2012): e35529. doi:10.1371/journal.pone.0035529 (link)

[J2] Tagkopoulos, Ilias, Yir-Chung Liu, and Saeed Tavazoie. “Predictive behavior within microbial genetic networks.” science 320, no. 5881 (2008): 1313-1317. doi:10.1126/science.1154456 (link)(pdf)

[J1] Kung, Sun-Yuan, Man-Wai Mak, and Ilias Tagkopoulos. “Symmetric and asymmetric multi-modality biclustering analysis for microarray data matrix.” Journal of bioinformatics and computational biology 4, no. 02 (2006): 275-298. doi:10.1142/S0219720006002065 (link)(pdf)

[C16] Huynh, Linh, and Ilias Tagkopoulos. ”Parameter inference for gene circuit models”, Proceedings of the 7th International Workshop on Bio-design Automation, IWBDA’15, Seattle, 2015

[C15] Huynh, Linh, Minseung Kim, and Ilias Tagkopoulos. ”Integration of circuit design automation and genome-scale modeling”, Proceedings of the 6th International Workshop on Bio-design Automation, IWBDA’14, Boston, 2014

[C14] Huynh, Linh, and Ilias 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] Gultepe, Eren, Hien Nguyen, Timothy Albertson, and Ilias 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] Huynh, Linh, and Ilias 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] Huynh, Linh, and Ilias 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] Miller, Robert, Vadim Mozhazskiy, Ilias Tagkopoulos, and Kwan-Liu 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] Mozhayskiy, Vadim, Bob Miller, Kwan-Liu Ma, and Ilias 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] Mozhayskiy, V. , and Ilias 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] Huynh, Linh, John Kececioglu, and Ilias 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] Tagkopoulos, Ilias, and Serpanos, D. “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] Tagkopoulos, Ilias. “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] Tagkopoulos, Ilias, Nikolai Slavov, and 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] Kung, S.Y., Man-Wai Mak, and Ilias 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] Tagkopoulos, Ilias, Charles Zukowski, German Cavelier, and Dimitris 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] Zervas, N.D., I. Tagkopoulos, V. Spiliotopoulos, P. Anagnostopoulos, D. Soudris, and 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.

[O16] Tagkopoulos, Ilias. “Petascale Simulations of Complex Biological Behavior in Fluctuating Environments”, 2nd NCSA Blue Waters Symposium for Petascale Science and Beyond, Champaign, IL, May, 2014 (link)

[O15] Kim, M., J. Carrera, L. Huynh, R. Estrela, N. Rai, A. Tsoukalas, and 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 (link)

[O14] Carrera, J., L. Huynh, and 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] Evitts, T., K. Gabric, and I. Tagkopoulos. “Quorum Sensing in Bacteria”, NSF BioMath Module, COMAP, pp. 1-42.

[O12] Mozhayskiy, V., M. Dragosits, and 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] Dragosits, M., et al. “Synthetic biology and evolutionary aspects of internal and external stress for industrial microbiology”, 4th ÖGMBT annual meeting, September 17-19, 2012, Graz, Austria.

[O10] Tagkopoulos, Ilias. “Cross-stress protection in bacteria: an evolutionary perspective”, Department of Microbiology and Environmental Toxicology, UCSC, 2013 (link)

[O9] Pavlogiannis, A., V. Mozhayskiy, and 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] Mozhayskiy, V., M. Dragosits, and I. Tagkopoulos. “Guided step-wise adaptation of microbial populations”, 7th Annual Systems-to-Synthesis Symposium, San Diego, CA, 2012.

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

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

[O5] Huynh, L., J. Kececioglu, and 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] Mozhayskiy, V., and 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] Mozhayskiy, V., and 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] Mozhayskiy, V., and 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] Mozhayskiy, V., and I. Tagkopoulos. “Simulations of Microbial Evolution in Fluctuating Environments”, Poster, 18th Annual International Conference on Intelligent Systems for Molecular Biology, ISMB’10, Boston, 2010.Ow