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Ilias Tagkopoulos

From EverybodyWiki Bios & Wiki




Ilias Tagkopoulos (born 1979) is a Greek computer scientist and systems biologist. He is a Professor of Computer Science and a faculty member at the Genome Center at the University of California, Davis. He is also the Director of the Artificial Intelligence Institute for Next Generation Food Systems (AIFS), a research initiative funded by the United States Department of Agriculture (USDA) and the National Science Foundation (NSF). His research focuses on the application of artificial intelligence (AI) and machine learning in biology, food systems, and health.

Early life and education

Tagkopoulos was born in Kavala, Greece, and completed high school in Reutlingen, Germany. He began his undergraduate studies at RWTH Aachen in 1998 and graduated from the University of Patras in 2001 with a Diploma in Electrical and Computer Engineering.

He received a Master of Science in Electrical Engineering from Columbia University in 2003 and earned a Ph.D. in Electrical Engineering from Princeton University in 2008. His doctoral research contributed to the discovery of anticipatory behavior in microbes, which was published in Science.[1]

Academic career

Following his Ph.D., Tagkopoulos worked in the financial industry as a relationship manager for fixed income derivatives at Credit Suisse. In 2009, he joined the University of California, Davis, as a faculty member in the Department of Computer Science. He was promoted to full professor in 2019.

His lab develops computational methods and experimental tools to integrate multi-omics data for predictive modeling, diagnostics, and biological design.[2] He has published over 100 peer-reviewed articles.[3] In 2025, his work was featured in the MIT Technology Review Insights report on artificial intelligence in computational biology.[4]

Awards and honors

  • NSF CAREER Award (2013–2018)[5]
  • Advisor, IGEM World Championship Grand Prize Winner (2014–2015)[6]
  • Burroughs Wellcome Fellowship, Princeton (2004–2006)[1]

Selected publications

  • Kim KJ, Moon SJ, Park KS, Tagkopoulos I. Network-based modeling of drug effects on disease module in systemic sclerosis [published correction appears in Sci Rep. 2021 Apr 9;11(1):8238. doi: 10.1038/s41598-021-87277-w.]. Sci Rep. 2020;10(1):13393. Published 2020 Aug 7. doi:10.1038/s41598-020-70280-y[7]
  • Cui Y, Riley M, Moreno MV, et al. Discovery of Potent Glycosidases Enables Quantification of Smoke-Derived Phenolic Glycosides through Enzymatic Hydrolysis. J Agric Food Chem. 2024;72(20):11617-11628. doi:10.1021/acs.jafc.4c01247[8]
  • Eetemadi A, Tagkopoulos I. Genetic Neural Networks: an artificial neural network architecture for capturing gene expression relationships. Bioinformatics. 2019;35(13):2226-2234. doi:10.1093/bioinformatics/bty945[9]
  • Freund GS, O'Brien TE, Vinson L, et al. Elucidating Substrate Promiscuity within the FabI Enzyme Family. ACS Chem Biol. 2017;12(9):2465-2473. doi:10.1021/acschembio.7b00400[10]
  • Rollins ZA, Huang J, Tagkopoulos I, Faller R, George SC. A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics. Comput Struct Biotechnol J. 2022;20:3473-3481. Published 2022 Jun 25. doi:10.1016/j.csbj.2022.06.048[11]
  • Kim KJ, Tagkopoulos I. Application of machine learning in rheumatic disease research. Korean J Intern Med. 2019;34(4):708-722. doi:10.3904/kjim.2018.349[12]
  • Gunning M, Tagkopoulos I. A systematic review of data and models for predicting food flavor and texture. Curr Res Food Sci. 2025;11:101127. doi:10.1016/j.crfs.2025.101127[13]
  • Wang X, Rai N, Merchel Piovesan Pereira B, Eetemadi A, Tagkopoulos I. Accelerated knowledge discovery from omics data by optimal experimental design. Nat Commun. 2020;11(1):5026. Published 2020 Oct 6. doi:10.1038/s41467-020-18785-y[14]
  • Taylor-Teeples M, Lin L, de Lucas M, et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature. 2015;517(7536):571-575. doi:10.1038/nature14099[15]
  • Aboud O, Liu Y, Dahabiyeh L, et al. Profile Characterization of Biogenic Amines in Glioblastoma Patients Undergoing Standard-of-Care Treatment. Biomedicines. 2023;11(8):2261. Published 2023 Aug 13. doi:10.3390/biomedicines11082261[16]
  • Yoo A, Li F, Youn J, et al. Prediction of adolescent depression from prenatal and childhood data from ALSPAC using machine learning. Sci Rep. 2024;14(1):23282. Published 2024 Oct 7. doi:10.1038/s41598-024-72158-9[17]
  • Eetemadi A, Rai N, Pereira BMP, Kim M, Schmitz H, Tagkopoulos I. The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health. Front Microbiol. 2020;11:393. Published 2020 Apr 3. doi:10.3389/fmicb.2020.00393[18]
  • Furuya, H., Nguyen, C.T., Chan, T., Marusina, A.I., Merleev, A.A., de la Luz Garcia Hernandez, M., Hsieh, S.L., Tsokos, G.C., Ritchlin, C.T., Tagkopoulos, I. and Maverakis, E., 2024. IL-23 induces CLEC5A+ IL-17A+ neutrophils and elicit skin inflammation associated with psoriatic arthritis. Journal of Autoimmunity, 143, p.103167.[19]
  • Naravane T., and Tagkopoulos I. ”Machine learning models to predict micronutrient profile in food after processing.” Current Research in Food Science 6 (2023): 100500.[20]
  • Youn, J., Navneet R., Tagkopoulos I. Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. Nature Communications (2022). doi: 10.1038/s41467-022-29993-z.[21]
  • Rai, N., Kim M., Tagkopoulos I. Understanding the formation and mechanism of anticipatory responses in Escherichia coli. International Journal of Molecular Sciences (2022). doi: 10.3390/ijms23115985.[22]
  • 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. PMID: 27713404; PMCID: PMC5059772.[2]
  • Tagkopoulos I., Liu Y., Tavazoie S. Predictive behavior within microbial genetic networks. Science. 2008;320(5881):1313-1317. doi:10.1126/science.1154456.[1]

References

  1. ↑ 1.0 1.1 1.2 Tagkopoulos, Ilias; Liu, Yiannis; Tavazoie, Saeed (2008). "Predictive behavior within microbial genetic networks". Science. 320 (5881): 1313–1317. Bibcode:2008Sci...320.1313T. doi:10.1126/science.1154456. PMC 2931280. PMID 18535241.
  2. ↑ 2.0 2.1 Kim, Minseung (October 7, 2016). "Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli". Nature Communications. 7. Bibcode:2016NatCo...713090K. doi:10.1038/ncomms13090. PMC 5059772. PMID 27713404. Unknown parameter |article-number= ignored (help)
  3. ↑ "Google Scholar". scholar.google.com. Retrieved 2025-07-09.
  4. ↑ "Powering the food industry with AI". MIT Technology Review. Retrieved 2025-07-09.
  5. ↑ Fell, Andy (April 1, 2013). "Four wn prestigious CAREER awards". Retrieved April 6, 2025.
  6. ↑ Bang, Derrick (December 9, 2014). "UC Davis Students Win Grand Prize at 2014 iGEM Competition". Retrieved April 1, 2025.
  7. ↑ Kim, Ki-Jo; Moon, Su-Jin; Park, Kyung-Su; Tagkopoulos, Ilias (2020-08-07). "Network-based modeling of drug effects on disease module in systemic sclerosis". Scientific Reports. 10 (1): 13393. doi:10.1038/s41598-020-70280-y. ISSN 2045-2322. PMC 7414841 Check |pmc= value (help). PMID 32770109 Check |pmid= value (help).
  8. ↑ Cui, Youtian; Riley, Mary; Moreno, Marcus V.; Cepeda, Mateo M.; Perez, Ignacio Arias; Wen, Yan; Lim, Lik Xian; Andre, Eric; Nguyen, An; Liu, Cody; Lerno, Larry; Nichols, Patrick K.; Schmitz, Harold; Tagkopoulos, Ilias; Kennedy, James A. (2024-05-22). "Discovery of Potent Glycosidases Enables Quantification of Smoke-Derived Phenolic Glycosides through Enzymatic Hydrolysis". Journal of Agricultural and Food Chemistry. 72 (20): 11617–11628. doi:10.1021/acs.jafc.4c01247. ISSN 1520-5118. PMC 11117406 Check |pmc= value (help). PMID 38728580 Check |pmid= value (help).
  9. ↑ Eetemadi, Ameen; Tagkopoulos, Ilias (2019-07-01). "Genetic Neural Networks: an artificial neural network architecture for capturing gene expression relationships". Bioinformatics (Oxford, England). 35 (13): 2226–2234. doi:10.1093/bioinformatics/bty945. ISSN 1367-4811. PMID 30452523.
  10. ↑ Freund, Gabriel S.; O'Brien, Terrence E.; Vinson, Logan; Carlin, Dylan Alexander; Yao, Andrew; Mak, Wai Shun; Tagkopoulos, Ilias; Facciotti, Marc T.; Tantillo, Dean J.; Siegel, Justin B. (2017-09-15). "Elucidating Substrate Promiscuity within the FabI Enzyme Family". ACS Chemical Biology. 12 (9): 2465–2473. doi:10.1021/acschembio.7b00400. ISSN 1554-8937. PMID 28820936.
  11. ↑ Rollins, Zachary A.; Huang, Jun; Tagkopoulos, Ilias; Faller, Roland; George, Steven C. (2022). "A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics". Computational and Structural Biotechnology Journal. 20: 3473–3481. doi:10.1016/j.csbj.2022.06.048. ISSN 2001-0370. PMC 9278023 Check |pmc= value (help). PMID 35860406 Check |pmid= value (help).
  12. ↑ Kim, Ki-Jo; Tagkopoulos, Ilias (2018-12-31). "Application of machine learning in rheumatic disease research". The Korean Journal of Internal Medicine. 34 (4): 708–722. doi:10.3904/kjim.2018.349. ISSN 2005-6648. PMC 6610179 Check |pmc= value (help). PMID 30616329.
  13. ↑ Gunning, Michael; Tagkopoulos, Ilias (2025-01-01). "A systematic review of data and models for predicting food flavor and texture". Current Research in Food Science. 11. doi:10.1016/j.crfs.2025.101127. ISSN 2665-9271. Unknown parameter |article-number= ignored (help)
  14. ↑ Wang, Xiaokang; Rai, Navneet; Merchel Piovesan Pereira, Beatriz; Eetemadi, Ameen; Tagkopoulos, Ilias (2020-10-06). "Accelerated knowledge discovery from omics data by optimal experimental design". Nature Communications. 11 (1): 5026. Bibcode:2020NatCo..11.5026W. doi:10.1038/s41467-020-18785-y. ISSN 2041-1723. PMID 33024104 Check |pmid= value (help).
  15. ↑ Taylor-Teeples, M.; Lin, L.; de Lucas, M.; Turco, G.; Toal, T. W.; Gaudinier, A.; Young, N. F.; Trabucco, G. M.; Veling, M. T.; Lamothe, R.; Handakumbura, P. P.; Xiong, G.; Wang, C.; Corwin, J.; Tsoukalas, A. (2015-01-29). "An Arabidopsis gene regulatory network for secondary cell wall synthesis". Nature. 517 (7536): 571–575. Bibcode:2015Natur.517..571T. doi:10.1038/nature14099. ISSN 1476-4687. PMC 4333722. PMID 25533953.
  16. ↑ Aboud, Orwa; Liu, Yin; Dahabiyeh, Lina; Abuaisheh, Ahmad; Li, Fangzhou; Aboubechara, John Paul; Riess, Jonathan; Bloch, Orin; Hodeify, Rawad; Tagkopoulos, Ilias; Fiehn, Oliver (2023-08-13). "Profile Characterization of Biogenic Amines in Glioblastoma Patients Undergoing Standard-of-Care Treatment". Biomedicines. 11 (8): 2261. doi:10.3390/biomedicines11082261. ISSN 2227-9059. PMC 10452138 Check |pmc= value (help). PMID 37626757 Check |pmid= value (help).
  17. ↑ Yoo, Arielle; Li, Fangzhou; Youn, Jason; Guan, Joanna; Guyer, Amanda E.; Hostinar, Camelia E.; Tagkopoulos, Ilias (2024-10-07). "Prediction of adolescent depression from prenatal and childhood data from ALSPAC using machine learning". Scientific Reports. 14 (1): 23282. Bibcode:2024NatSR..1423282Y. doi:10.1038/s41598-024-72158-9. ISSN 2045-2322. PMC 11458604 Check |pmc= value (help). PMID 39375420 Check |pmid= value (help).
  18. ↑ Eetemadi, Ameen; Rai, Navneet; Pereira, Beatriz Merchel Piovesan; Kim, Minseung; Schmitz, Harold; Tagkopoulos, Ilias (2020-04-03). "The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health". Frontiers in Microbiology. 11. doi:10.3389/fmicb.2020.00393. ISSN 1664-302X.
  19. ↑ Furuya, Hiroki (February 1, 2024). "IL-23 induces CLEC5A+ IL-17A+ neutrophils and elicit skin inflammation associated with psoriatic arthritis". Journal of Autoimmunity. 143. doi:10.1016/j.jaut.2024.103167. PMC 10981569 Check |pmc= value (help). PMID 38301504 Check |pmid= value (help). Unknown parameter |article-number= ignored (help)
  20. ↑ Naravane, Tarini; Tagkopoulos, Ilias (June 1, 2023). "Machine learning models to predict micronutrient profile in food after processing". Current Research in Food Science. 6 (100500). doi:10.1016/j.crfs.2023.100500. PMC 10160345 Check |pmc= value (help). PMID 37151381 Check |pmid= value (help). Unknown parameter |article-number= ignored (help)
  21. ↑ Jason, Youn; Rai, Navneet; Tagkopoulos, Ilias (April 29, 2022). "Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes". Nature Communications. 13 (1): 2360. Bibcode:2022NatCo..13.2360Y. doi:10.1038/s41467-022-29993-z. PMC 9055065 Check |pmc= value (help). PMID 35487919 Check |pmid= value (help).
  22. ↑ Rai, Navneet; Kim, Minseung; Tagkopoulos, Ilias (May 26, 2022). "Understanding the Formation and Mechanism of Anticipatory Responses in Escherichia coli". International Journal of Molecular Sciences. 23 (11): 5985. doi:10.3390/ijms23115985. PMC 9181292 Check |pmc= value (help). PMID 35682665 Check |pmid= value (help).



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