Publications

[J68] Aboud, Orwa, Yin Liu, Lina Dahabiyeh, Ahmad Abuaisheh, Fangzhou Li, John Paul Aboubechara, Jonathan Riess, Orin Bloch Rawad Hodeify, Ilias Tagkopoulos, and Oliver Fiehn. “Profile Characterization of Biogenic Amines in Glioblastoma Patients Undergoing Standard-of-Care Treatment.” Biomedicines (2023). doi: 10.3390/biomedicines11082261 (link)

[J67] Naravane, Tarini, and Ilias Tagkopoulos. “Machine learning models to predict micronutrient profile in food after processing.” Current Research in Food Science (2023): 100500. doi: 10.1016/j.crfs.2023.100500 (link), (GitHub coming soon)

[J66] Chan, Trevor, Cheng-En Tan, and Ilias Tagkopoulos. “Audit lead selection and yield prediction from historical tax data using artificial neural networks.” PLOS One (2022). doi: 10.1371/journal.pone.0278121 (link), (pdf), (GitHub)

[J65] Holt, Roberta R., Daniela Barile, Selina C. Wang, John P. Munafo Jr, Torey Arvik, Xueqi Li, Fanny Lee, Carl L. Keen, Ilias Tagkopoulos, and Harold H. Schmitz. “Chardonnay Marc as a New Model for Upcycled Co-products in the Food Industry: Concentration of Diverse Natural Products Chemistry for Consumer Health and Sensory Benefits.” Journal of Agricultural and Food Chemistry (2022) doi: 10.1021/acs.jafc.2c04519 (link), (pdf)

[J64] Eetemadi, Ameen, Ilias Tagkopoulos. “Algorithmic lifestyle optimization.” Journal of the American Medical Informatics Association (2022). doi: 10.1093/jamia/ocac186 (link), (pdf), (GitHub coming soon)

[J63] Kokkinos, Yiannis, JoAnn Morrison, Richard Bradley, Theodoros Panagiotakos, Jennifer Ogeer, Dennis Chew, Ciaran O’Flynn, Geert De Meyer, Phillip Watson, Ilias Tagkopoulos. “An early prediction model for canine chronic kidney disease based on routine clinical laboratory tests.” Scientific Reports (2022). doi: s41598-022-18793-6 (link)

[J62] Rollins, Zachary A., Jun Huang, Ilias Tagkopoulos, Roland Faller, Steven C. George. “A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics.” Computational and Structural Biotechnology Journal (2022). doi: 10.1016/j.csbj.2022.06.048 (link)

[J61] Rai, Navneet, Minseung Kim, Ilias Tagkopoulos. “Understanding the formation and mechanism of anticipatory responses in Escherichia coli.” International Journal of Molecular Sciences (2022). doi: 10.3390/ijms23115985 (link)

[J60] Youn, Jason, Navneet Rai, Ilias Tagkopoulos. “Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes.” Nature Communications (2022). doi: 10.1038/s41467-022-29993-z (link), (GitHub)

[J59] Tagkopoulos, Ilias, Stephen F Brown, Xin Liu, Qing Zhao, Tarek I Zohdi, J Mason Earles, Nitin Nitin, Daniel E Runcie, Danielle G Lemay, Aaron D Smith, Pamela C Ronald, Hao Feng, Gabriel David Youtsey. “Special report: AI Institute for next generation food systems (AIFS).” Computers and Electronics in Agriculture (2022). doi: 10.1016/j.compag.2022.106819 (link)

[J58] Lee, Bo Mi, Ameen Eetemadi, Ilias Tagkopoulos. “Reduced graphene oxide-metalloporphyrin sensors for human breath screening.” Applied Sciences (2021). doi: 10.3390/app112311290 (link)

[J57] Matson, Morgan M., Mateo M. Cepeda, Angela Zhang, Anna E. Case, Erol S. Kavvas, Xiaokang Wang, Austin L. Carroll, Ilias Tagkopoulos, Shota Atsumi. “Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli.” Metabolic Engineering (2021). doi: 10.1016/j.ymben.2021.11.002 (link), (GitHub)

[J56] de Oliveira, Eduardo Barros, Fernanda Ferreira, Klibs Galvao, Jason Youn, Ilias Tagkopoulos, Noelia Silva-del-Rio, Richard Van Vleck Pereira, Vinicius Machado, Fabio Lima. “Integration of statistical inferences and machine learning algorithms for prediction of metritis cure in dairy cows.” Journal of Dairy Science (2021). doi: 10.3168/jds.2021-20262 (link), (GitHub)

[J55] Pereira, Beatriz Merchel Piovesan, Muhammad Adil Salim, Navneet Rai, Ilias Tagkopoulos. “Tolerance to glutaraldehyde in Escherichia coli mediated by overexpression of the aldehyde reductase YqhD by YqhC.” Frontiers in Microbiology (2021). doi: 10.3389/fmicb.2021.680553 (link)

[J54] Kim, Ki-Jo, Su-Jin Moon, Kyung-Su Park, Ilias Tagkopoulos. “Network‑based modeling of drug effects on disease module in systemic sclerosis.” Scientific Reports (2021). doi: 10.1038/s41598-020-70280-y (link), (pdf)

[J53] Pereira, Beatriz Merchel Piovesan, Xiaokang Wang, Ilias Tagkopoulos. “Biocide-induced emergence of antibiotic resistance in Escherichia coli.” Frontiers in Microbiology (2021). doi: 10.3389/fmicb.2021.640923 (link), (pdf), (GitHub)

[J52] Eetemadi, Ameen, Ilias Tagkopoulos. “Methane and fatty acid metabolism pathways are predictive of Low-FODMAP diet efficacy for patients with irritable bowel syndrome.” Clinical Nutrition (2021). doi: 10.1016/j.clnu.2020.12.041 (link), (pdf), (GitHub)

[J51] Risner, Derrick, Fangzhou Li, Jason Fell, Sara Pace, Ilias Tagkopoulos, Justin Siegel, Edward Spang. “Preliminary techno-economic assessment of animal cell-based meat.” Foods (2021). doi: 10.1101/2020.09.10.292144 (link), (GitHub)

[J50] Youn, Jason, Tarini Naravane, Ilias Tagkopoulos. “Using word embeddings to learn a better food ontology.” Frontiers in Artificial Intelligence (2020). doi: 10.3389/frai.2020.584784 (link), (GitHub)

[J49] Mak, Wai Shun, Xiaokang Wang, Rigoberto Arenas, Youtian Cui, Steve J Bertolani, Wen Qiao Deng, Ilias Tagkopoulos, David K Wilson, Justin B Siegel. “Discovery, design, and structural characterization of alkane producing enzymes across the ferritin-like superfamily.” Biochemistry (2020). doi: 10.1021/acs.biochem.0c00665 (link), (pdf)

[J48] Joo, Young Bin, In-Woon Baek, Kyung-Su Park, Ilias Tagkopoulos, Ki-Jo Kim. “Novel classification of axial spondyloarthritis to predict radiographic progression using machine learning.” Clinical and Experimental Rheumatology (2020). [Online ahead of print] (link), (pdf)

[J47] Wang, Xiaokang, Navneet Rai, Beatriz Merchel Piovesan Pereira, Ameen Eetemadi, Ilias Tagkopoulos. “Accelerated knowledge discovery from omics data by optimal experimental design.” Nature Communications (2020). doi: 10.1038/s41467-020-18785-y (link), (GitHub)

[J46] Pereira, Beatriz Merchel Piovesan, Xiaokang Wang, Ilias Tagkopoulos. “Short- and long-term transcriptomic responses of Escherichia coli to biocides: a systems analysis.” Applied and Environmental Microbiology (2020). doi: 10.1128/AEM.00708-20 (link)

[J45] Eetemadi, Ameen, Navneet Rai, Beatriz Merchel Piovesan Pereira, Minseung Kim, Harold Schmitz, 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)

[J44] Bradley, Richard, Ilias Tagkopoulos, Minseung Kim, Yiannis Kokkinos, Theodoros Panagiotakos, James Kennedy, Geert De Meyer, Phillip Watson, Jonathan Elliott. “Predicting early risk of chronic kidney disease in cats using routine clinical laboratory tests and machine learning.” Journal of veterinary internal medicine (2019). doi:10.1111/jvim.15623 (link)

[J43] Elizabeth Chin, Gabriel Simmons, Yasmine Bouzid, Annie Kan, Dustin Burnett, Ilias Tagkopoulos,  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), (GitHub)

[J42] Pereira, Beatriz Merchel Piovesan, 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, 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, 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, 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), (GitHub)

[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), (pdf), (GitHub)

[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), (GitHub), (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), (GitHub), (Ecomics portal)

[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.” Nature 517, 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), (GitHub)

[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)