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ilias tagkopoulos - Publications

Affiliations: 
Princeton University, Princeton, NJ 
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21/77 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Mak WS, Wang X, Arenas R, Cui Y, Bertolani SJ, Deng WQ, Tagkopoulos I, Wilson DK, Siegel JB. Discovery, Design, and Structural Characterization of Alkane Producing Enzymes across the Ferritin-like Superfamily. Biochemistry. PMID 32935984 DOI: 10.1021/Acs.Biochem.0C00665  0.326
2020 Merchel Piovesan Pereira B, Wang X, Tagkopoulos I. A systems analysis of short and long-term transcriptomic response to biocides. Applied and Environmental Microbiology. PMID 32385082 DOI: 10.1128/AEM.00708-20  0.316
2019 Kim KJ, Kim M, Adamopoulos I, Tagkopoulos I. Compendium of synovial signatures identifies pathologic characteristics for predicting treatment response in rheumatoid arthritis patients. Clinical Immunology (Orlando, Fla.). PMID 30831253 DOI: 10.1016/j.clim.2019.03.002  0.313
2018 Rai N, Huynh L, Kim M, Tagkopoulos I. Population collapse and adaptive rescue during long-term chemostat fermentation. Biotechnology and Bioengineering. PMID 30536368 DOI: 10.1002/bit.26898  0.327
2018 Eetemadi A, Tagkopoulos I. Genetic Neural Networks: An artificial neural network architecture for capturing gene expression relationships. Bioinformatics (Oxford, England). PMID 30452523 DOI: 10.1093/bioinformatics/bty945  0.386
2017 Bjornson M, Balcke GU, Xiao Y, de Souza A, Wang JZ, Zhabinskaya D, Tagkopoulos I, Tissier A, Dehesh K. Integrated omics analyses of retrograde signaling mutant delineate interrelated stress response strata. The Plant Journal : For Cell and Molecular Biology. PMID 28370892 DOI: 10.1111/Tpj.13547  0.327
2016 Kim M, Rai N, Zorraquino V, Tagkopoulos I. Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. Nature Communications. 7: 13090. PMID 27713404 DOI: 10.1038/ncomms13090  0.361
2016 Huynh L, Tagkopoulos I. A Parts Database with Consensus Parameter Estimation for Synthetic Circuit Design. Acs Synthetic Biology. PMID 27454439 DOI: 10.1021/acssynbio.5b00205  0.302
2015 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. Scientific Reports. 5: 10658. PMID 26023068 DOI: 10.1038/Srep10658  0.329
2015 Kim M, Zorraquino V, Tagkopoulos I. Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles. Plos Computational Biology. 11: e1004127. PMID 25774498 DOI: 10.1371/journal.pcbi.1004127  0.378
2015 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, ... ... Tagkopoulos I, et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature. 517: 571-5. PMID 25533953 DOI: 10.1038/Nature14099  0.354
2014 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. Molecular Systems Biology. 10: 735. PMID 24987114 DOI: 10.15252/msb.20145108  0.395
2013 Pavlogiannis A, Mozhayskiy V, Tagkopoulos I. A flood-based information flow analysis and network minimization method for gene regulatory networks. Bmc Bioinformatics. 14: 137. PMID 23617932 DOI: 10.1186/1471-2105-14-137  0.355
2013 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. Molecular Systems Biology. 9: 643. PMID 23385483 DOI: 10.1038/Msb.2012.76  0.304
2012 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. The Journal of Biological Chemistry. 287: 33533-44. PMID 22875853 DOI: 10.1074/Jbc.M112.392332  0.495
2012 Mozhayskiy V, Tagkopoulos I. Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution. Bmc Bioinformatics. 13: S13. PMID 22759418 DOI: 10.1186/1471-2105-13-S10-S13  0.351
2012 Huynh L, Kececioglu J, Köppe M, Tagkopoulos I. Automatic design of synthetic gene circuits through mixed integer non-linear programming. Plos One. 7: e35529. PMID 22536398 DOI: 10.1371/Journal.Pone.0035529  0.321
2008 Tagkopoulos I, Liu YC, Tavazoie S. Predictive behavior within microbial genetic networks. Science (New York, N.Y.). 320: 1313-7. PMID 18467556 DOI: 10.3731/Topologica.2.018  0.581
2006 Kung SY, Mak MW, Tagkopoulos I. Symmetric and asymmetric multi-modality biclustering analysis for microarray data matrix. Journal of Bioinformatics and Computational Biology. 4: 275-98. PMID 16819784 DOI: 10.1142/S0219720006002065  0.553
2005 Kung SY, Mak MW, Tagkopoulos I. Multi-metric and multi-substructure biclustering analysis for gene expression data. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 123-34. PMID 16447970 DOI: 10.1109/CSB.2005.40  0.5
2005 Tagkopoulos I, Slavov N, Kung SY. Multi-class biclustering and classification based or modeling of gene regulatory networks Proceedings - Bibe 2005: 5th Ieee Symposium On Bioinformatics and Bioengineering. 2005: 89-96. DOI: 10.1109/BIBE.2005.40  0.487
Low-probability matches (unlikely to be authored by this person)
2013 Mozhayskiy V, Tagkopoulos I. Microbial evolution in vivo and in silico: methods and applications. Integrative Biology : Quantitative Biosciences From Nano to Macro. 5: 262-77. PMID 23096365 DOI: 10.1039/C2Ib20095C  0.297
2017 Kim M, Eetemadi A, Tagkopoulos I. DeepPep: Deep proteome inference from peptide profiles. Plos Computational Biology. 13: e1005661. PMID 28873403 DOI: 10.1371/journal.pcbi.1005661  0.297
2016 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, et al. Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants. Plos One. 11: e0147596. PMID 26815142 DOI: 10.1371/Journal.Pone.0147596  0.297
2016 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. Molecular Biology and Evolution. PMID 28007978 DOI: 10.1093/molbev/msw269  0.296
2015 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 Medical Informatics. 3: e11. PMID 25710907 DOI: 10.2196/medinform.3445  0.295
2018 Kim KJ, Tagkopoulos I. Application of machine learning in rheumatic disease research. The Korean Journal of Internal Medicine. PMID 30616329 DOI: 10.3904/kjim.2018.349  0.293
2014 Huynh L, Tagkopoulos I. Optimal part and module selection for synthetic gene circuit design automation. Acs Synthetic Biology. 3: 556-64. PMID 24933033 DOI: 10.1021/sb400139h  0.291
2018 Wang X, Zorraquino V, Kim M, Tsoukalas A, Tagkopoulos I. Predicting the evolution of Escherichia coli by a data-driven approach. Nature Communications. 9: 3562. PMID 30177705 DOI: 10.1038/s41467-018-05807-z  0.29
2013 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 Synthetic Biology. 2: 111-20. PMID 23656374 DOI: 10.1021/Sb300114D  0.289
2013 Huynh L, Tsoukalas A, Köppe M, Tagkopoulos I. SBROME: a scalable optimization and module matching framework for automated biosystems design. Acs Synthetic Biology. 2: 263-73. PMID 23654271 DOI: 10.1021/Sb300095M  0.287
2012 Mozhayskiy V, Tagkopoulos I. Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation. Bmc Bioinformatics. 13: S10. PMID 22759415 DOI: 10.1186/1471-2105-13-S10-S10  0.287
2015 Huynh L, Tagkopoulos I. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching. Acs Synthetic Biology. 4: 890-7. PMID 25916918 DOI: 10.1021/sb500339k  0.284
2013 Tagkopoulos I. Microbial factories under control: auto-regulatory control through engineered stress-induced feedback. Bioengineered. 4: 5-8. PMID 22922761 DOI: 10.4161/bioe.21935  0.283
2012 Dragosits M, Nicklas D, Tagkopoulos I. A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli. Journal of Biological Engineering. 6: 2. PMID 22463687 DOI: 10.1186/1754-1611-6-2  0.276
2016 Meisner MH, Rosenheim JA, Tagkopoulos I, Peters DPC. A data-driven, machine learning framework for optimal pest management in cotton Ecosphere. 7. DOI: 10.1002/ecs2.1263  0.273
2019 Merchel Piovesan Pereira B, Tagkopoulos I. Benzalkonium chlorides: Uses, regulatory status, and microbial resistance. Applied and Environmental Microbiology. PMID 31028024 DOI: 10.1128/AEM.00377-19  0.27
2019 Bradley R, Tagkopoulos I, Kim M, Kokkinos Y, Panagiotakos T, Kennedy J, De Meyer G, Watson P, Elliott J. Predicting early risk of chronic kidney disease in cats using routine clinical laboratory tests and machine learning. Journal of Veterinary Internal Medicine. PMID 31557361 DOI: 10.1111/jvim.15623  0.269
2020 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. Frontiers in Microbiology. 11: 393. PMID 32318028 DOI: 10.3389/fmicb.2020.00393  0.266
2019 Moon SJ, Bae JM, Park KS, Tagkopoulos I, Kim KJ. Compendium of skin molecular signatures identifies key pathological features associated with fibrosis in systemic sclerosis. Annals of the Rheumatic Diseases. PMID 30952646 DOI: 10.1136/annrheumdis-2018-214778  0.258
2019 Chin EL, Simmons G, Bouzid YY, Kan A, Burnett DJ, Tagkopoulos I, Lemay DG. Nutrient Estimation from 24-Hour Food Recalls Using Machine Learning and Database Mapping: A Case Study with Lactose. Nutrients. 11. PMID 31847188 DOI: 10.3390/nu11123045  0.254
2014 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. Journal of the American Medical Informatics Association : Jamia. 21: 315-25. PMID 23959843 DOI: 10.1136/amiajnl-2013-001815  0.247
2005 Tagkopoulos I, Serpanos D. Gene classification and regulatory prediction based on transcriptional modeling Proceedings of the Fifth Ieee International Symposium On Signal Processing and Information Technology. 2005: 29-34. DOI: 10.1109/ISSPIT.2005.1577065  0.242
2020 Wang X, Rai N, Merchel Piovesan Pereira B, Eetemadi A, Tagkopoulos I. Accelerated knowledge discovery from omics data by optimal experimental design. Nature Communications. 11: 5026. PMID 33024104 DOI: 10.1038/s41467-020-18785-y  0.238
2017 Freund GS, O'Brien TE, Vinson L, Carlin DA, Yao A, Mak WS, Tagkopoulos I, Facciotti MT, Tantillo DJ, Siegel JB. Elucidating Substrate Promiscuity within the FabI Enzyme Family. Acs Chemical Biology. PMID 28820936 DOI: 10.1021/Acschembio.7B00400  0.237
2018 Kim M, Tagkopoulos I. Data integration and predictive modeling methods for multi-omics datasets. Molecular Omics. 14: 8-25. PMID 29725673 DOI: 10.1039/c7mo00051k  0.21
2003 Tagkopoulos I, Zukowski C, Cavelier G, Anastassiou D. A custom FPGA for the simulation of gene regulatory networks Proceedings of the Ieee Great Lakes Symposium On Vlsi. 132-135.  0.205
2013 Yao AI, Fenton TA, Owsley K, Seitzer P, Larsen DJ, Sit H, Lau J, Nair A, Tantiongloc J, Tagkopoulos I, Facciotti MT. Correction to Promoter Element Arising from the Fusion of Standard BioBrick Parts Acs Synthetic Biology. 2: 351-351. DOI: 10.1021/Sb400031E  0.202
2022 Chan T, Tan CE, Tagkopoulos I. Audit lead selection and yield prediction from historical tax data using artificial neural networks. Plos One. 17: e0278121. PMID 36449508 DOI: 10.1371/journal.pone.0278121  0.201
2014 Aung HH, Tsoukalas A, Rutledge JC, Tagkopoulos I. A systems biology analysis of brain microvascular endothelial cell lipotoxicity. Bmc Systems Biology. 8: 80. PMID 24993133 DOI: 10.1186/1752-0509-8-80  0.2
2022 Kokkinos Y, Morrison J, Bradley R, Panagiotakos T, Ogeer J, Chew D, O'Flynn C, De Meyer G, Watson P, Tagkopoulos I. An early prediction model for canine chronic kidney disease based on routine clinical laboratory tests. Scientific Reports. 12: 14489. PMID 36008537 DOI: 10.1038/s41598-022-18793-6  0.193
2021 Merchel Piovesan Pereira B, Adil Salim M, Rai N, Tagkopoulos I. Tolerance to Glutaraldehyde in Mediated by Overexpression of the Aldehyde Reductase YqhD by YqhC. Frontiers in Microbiology. 12: 680553. PMID 34248896 DOI: 10.3389/fmicb.2021.680553  0.187
2012 Hunyh L, Tagkopoulos I. A robust, library-based, optimization-driven method for automatic gene circuit design 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182639  0.182
2022 Youn J, Rai N, Tagkopoulos I. Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. Nature Communications. 13: 2360. PMID 35487919 DOI: 10.1038/s41467-022-29993-z  0.175
2011 Mozhayskiy V, Tagkopoulos I. In silico evolution of multi-scale microbial systems in the presence of mobile genetic elements and horizontal gene transfer Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6674: 262-273. DOI: 10.1007/978-3-642-21260-4_26  0.172
2020 Joo YB, Baek IW, Park KS, Tagkopoulos I, Kim KJ. Novel classification of axial spondyloarthritis to predict radiographic progression using machine learning. Clinical and Experimental Rheumatology. PMID 32662400  0.169
2022 Rai N, Kim M, Tagkopoulos I. Understanding the Formation and Mechanism of Anticipatory Responses in . International Journal of Molecular Sciences. 23. PMID 35682665 DOI: 10.3390/ijms23115985  0.163
2020 Simmons G, Lee F, Kim M, Holt R, Tagkopoulos I. Identification of Differential, Health-Related Compounds in Chardonnay Marc through Network-Based Meta-Analysis Current Developments in Nutrition. 4: 475-475. DOI: 10.1093/cdn/nzaa045_108  0.157
2005 Tagkopoulos I. A transcriptional approach to gene clustering Proceedings of the 2005 Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology, Cibcb '05. 2005.  0.147
2023 Naravane T, Tagkopoulos I. Machine learning models to predict micronutrient profile in food after processing. Current Research in Food Science. 6: 100500. PMID 37151381 DOI: 10.1016/j.crfs.2023.100500  0.137
2021 Matson MM, Cepeda MM, Zhang A, Case AE, Kavvas ES, Wang X, Carroll AL, Tagkopoulos I, Atsumi S. Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli. Metabolic Engineering. 69: 50-58. PMID 34763090 DOI: 10.1016/j.ymben.2021.11.002  0.129
2012 Gultepe E, Nguyen H, Albertson T, Tagkopoulos I. A Bayesian network for early diagnosis of sepsis patients: A basis for a clinical decision support system 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182636  0.127
2021 Kim KJ, Moon SJ, Park KS, Tagkopoulos I. Author Correction: Network-based modeling of drug effects on disease module in systemic sclerosis. Scientific Reports. 11: 8238. PMID 33837228 DOI: 10.1038/s41598-021-87277-w  0.125
2024 Tan CE, Neupane BP, Wen Y, Lim LX, Medina Plaza C, Oberholster A, Tagkopoulos I. Volatile Organic Compound-Based Predictive Modeling of Smoke Taint in Wine. Journal of Agricultural and Food Chemistry. PMID 38533667 DOI: 10.1021/acs.jafc.3c07019  0.12
2020 Risner D, Li F, Fell JS, Pace SA, Siegel JB, Tagkopoulos I, Spang ES. Preliminary Techno-Economic Assessment of Animal Cell-Based Meat. Foods (Basel, Switzerland). 10. PMID 33374916 DOI: 10.3390/foods10010003  0.118
2015 Huynh L, Tagkopoulos I. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching Acs Synthetic Biology. 4: 890-897. DOI: 10.1021/sb500339k  0.108
2022 Holt RR, Barile D, Wang SC, Munafo JP, Arvik T, Li X, Lee F, Keen CL, Tagkopoulos I, Schmitz HH. 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. PMID 36409321 DOI: 10.1021/acs.jafc.2c04519  0.107
2020 Youn J, Naravane T, Tagkopoulos I. Using Word Embeddings to Learn a Better Food Ontology. Frontiers in Artificial Intelligence. 3: 584784. PMID 33733222 DOI: 10.3389/frai.2020.584784  0.102
2021 Merchel Piovesan Pereira B, Wang X, Tagkopoulos I. Biocide-Induced Emergence of Antibiotic Resistance in . Frontiers in Microbiology. 12: 640923. PMID 33717036 DOI: 10.3389/fmicb.2021.640923  0.098
2022 Rollins ZA, Huang J, Tagkopoulos I, Faller R, George SC. A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics. Computational and Structural Biotechnology Journal. 20: 3473-3481. PMID 35860406 DOI: 10.1016/j.csbj.2022.06.048  0.092
2012 Alexopoulos C, Loukis E, Charalabidis Y, Tagkopoulos I. A methodology for evaluating PSI e-infrastructures based on multiple value models Proceedings of the 2012 16th Panhellenic Conference On Informatics, Pci 2012. 37-43. DOI: 10.1109/PCi.2012.80  0.091
2021 Eetemadi A, Tagkopoulos I. Methane and fatty acid metabolism pathways are predictive of Low-FODMAP diet efficacy for patients with irritable bowel syndrome. Clinical Nutrition (Edinburgh, Scotland). PMID 33504454 DOI: 10.1016/j.clnu.2020.12.041  0.088
2011 Mozhayskiy V, Miller B, Ma KL, Tagkopoulos I. A scalable multi-scale framework for parallel simulation and visualization of microbial evolution Proceedings of the Teragrid 2011 Conference: Extreme Digital Discovery, Tg'11. DOI: 10.1145/2016741.2016749  0.072
2022 Eetemadi A, Tagkopoulos I. Algorithmic lifestyle optimization. Journal of the American Medical Informatics Association : Jamia. PMID 36308771 DOI: 10.1093/jamia/ocac186  0.07
2023 Aboud O, Liu Y, Dahabiyeh L, Abuaisheh A, Li F, Aboubechara JP, Riess J, Bloch O, Hodeify R, Tagkopoulos I, Fiehn O. Profile Characterization of Biogenic Amines in Glioblastoma Patients Undergoing Standard-of-Care Treatment. Biomedicines. 11. PMID 37626757 DOI: 10.3390/biomedicines11082261  0.062
2024 Furuya H, Nguyen CT, Chan T, Marusina AI, Merleev AA, Garcia-Hernandez ML, Hsieh SL, Tsokos GC, Ritchlin CT, Tagkopoulos I, Maverakis E, Adamopoulos IE. IL-23 induces CLEC5A IL-17A neutrophils and elicit skin inflammation associated with psoriatic arthritis. Journal of Autoimmunity. 143: 103167. PMID 38301504 DOI: 10.1016/j.jaut.2024.103167  0.056
2009 Tagkopoulos I. Rocks of ages Economist. 392.  0.01
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