| Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0 L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ... Nature protocols 14 (3), 639-702, 2019 | 554 | 2019 |
| Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance ES Kavvas, E Catoiu, N Mih, JT Yurkovich, Y Seif, N Dillon, D Heckmann, ... Nature communications 9 (1), 1-9, 2018 | 105 | 2018 |
| Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics A Bordbar, JT Yurkovich, G Paglia, O Rolfsson, ÓE Sigurjónsson, ... Scientific reports 7 (1), 1-12, 2017 | 104* | 2017 |
| BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree CJ Norsigian, N Pusarla, JL McConn, JT Yurkovich, A Dräger, BO Palsson, ... Nucleic acids research 48 (D1), D402-D406, 2020 | 87 | 2020 |
| Gut microbiome pattern reflects healthy ageing and predicts survival in humans T Wilmanski, C Diener, N Rappaport, S Patwardhan, J Wiedrick, ... Nature metabolism 3 (2), 274-286, 2021 | 85 | 2021 |
| Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities X Fang, A Sastry, N Mih, D Kim, J Tan, JT Yurkovich, CJ Lloyd, Y Gao, ... Proceedings of the National Academy of Sciences 114 (38), 10286-10291, 2017 | 75 | 2017 |
| Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits Y Seif, E Kavvas, JC Lachance, JT Yurkovich, SP Nuccio, X Fang, ... Nature communications 9 (1), 1-12, 2018 | 70 | 2018 |
| Toward community standards and software for whole-cell modeling D Waltemath, JR Karr, FT Bergmann, V Chelliah, M Hucka, M Krantz, ... IEEE Transactions on Biomedical Engineering 63 (10), 2007-2014, 2016 | 58 | 2016 |
| Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 Y Gao, JT Yurkovich, SW Seo, I Kabimoldayev, A Dräger, K Chen, ... Nucleic Acids Research, gky752, 2018 | 54 | 2018 |
| Cellular responses to reactive oxygen species are predicted from molecular mechanisms L Yang, N Mih, A Anand, JH Park, J Tan, JT Yurkovich, JM Monk, CJ Lloyd, ... Proceedings of the National Academy of Sciences 116 (28), 14368-14373, 2019 | 49 | 2019 |
| Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions ES Kavvas, Y Seif, JT Yurkovich, C Norsigian, S Poudel, WW Greenwald, ... BMC systems biology 12 (1), 1-15, 2018 | 41 | 2018 |
| Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data L Yang, J Tan, EJ O’Brien, JM Monk, D Kim, HJ Li, P Charusanti, ... Proceedings of the National Academy of Sciences 112 (34), 10810-10815, 2015 | 39 | 2015 |
| Metabolic network analysis reveals altered bile acid synthesis and metabolism in Alzheimer’s disease P Baloni, CC Funk, J Yan, JT Yurkovich, A Kueider-Paisley, K Nho, ... Cell Reports Medicine 1 (8), 100138, 2020 | 37* | 2020 |
| Modeling the multi-scale mechanisms of macromolecular resource allocation L Yang, JT Yurkovich, ZA King, BO Palsson Current opinion in microbiology 45, 8-15, 2018 | 37 | 2018 |
| Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks JT Yurkovich, DC Zielinski, L Yang, G Paglia, O Rolfsson, ... Journal of Biological Chemistry 292 (48), 19556-19564, 2017 | 35 | 2017 |
| Principles of proteome allocation are revealed using proteomic data and genome-scale models L Yang, JT Yurkovich, CJ Lloyd, A Ebrahim, MA Saunders, BO Palsson Scientific reports 6 (1), 1-8, 2016 | 34 | 2016 |
| Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow E Brunk, RL Chang, J Xia, H Hefzi, JT Yurkovich, D Kim, E Buckmiller, ... Proceedings of the National Academy of Sciences 115 (43), 11096-11101, 2018 | 31 | 2018 |
| Temperature-dependent estimation of Gibbs energies using an updated group-contribution method B Du, Z Zhang, S Grubner, JT Yurkovich, BO Palsson, DC Zielinski Biophysical journal 114 (11), 2691-2702, 2018 | 26 | 2018 |
| A systems approach to clinical oncology uses deep phenotyping to deliver personalized care JT Yurkovich, Q Tian, ND Price, L Hood Nature Reviews Clinical Oncology 17 (3), 183-194, 2020 | 25 | 2020 |
| Community standards to facilitate development and address challenges in metabolic modeling MA Carey, A Dräger, ME Beber, JA Papin, JT Yurkovich Molecular Systems Biology 16 (8), e9235, 2020 | 24 | 2020 |
Bernhard PalssonUCSDVerified email at eng.ucsd.edu
