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| 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), 4306, 2018 | 189 | 2018 |
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| 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 | 113 | 2017 |
| 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, ... Proc Natl Acad Sci USA 116 (28), 14368-14373, 2019 | 105 | 2019 |
| 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 46 (20), 10682-10696, 2018 | 101 | 2018 |
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| BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data JC Lachance, CJ Lloyd, JM Monk, L Yang, AV Sastry, Y Seif, BO Palsson, ... PLoS computational biology 15 (4), e1006971, 2019 | 92 | 2019 |
| Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design K Zhuang, L Yang, WR Cluett, R Mahadevan BMC biotechnology 13, 1-15, 2013 | 82 | 2013 |
| A biochemically-interpretable machine learning classifier for microbial GWAS ES Kavvas, L Yang, JM Monk, D Heckmann, BO Palsson Nature communications 11 (1), 2580, 2020 | 78 | 2020 |
| Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration A Anand, KE Chen, L Yang, AV Sastry, CA Olson, S Poudel, Y Seif, ... Proceedings of the National Academy of Sciences 116 (50), 25287-25292, 2019 | 66 | 2019 |
| OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states A Anand, K Chen, E Catoiu, AV Sastry, CA Olson, TE Sandberg, Y Seif, ... Molecular biology and evolution 37 (3), 660-667, 2020 | 62 | 2020 |
| 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 | 62 | 2017 |
| solveME: fast and reliable solution of nonlinear ME models L Yang, D Ma, A Ebrahim, CJ Lloyd, MA Saunders, BO Palsson BMC Bioinformatics 17 (1), 391, 2016 | 59 | 2016 |
| DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression L Yang, A Ebrahim, CJ Lloyd, MA Saunders, BO Palsson BMC systems biology 13, 1-15, 2019 | 56 | 2019 |
| 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 | 55 | 2018 |
| Metabolic and genetic basis for auxotrophies in Gram-negative species Y Seif, KS Choudhary, Y Hefner, A Anand, L Yang, BO Palsson Proceedings of the National Academy of Sciences 117 (11), 6264-6273, 2020 | 54 | 2020 |
| Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli B Du, L Yang, CJ Lloyd, X Fang, BO Palsson PLoS computational biology 15 (12), e1007525, 2019 | 53 | 2019 |