| EMILiO: a fast algorithm for genome-scale strain design L Yang, WR Cluett, R Mahadevan Metabolic engineering 13 (3), 272-281, 2011 | 123 | 2011 |
| COBRAme: A computational framework for genome-scale models of metabolism and gene expression CJ Lloyd, A Ebrahim, L Yang, ZA King, E Catoiu, EJ O’Brien, JK Liu, ... PLoS computational biology 14 (7), e1006302, 2018 | 66* | 2018 |
| Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow E Brunk, KW George, J Alonso-Gutierrez, M Thompson, E Baidoo, ... Cell systems 2 (5), 335-346, 2016 | 60 | 2016 |
| 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 | 59 | 2018 |
| 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), 8, 2013 | 54 | 2013 |
| 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 | 51 | 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 | 43 | 2016 |
| 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 | 35 | 2015 |
| The Escherichia coli transcriptome mostly consists of independently regulated modules AV Sastry, Y Gao, R Szubin, Y Hefner, S Xu, D Kim, KS Choudhary, ... Nature communications 10 (1), 1-14, 2019 | 34 | 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 | 31 | 2018 |
| Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation K Chen, Y Gao, N Mih, EJ O’Brien, L Yang, BO Palsson Proceedings of the National Academy of Sciences 114 (43), 11548-11553, 2017 | 31 | 2017 |
| Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression D Ma, L Yang, RMT Fleming, I Thiele, BO Palsson, MA Saunders Scientific Reports 7, 40863, 2017 | 31 | 2017 |
| 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), 2, 2019 | 25 | 2019 |
| 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 | 25 | 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, 36734, 2016 | 25 | 2016 |
| 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 | 21 | 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 | 20 | 2018 |
| A bilevel optimization algorithm to identify enzymatic capacity constraints in metabolic networks L Yang, R Mahadevan, WR Cluett Computers & Chemical Engineering 32 (9), 2072-2085, 2008 | 19 | 2008 |
| Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling S Garg, L Yang, R Mahadevan BMC research notes 3 (1), 1-7, 2010 | 16 | 2010 |
| 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 | 15 | 2019 |
