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), 5536, 2019 | 211 | 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), 4306, 2018 | 189 | 2018 |
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 | 171 | 2018 |
EMILiO: a fast algorithm for genome-scale strain design L Yang, WR Cluett, R Mahadevan Metabolic engineering 13 (3), 272-281, 2011 | 152 | 2011 |
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 | 114 | 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 | 106 | 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 | 105 | 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 | 101 | 2016 |
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 | 98 | 2017 |
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 | 83 | 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 | 69 | 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 | 65 | 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 | 61 | 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 | 60 | 2016 |
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 | 56 | 2020 |
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 | 56 | 2018 |
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 | 54 | 2019 |