|Next-generation genome-scale models for metabolic engineering|
ZA King, CJ Lloyd, AM Feist, BO Palsson
Current opinion in biotechnology 35, 23-29, 2015
|i ML1515, a knowledgebase that computes Escherichia coli traits|
JM Monk, CJ Lloyd, E Brunk, N Mih, A Sastry, Z King, R Takeuchi, ...
Nature biotechnology 35 (10), 904-908, 2017
|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
|Laboratory evolution to alternating substrate environments yields distinct phenotypic and genetic adaptive strategies|
TE Sandberg, CJ Lloyd, BO Palsson, AM Feist
Applied and environmental microbiology 83 (13), 2017
|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
|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
|Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models|
D Heckmann, CJ Lloyd, N Mih, Y Ha, DC Zielinski, ZB Haiman, ...
Nature communications 9 (1), 1-10, 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
|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
|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
|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
|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
|Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen|
JK Liu, C Lloyd, M Al-Bassam, A Ebrahim, JN Kim, C Olson, A Aksenov, ...
PLoS computational biology 15 (3), e1006848, 2019
|The genetic basis for adaptation of model-designed syntrophic co-cultures|
CJ Lloyd, ZA King, TE Sandberg, Y Hefner, CA Olson, PV Phaneuf, ...
PLoS computational biology 15 (3), e1006213, 2019
|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
|Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers|
D Heckmann, A Campeau, CJ Lloyd, PV Phaneuf, Y Hefner, ...
Proceedings of the National Academy of Sciences 117 (37), 23182-23190, 2020
|Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth|
CJ Lloyd, J Monk, A Ebrahim, L Yang, B Palsson
|Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets|
OS Mohite, CJ Lloyd, JM Monk, T Weber, BO Palsson
BioRxiv, 781328, 2019
|Reconstructing organisms in silico: genome-scale models and their emerging applications|
X Fang, CJ Lloyd, BO Palsson
Nature Reviews Microbiology, 1-13, 2020
|Expanding the Scope of Genome-scale Models of Metabolism and Gene Expression|
UC San Diego, 2019