Colton Lloyd
Colton Lloyd
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Cited by
Cited by
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
bioRxiv, 2020
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
CJ Lloyd
UC San Diego, 2019
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