Academic lineage
Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets
- Omkar S Mohite, Colton J Lloyd, Jonathan M Monk, Tilmann Weber, Bernhard O Palsson
- None, 10.1016/j.synbio.2022.04.011
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth
- Colton J Lloyd, Jonathan Monk, Laurence Yang, Ali Ebrahim, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1007817
Reconstructing organisms in silico: genome-scale models and their emerging applications
- Xin Fang, Colton J Lloyd, Bernhard O Palsson
- Nat Rev Microbiol, 10.1038/s41579-020-00440-4
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers
- David Heckmann, Anaamika Campeau, Colton J Lloyd, …, Adam M Feist, David J Gonzalez, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.2001562117
Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli
- Bin Du, Laurence Yang, Colton J Lloyd, Xin Fang, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1007525
Cellular responses to reactive oxygen species are predicted from molecular mechanisms
- Laurence Yang, Nathan Mih, Amitesh Anand, …, Ying Hefner, Adam M Feist, Bernhard O Palsson
- Proc Natl Acad Sci U S A, 10.1073/pnas.1905039116
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
- Jean-Christophe Lachance, Colton J Lloyd, Jonathan M Monk, …, Adam M Feist, Zachary A King, Pierre-Étienne Jacques
- PLoS Comput Biol, 10.1371/journal.pcbi.1006971
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
- Joanne K Liu, Colton Lloyd, Mahmoud M Al-Bassam, …, Alexander Aksenov, Pieter Dorrestein, Karsten Zengler
- PLoS Comput Biol, 10.1371/journal.pcbi.1006848
The genetic basis for adaptation of model-designed syntrophic co-cultures
- Colton J Lloyd, Zachary A King, Troy E Sandberg, …, Gregory Humphrey, Rob Knight, Adam M Feist
- PLoS Comput Biol, 10.1371/journal.pcbi.1006213
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
- Laurence Yang, Ali Ebrahim, Colton J Lloyd, Michael A Saunders, Bernhard O Palsson
- None, 10.1186/s12918-018-0675-6
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
- David Heckmann, Colton J Lloyd, Nathan Mih, …, Abdelmoneim Amer Desouki, Martin J Lercher, Bernhard O Palsson
- Nat Commun, 10.1038/s41467-018-07652-6
COBRAme: A computational framework for genome-scale models of metabolism and gene expression
- Colton J Lloyd, Ali Ebrahim, Laurence Yang, …, Edward J O’Brien, Joanne K Liu, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1006302
iML1515, a knowledgebase that computes Escherichia coli traits
- Jonathan M Monk, Colton J Lloyd, Elizabeth Brunk, …, Hirotada Mori, Adam M Feist, Bernhard O Palsson
- Nat Biotechnol, 10.1038/nbt.3956
Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies
- Troy E Sandberg, Colton J Lloyd, Bernhard O Palsson, Adam M Feist
- Appl Environ Microbiol, 10.1128/aem.00410-17