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Colton Lloyd - Publications

Affiliations: 
2019 University of California, San Diego, La Jolla, CA 
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21 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Tibocha-Bonilla JD, Zuñiga C, Lekbua A, Lloyd C, Rychel K, Short K, Zengler K. Predicting stress response and improved protein overproduction in Bacillus subtilis. Npj Systems Biology and Applications. 8: 50. PMID 36575180 DOI: 10.1038/s41540-022-00259-0  0.404
2022 Mohite OS, Lloyd CJ, Monk JM, Weber T, Palsson BO. Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets. Synthetic and Systems Biotechnology. 7: 900-910. PMID 35647330 DOI: 10.1016/j.synbio.2022.04.011  0.696
2021 Lachance JC, Matteau D, Brodeur J, Lloyd CJ, Mih N, King ZA, Knight TF, Feist AM, Monk JM, Palsson BO, Jacques PÉ, Rodrigue S. Genome-scale metabolic modeling reveals key features of a minimal gene set. Molecular Systems Biology. 17: e10099. PMID 34288418 DOI: 10.15252/msb.202010099  0.81
2021 Lloyd CJ, Monk J, Yang L, Ebrahim A, Palsson BO. Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. Plos Computational Biology. 17: e1007817. PMID 34161321 DOI: 10.1371/journal.pcbi.1007817  0.817
2020 Fang X, Lloyd CJ, Palsson BO. Reconstructing organisms in silico: genome-scale models and their emerging applications. Nature Reviews. Microbiology. PMID 32958892 DOI: 10.1038/S41579-020-00440-4  0.651
2020 Heckmann D, Campeau A, Lloyd CJ, Phaneuf PV, Hefner Y, Carrillo-Terrazas M, Feist AM, Gonzalez DJ, Palsson BO. Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers. Proceedings of the National Academy of Sciences of the United States of America. PMID 32873645 DOI: 10.1073/Pnas.2001562117  0.782
2019 Du B, Yang L, Lloyd CJ, Fang X, Palsson BO. Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. Plos Computational Biology. 15: e1007525. PMID 31809503 DOI: 10.1371/Journal.Pcbi.1007525  0.695
2019 Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270234 DOI: 10.1073/Pnas.1905039116  0.615
2019 Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. Plos Computational Biology. 15: e1006971. PMID 31009451 DOI: 10.1371/Journal.Pcbi.1006971  0.789
2019 Liu JK, Lloyd C, Al-Bassam M, Ebrahim A, Kim JN, Olson C, Aksenov A, Dorrestein P, Zengler K. Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. Plos Computational Biology. 15: e1006848. PMID 30845144 DOI: 10.1371/Journal.Pcbi.1006848  0.717
2019 Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O'Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R, Feist AM. The genetic basis for adaptation of model-designed syntrophic co-cultures. Plos Computational Biology. 15: e1006213. PMID 30822347 DOI: 10.1371/Journal.Pcbi.1006213  0.77
2019 Yang L, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO. DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. Bmc Systems Biology. 13: 2. PMID 30626386 DOI: 10.1186/S12918-018-0675-6  0.757
2018 Heckmann D, Lloyd CJ, Mih N, Ha Y, Zielinski DC, Haiman ZB, Desouki AA, Lercher MJ, Palsson BO. Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. Nature Communications. 9: 5252. PMID 30531987 DOI: 10.1038/S41467-018-07652-6  0.777
2018 Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO. COBRAme: A computational framework for genome-scale models of metabolism and gene expression. Plos Computational Biology. 14: e1006302. PMID 29975681 DOI: 10.1371/Journal.Pcbi.1006302  0.809
2017 Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. iML1515, a knowledgebase that computes Escherichia coli traits. Nature Biotechnology. 35: 904-908. PMID 29020004 DOI: 10.1038/Nbt.3956  0.718
2017 Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Proceedings of the National Academy of Sciences of the United States of America. PMID 28874552 DOI: 10.1073/Pnas.1702581114  0.737
2017 Sandberg TE, Lloyd CJ, Palsson BO, Feist AM. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Applied and Environmental Microbiology. PMID 28455337 DOI: 10.1128/Aem.00410-17  0.669
2016 Yang L, Yurkovich JT, Lloyd CJ, Ebrahim A, Saunders MA, Palsson BO. Principles of proteome allocation are revealed using proteomic data and genome-scale models. Scientific Reports. 6: 36734. PMID 27857205 DOI: 10.1038/Srep36734  0.82
2016 Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO. solveME: fast and reliable solution of nonlinear ME models. Bmc Bioinformatics. 17: 391. PMID 27659412 DOI: 10.1186/S12859-016-1240-1  0.74
2015 Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, et al. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences of the United States of America. PMID 26261351 DOI: 10.1073/Pnas.1501384112  0.767
2015 King ZA, Lloyd CJ, Feist AM, Palsson BO. Next-generation genome-scale models for metabolic engineering. Current Opinion in Biotechnology. 35: 23-29. PMID 25575024 DOI: 10.1016/J.Copbio.2014.12.016  0.702
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