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2020

Adaptive laboratory evolution of Escherichia coli under acid stress

Du, B., Olson, C. A., Sastry, A. V., Fang, X., Phaneuf, P. V., Chen, K., Wu, M., Szubin, R., Xu, S., Gao, Y., Hefner, Y., Feist, A. M. & Palsson, B. O., 2020, In : Microbiology. 166, 2, 141 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Lipid and carotenoid production from wheat straw hydrolysates by different oleaginous yeasts

Liu, Z., Feist, A., Dragone, G. & Mussatto, S. I., 2020, In : Journal of Cleaner Production. 249, 119308.

Research output: Contribution to journalJournal articleResearchpeer-review

2019

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

Anand, A., Chen, K., Yang, L., Sastry, A. V., Olson, C. A., Poudel, S., Seif, Y., Hefner, Y., Phaneuf, P. V., Xu, S., Szubin, R., Feist, A. & Palsson, B., 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 50, p. 25287-25292

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Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

Pereira, R., Wei, Y., Mohamed, E. T. T., Radi, M., Malina, C., Herrgård, M. J., Feist, A. M., Nielsen, J. & Chen, Y., 2019, In : Metabolic Engineering. 56, p. 130-141 12 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Aledb 1.0: A database of mutations from adaptive laboratory evolution experimentation

Phaneuf, P. V., Gosting, D., Palsson, B. O. & Feist, A. M., 2019, In : Nucleic acids research. 47, D1, p. D1164-D1171 8 p., gky983.

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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Lachance, J. C., Lloyd, C. J., Monk, J. M., Yang, L., Sastry, A. V., Seif, Y., Palsson, B. O., Rodrigue, S., Feist, A. M., King, Z. A. & Jacques, P. É., 2019, In : PLOS Computational Biology. 15, 4, e1006971.

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Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Yang, L., Mih, N., Anand, A., Park, J. H., Tan, J., Yurkovich, J. T., Monk, J. M., Lloyd, C. J., Sandberg, T. E., Seo, S. W., Kim, D., Sastry, A. V., Phaneuf, P., Gao, Y., Broddrick, J. T., Chen, K., Heckmann, D., Szubin, R., Hefner, Y., Feist, A. M. & 1 others, Palsson, B. O., 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 28, p. 14368-14373

Research output: Contribution to journalJournal articleResearchpeer-review

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

Poudel, S., Tsunemoto, H., Meehan, M., Szubin, R., Olson, C. A., Lamsa, A., Seif, Y., Dillon, N., Vrbanac, A., Sugie, J., Dahesh, S., Monk, J. M., Dorrestein, P. C., Pogliano, J., Knight, R., Nizet, V., Palsson, B. O. & Feist, A. M., 2019, In : Scientific Data. 6, 1, 43.

Research output: Contribution to journalJournal articleResearchpeer-review

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Enzyme promiscuity shapes adaptation to novel growth substrates

Guzmán, G. I., Sandberg, T. E., LaCroix, R. A., Nyerges, Á., Papp, H., de Raad, M., King, Z. A., Hefner, Y., Northen, T. R., Notebaart, R. A., Pál, C., Palsson, B. O., Papp, B. & Feist, A. M., 2019, In : Molecular Systems Biology. 15, 4, e8462.

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Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution

Mohamed, E. T. T., Mundhada, H., Landberg, J. M., Cann, I., Mackie, R. I., Nielsen, A. T., Herrgard, M. J. & Feist, A. M., 2019, In : Microbial Cell Factories. 18, 116.

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Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media

Rajput, A., Poudel, S., Tsunemoto, H., Meehan, M., Szubin, R., Olson, C. A., Lamsa, A., Seif, Y., Dillon, N., Vrbanac, A., Sugie, J., Dahesh, S., Monk, J. M., Dorrestein, P. C., Knight, R., Nizet, V., Palsson, B. O. & Feist, A. M., 2019, In : Scientific Data. 6, 1, 322.

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Pseudogene repair driven by selection pressure applied in experimental evolution

Anand, A., Olson, C. A., Yang, L., Sastry, A. V., Catoiu, E., Choudhary, K. S., Phaneuf, P. V., Sandberg, T. E., Xu, S., Hefner, Y., Szubin, R., Feist, A. & Palsson, B., 2019, In : Nature Microbiology. 4, 3, p. 386-389

Research output: Contribution to journalJournal articleResearchpeer-review

Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus

Machado, H., Weng, L. L., Dillon, N., Seif, Y., Holland, M., Pekar, J. E., Monk, J. M., Nizet, V., Palsson, B. O. & Feist, A. M., 2019, In : Applied and Environmental Microbiology. 85, 21, p. 1-13 13 p., e01773-19.

Research output: Contribution to journalJournal articleResearchpeer-review

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

Sandberg, T. E., Salazar, M. J., Weng, L. L., Palsson, B. O. & Feist, A. M., 2019, In : Metabolic Engineering. 56, p. 1-16 16 p.

Research output: Contribution to journalJournal articleResearchpeer-review

The genetic basis for adaptation of model-designed syntrophic co-cultures

Lloyd, C. J., King, Z. A., Sandberg, T. E., Hefner, Y., Olson, C. A., Phaneuf, P. V., O'Brien, E. J., Sanders, J. G., Salido, R. A., Sanders, K., Brennan, C., Humphrey, G., Knight, R. & Feist, A. M., 2019, In : PLOS Computational Biology. 15, 3, 28 p., e1006213.

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2018

Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Metabolic Engineering. 48, p. 82-93

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Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Metabolic Engineering. 48, p. 233-242

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Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli

Long, C. P., Gonzalez, J. E., Feist, A. M., Palsson, B. O. & Antoniewicz, M. R., 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 1, p. 222-227 6 p.

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Enhanced Metabolite Productivity of Escherichia coli Adapted to Glucose M9 Minimal Medium

Rugbjerg, P., Feist, A. M. & Sommer, M. O. A., 2018, In : Frontiers in Bioengineering and Biotechnology. 6, 6 p., 166.

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Evolution of gene knockout strains of E-coli reveal regulatory architectures governed by metabolism

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Nature Communications. 9, 15 p., 3796.

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Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Frontiers in Microbiology. 9, 16 p., 1793.

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Identification of growth-coupled production strains considering protein costs and kinetic variability

Dinh, H. V., King, Z. A., Palsson, B. O. & Feist, A. M., 2018, In : Metabolic Engineering Communications. 7, e00080.

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Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae

Strucko, T., Zirngibl, K., Pereira, F., Kafkia, E., Mohamed, E. T., Rettel, M., Stein, F., Feist, A. M., Jouhten, P., Patil, K. R. & Forster, J., 2018, In : Metabolic Engineering. 47, p. 73-82 10 p.

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Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

McCloskey, D., Xu, S., Sandberg, T. E., Brunk, E., Hefner, Y., Szubin, R., Feist, A. M. & Palsson, B. O., 2018, In : Applied and Environmental Microbiology. 84, 19, 17 p., e00823-18.

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Reframing gene essentiality in terms of adaptive flexibility

Guzmán, G. I., Olson, C. A., Hefner, Y., Phaneuf, P. V., Catoiu, E., Crepaldi, L. B., Micas, L. G., Palsson, B. O. & Feist, A. M., 2018, In : BMC Systems Biology. 12, 20 p., 143.

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Underground metabolism: network-level perspective and biotechnological potential

Notebaart, R. A., Kintses, B., Feist, A. & Papp, B., 2018, In : Current Opinion in Biotechnology. 49, p. 108-114

Research output: Contribution to journalJournal articleResearchpeer-review

2017

A Model for Designing Adaptive Laboratory Evolution Experiments

LaCroix, R. A., Palsson, B. O., Feist, A. M. & Kivisaar, M. (ed.), 2017, In : Applied and Environmental Microbiology. 83, 8, 14 p., e03115-16.

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Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

Long, C. P., Gonzalez, J. E., Feist, A. M., Palsson, B. O. & Antoniewicz, M. R., 2017, In : Metabolic Engineering. 44, p. 100-107

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Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution

Mohamed, E. T., Wang, S., Lennen, R. M., Herrgård, M. J., Simmons, B. A., Singer, S. W. & Feist, A. M., 2017, In : Microbial Cell Factories. 16, 1, 15 p., 204.

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iML1515, a knowledgebase that computes Escherichia coli traits

Monk, J. M., Lloyd, C. J., Brunk, E., Mih, N., Sastry, A., King, Z., Takeuchi, R., Nomura, W., Zhang, Z., Mori, H., Feist, A. M. & Palsson, B. O., 2017, In : Nature Biotechnology. 35, 10, p. 904-908

Research output: Contribution to journalJournal articleResearchpeer-review

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution

Mundhada, H., Seoane, J. M., Schneider, K., Christensen, H. B., Koza, A., Herrgard, M., Feist, A. & Nielsen, A. T., 2017, In : Metabolic Engineering. 39, p. 141–150 24 p.

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Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

Sandberg, T. E., Lloyd, C. J., Palsson, B. O., Feist, A. M. & Kivisaar, M. (ed.), 2017, In : APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 83, 13, 15 p., e00410-17.

Research output: Contribution to journalJournal articleResearchpeer-review

Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion

King, Z. A., O'Brien, E. J., Feist, A. M. & Palsson, B. O., 2017, In : Metabolic Engineering. 39, p. 220–227 8 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2016

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

Brunk, E., George, K. W., Alonso-Gutierrez, J., Tjompson, M., Baidoo, E., Wang, G., Petzold, C. J., McCloskey, D., Monk, J., Yang, L., O’Brien, E. J., Batth, T. S., Garcia Martin, H., Feist, A., Adams, P. D., Keasling, J. D., Palsson, B. & Soon Lee, T., 2016, In : Cell Systems. 2, 5, p. 335-346 13 p.

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Evolution of E. coli on [U-13C] Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology

Sandberg, T. E., Long, C. P., Gonzalez, J. E., Feist, A., Antoniewicz, M. R. & Palsson, B., 2016, In : P L o S One. 11, 3, 14 p., e0151130.

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Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

Utrilla, J., O'Brien, E. J., Chen, K., McCloskey, D., Cheung, J., Wang, H., Armenta-Medina, D., Feist, A. & Palsson, B., 2016, In : Cell. 2, p. 260-271 12 p.

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MID Max: LC–MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications

McCloskey, D., Young, J. D., Xu, S., Palsson, B. & Feist, A., 2016, In : Analytical Chemistry. 88, 2, p. 1362–1370 9 p.

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Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

McCloskey, D., Young, J. D., Xu, S., Palsson, B. & Feist, A., 2016, In : Analytical chemistry. 88, 7, p. 3844-3852 9 p.

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Multi-omic data integration enables discovery of hidden biological regularities

Ebrahim, A., Brunk, E., Tan, J., O'Brien, E. J., Kim, D., Szubin, R., Lerman, J. A., Lechner, A., Sastry, A., Bordbar, A., Feist, A. & Palsson, B., 2016, In : Nature Communications. 7, 9 p., 13091.

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Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Monk, JM., Koza, A., Campodonico, MA., Machado, D., Seoane, J. M., Palsson, B., Herrgard, M. & Feist, A., 2016, In : Cell Systems. 3, 3, p. 238-251 26 p.

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2015

A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites

McCloskey, D., Gangoiti, J. A., Palsson, B. O. & Feist, A. M., 2015, In : Metabolomics. 11, 5, p. 1338-1350 13 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Fast Swinnex Filtration (FSF): A fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media

McCloskey, D., Utrilla, J., Naviaux, R. K., Palsson, B. O. & Feist, A., 2015, In : Metabolomics. 11, 1, p. 198-209 12 p.

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1 Downloads (Pure)

Model-driven discovery of underground metabolic functions in Escherichia coli

Guzmán, G. I., Utrilla, J., Nurk, S., Brunk, E., Monk, J. M., Ebrahim, A., Palsson, B. O. & Feist, A. M., 2015, In : Proceedings of the National Academy of Sciences. 112, 3, p. 929-934 6 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Next-generation genome-scale models for metabolic engineering

King, Z. A., Lloyd, C. J., Feist, A. M. & Palsson, B. O., 2015, In : Current Opinion in Biotechnology. 35, p. 23-29 7 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

LaCroix, R. A., Sandberg, T. E., O'Brien, E. J., Utrilla, J., Ebrahim, A., Guzman, G. I., Szubin, R., Palsson, B. & Feist, A., 2015, In : APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 81, 1, p. 17-30 14 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2014

A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent

McCloskey, D., Gangoiti, J. A., King, Z. A., Naviaux, R. K., Barshop, B. A., Palsson, B. & Feist, A., 2014, In : Biotechnology and Bioengineering. 111, 4, p. 803-815

Research output: Contribution to journalJournal articleResearchpeer-review

3 Downloads (Pure)

Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds

Geertz-Hansen, H. M., Blom, N., Feist, A., Brunak, S. & Petersen, T. N., 2014, In : Proteins: Structure, Function, and Bioinformatics. 82, 9, p. 1819-1828

Research output: Contribution to journalJournal articleResearchpeer-review

Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations.

Sandberg, T. E., Pedersen, M., LaCroix, R. A., Ebrahim, A., Bonde, M., Herrgard, M., Palsson, B., Sommer, M. & Feist, A., 2014, In : Molecular Biology and Evolution. 31, 10, p. 2647-2662

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