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Research Output 2017 2019

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2019
5 Downloads (Pure)

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

Research output: Contribution to journalJournal articleResearchpeer-review

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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., 2019, (Accepted/In press) In : Microbiology.

Research output: Contribution to journalJournal articleResearchpeer-review

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

114 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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70 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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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

84 Downloads (Pure)

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

Open Access
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188 Downloads (Pure)
Open Access
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154 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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80 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

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

Liu, Z., Feist, A., Dragone, G. & Mussatto, S. I., 2019, (Accepted/In press) In : Journal of Cleaner Production.

Research output: Contribution to journalJournal articleResearchpeer-review

4 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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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

312 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2018
94 Downloads (Pure)

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

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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99 Downloads (Pure)

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

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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296 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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144 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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167 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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167 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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89 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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539 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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87 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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121 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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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
169 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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125 Downloads (Pure)

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

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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201 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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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

480 Downloads (Pure)

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.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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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