Research Output

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, (Accepted/In press) In : Microbiology.

Research output: Contribution to journalJournal articleResearchpeer-review

A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Norsigian, C. J., Fang, X., Seif, Y., Monk, J. M. & Palsson, B. O., 2020, In : Nature Protocols. 15, 1, p. 1-14

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, (Accepted/In press) In : Journal of Cleaner Production.

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

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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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.

Research output: Contribution to journalJournal articleResearchpeer-review

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118 Downloads (Pure)

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

Yang, J. H., Wright, S. N., Hamblin, M., McCloskey, D., Alcantar, M. A., Schrübbers, L., Lopatkin, A. J., Satish, S., Nili, A., Palsson, B. O., Walker, G. C. & Collins, J. J., 2019, In : CELL. 177, 6, p. 1649-1661.e9

Research output: Contribution to journalJournal articleResearchpeer-review

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

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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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92 Downloads (Pure)
Open Access
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197 Downloads (Pure)

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A., Haraldsdottir, H. S., Wachowiak, J., Keating, S. M., Vlasov, V., Magnusdottir, S., Ng, C. Y., Preciat, G., Zagare, A., Chan, S. H. J., Aurich, M. K., Clancy, C. M., Modamio, J., Sauls, J. T., Noronha, A. & 35 others, Bordbar, A., Cousins, B., El Assal, D. C., Valcarcel, L. V., Apaolaza, I., Ghaderi, S., Ahookhosh, M., Ben Guebila, M., Kostromins, A., Sompairac, N., Le, H. M., Ma, D., Sun, Y., Wang, L., Yurkovich, J. T., Oliveira, M. A. P., Vuong, P. T., El Assal, L. P., Kuperstein, I., Zinovyev, A., Hinton, H. S., Bryant, W. A., Aragon Artacho, F. J., Planes, F. J., Stalidzans, E., Maass, A., Vempala, S., Hucka, M., Saunders, M. A., Maranas, C. D., Lewis, N. E., Sauter, T., Palsson, B. O., Thiele, I. & Fleming, R. M. T., 2019, In : Nature Protocols. 14, 3, p. 639-702 64 p.

Research output: Contribution to journalJournal articleResearchpeer-review

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Yang, L., Ebrahim, A., Lloyd, C. J., Saunders, M. A. & Palsson, B., 2019, In : BMC Systems Biology. 13, 2, 15 p.

Research output: Contribution to journalJournal articleResearchpeer-review

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148 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

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160 Downloads (Pure)

Expanding the uses of genome-scale models with protein structures

Mih, N. & Palsson, B. O., 2019, In : Molecular Systems Biology. 15, 11, 5 p., e8601.

Research output: Contribution to journalComment/debateResearchpeer-review

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23 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

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Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Du, B., Yang, L., Lloyd, C. J., Fang, X. & Palsson, B., 2019, In : PLOS Computational Biology. 15, 12, 21 p., e1007525.

Research output: Contribution to journalJournal articleResearchpeer-review

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Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Cheng, C., O'Brien, E. J., McCloskey, D., Utrilla, J., Olson, C., LaCroix, R. A., Sandberg, T. E., Feist, A. M., Palsson, B. O. & King, Z. A., 2019, In : PLOS Computational Biology. 15, 6, e1007066.

Research output: Contribution to journalJournal articleResearchpeer-review

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293 Downloads (Pure)

Minimal cells, maximal knowledge

Lachance, J. C., Rodrigue, S. & Palsson, B. O., 2019, In : eLife. 8, 4 p., e45379.

Research output: Contribution to journalJournal articleResearchpeer-review

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110 Downloads (Pure)

Multi-omics analysis of fatty alcohol production in engineered yeasts saccharomyces cerevisiae and yarrowia lipolytica

Dahlin, J., Holkenbrink, C., Marella, E. R., Wang, G., Liebal, U., Lieven, C., Weber, D., McCloskey, D., Ebert, B. E., Herrgård, M. J., Blank, L. M. & Borodina, I., 2019, In : Frontiers in Genetics. 10, 747.

Research output: Contribution to journalJournal articleResearchpeer-review

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14 Downloads (Pure)

Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome

Hwang, S., Lee, N., Jeong, Y., Lee, Y., Kim, W., Cho, S., Palsson, B. O. & Cho, B-K., 2019, In : Nucleic acids research. 47, 12, p. 6114-6129

Research output: Contribution to journalJournal articleResearchpeer-review

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43 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

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6 Downloads (Pure)

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

Synthetic biology tools for novel secondary metabolite discovery in streptomyces

Lee, N., Hwang, S., Lee, Y., Cho, S. & Palsson, B., 2019, In : Journal of Microbiology and Biotechnology. 29, 5, p. 667-686

Research output: Contribution to journalJournal articleResearchpeer-review

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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.

Research output: Contribution to journalJournal articleResearchpeer-review

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318 Downloads (Pure)

The Transcription Unit Architecture of Streptomyces lividans TK24

Lee, Y., Lee, N., Jeong, Y., Hwang, S., Kim, W., Cho, S., Palsson, B. O. & Cho, B-K., 2019, In : Frontiers in Microbiology. 10, 13 p., 2074.

Research output: Contribution to journalJournal articleResearchpeer-review

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40 Downloads (Pure)

The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

Ghatak, S., King, Z. A., Sastry, A. & Palsson, B. O., 2019, In : Nucleic acids research. 47, 5, p. 2446-2454

Research output: Contribution to journalJournal articleResearchpeer-review

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88 Downloads (Pure)
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

Research output: Contribution to journalJournal articleResearchpeer-review

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102 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

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A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

Santos-Zavaleta, A., Sanchez-Perez, M., Salgado, H., Velazquez-Ramirez, D. A., Gama-Castro, S., Tierrafria, V. H., Busby, S. J. W., Aquino, P., Fang, X., Palsson, B. O., Galagan, J. E. & Collado-Vides, J., 2018, In : B M C Biology. 16, 91.

Research output: Contribution to journalJournal articleResearchpeer-review

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136 Downloads (Pure)

Bacterial cells with improved tolerance to diacids

Lennen, R., Nielsen, A. T., Herrgard, M., Sommer, M. O. A., Feist, A. & Tharwat Tolba Mohamed, E., 2018, IPC No. C12N1/20; C12P7/44; C12P7/46, Patent No. WO2018091525 , 24 May 2018, Priority date 15 Nov 2016, Priority No. US201662422457P

Research output: Patent

Open Access
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179 Downloads (Pure)

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

Brunk, E., Chang, R. L., Xia, J., Hefzi, H., Yurkovich, J. T., Kim, D., Buckmiller, E., Wang, H. H., Cho, B-K., Yang, C., Palsson, B. O., Church, G. M. & Lewis, N. E., 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 43, p. 11096-11101

Research output: Contribution to journalJournal articleResearchpeer-review

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47 Downloads (Pure)

ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions

Latif, H., Federowicz, S., Ebrahim, A., Tarasova, J., Szubin, R., Utrilla, J., Zengler, K. & Palsson, B. O., 2018, In : P L o S One. 13, 5, 20 p., e0197272.

Research output: Contribution to journalJournal articleResearchpeer-review

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156 Downloads (Pure)

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Lloyd, C. J., Ebrahim, A., Yang, L., King, Z. A., Catoiu, E., O'Brien, E. J., Liu, J. K. & Polsson, B. O., 2018, In : P L o S Computational Biology (Online). 14, 7, 14 p., e1006302.

Research output: Contribution to journalJournal articleResearchpeer-review

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78 Downloads (Pure)

Computational Methods to Assess the Production Potential of Bio-Based Chemicals

Campodonico, M. A., Sukumara, S., Feist, A. M. & Herrgård, M. J., 2018, Synthetic Metabolic Pathways. Vol. 1671. p. 97-116 (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

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

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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.

Research output: Contribution to journalJournal articleResearchpeer-review

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152 Downloads (Pure)

Escher-FBA: a web application for interactive flux balance analysis

Rowe, E., Palsson, B. O. & King, Z. A., 2018, In : BMC Systems Biology. 12, 7 p., 84.

Research output: Contribution to journalJournal articleResearchpeer-review

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158 Downloads (Pure)

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Fang, X., Monk, J. M., Mih, N., Du, B., Sastry, A. V., Kavvas, E., Seif, Y., Smarr, L. & Palsson, B. O., 2018, In : B M C Systems Biology. 12, 66.

Research output: Contribution to journalJournal articleResearchpeer-review

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145 Downloads (Pure)

Estimating Metabolic Equilibrium Constants: Progress and Future Challenges

Du, B., Zielinski, D. C. & Palsson, B. O., 2018, In : Trends in Biochemical Sciences. 43, 12, p. 960-969

Research output: Contribution to journalJournal articleResearchpeer-review

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

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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Seif, Y., Kavvas, E., Lachance, J-C., Yurkovich, J. T., Nuccio, S-P., Fang, X., Catoiu, E., Raffatellu, M., Palsson, B. O. & Monk, J. M., 2018, In : Nature Communications. 9, 12 p., 3771.

Research output: Contribution to journalJournal articleResearchpeer-review

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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.

Research output: Contribution to journalJournal articleResearchpeer-review

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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.

Research output: Contribution to journalJournal articleResearchpeer-review

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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.

Research output: Contribution to journalJournal articleResearchpeer-review

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Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Heckmann, D., Lloyd, C. J., Mih, N., Ha, Y., Zielinski, D. C., Haiman, Z. B., Desouki, A. A., Lercher, M. J. & Palsson, B. O., 2018, In : Nature Communications. 9, 10 p., 5252.

Research output: Contribution to journalJournal articleResearchpeer-review

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Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

Fang, X., Monk, J. M., Nurk, S., Akseshina, M., Zhu, Q., Gemmell, C., Gianetto-Hill, C., Leung, N., Szubin, R., Sanders, J., Beck, P. L., Li, W., Sandborn, W. J., Gray-Owen, S. D., Knight, R., Allen-Vercoe, E., Palsson, B. O. & Smarr, L., 2018, In : Frontiers in Microbiology. 9, 14 p., 2559.

Research output: Contribution to journalJournal articleResearchpeer-review

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Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

Heckmann, D., Zielinski, D. C. & Palsson, B. O., 2018, In : Nature Communications. 9, 9 p., 5270.

Research output: Contribution to journalJournal articleResearchpeer-review

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