Research Output 2011 2019

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2019
6 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

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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.

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115 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.

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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

73 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.

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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

88 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.

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191 Downloads (Pure)
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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

146 Downloads (Pure)

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.

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155 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.

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83 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.

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5 Downloads (Pure)

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.

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288 Downloads (Pure)

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.

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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

105 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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8 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.

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41 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

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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

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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

250 Downloads (Pure)

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

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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

316 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.

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38 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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87 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

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2018
97 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

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101 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

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133 Downloads (Pure)

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.

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43 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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149 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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76 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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297 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.

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148 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.

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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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142 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.

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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

168 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.

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128 Downloads (Pure)

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.

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170 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.

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90 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.

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547 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.

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123 Downloads (Pure)

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.

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126 Downloads (Pure)

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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120 Downloads (Pure)

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.

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Modeling the multi-scale mechanisms of macromolecular resource allocation

Yang, L., Yurkovich, J. T., King, Z. A. & Palsson, B. O., 2018, In : Current opinion in Microbiology. 45, p. 8-15

Research output: Contribution to journalJournal articleResearchpeer-review

88 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.

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322 Downloads (Pure)

RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli

McCloskey, D., Xu, J., Schrübbers, L., Christensen, H. B. & Herrgård, M. J., 2018, In : Metabolic Engineering. 47, p. 383-392

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53 Downloads (Pure)

Recon3D enables a three-dimensional view of gene variation in human metabolism

Brunk, E., Sahoo, S., Zielinski, D. C., Altunkaya, A., Dräger, A., Mih, N., Gatto, F., Nilsson, A., Preciat Gonzalez, G. A., Aurich, M. K., Prlic, A., Sastry, A., Danielsdottir, A. D., Heinken, A., Noronha, A., Rose, P. W., Burley, S. K., Fleming, R. M. T., Nielsen, J., Thiele, I. & 1 others, Palsson, B. O., 2018, In : Nature Biotechnology. 36, 3, p. 272-281

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