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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

An atlas of human metabolism

Robinson, J. L., Kocabaş, P., Wang, H., Cholley, P. E., Cook, D., Nilsson, A., Anton, M., Ferreira, R., Domenzain, I., Billa, V., Limeta, A., Hedin, A., Gustafsson, J., Kerkhoven, E. J., Svensson, L. T., Palsson, B. O., Mardinoglu, A., Hansson, L., Uhlén, M. & Nielsen, J., 2020, In : Science Signaling. 13, 624, eaaz1482.

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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

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BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O. & King, Z., 2020, In : Nucleic acids research. 48, 1, p. D402-D406

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Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli

Luo, H., Yang, L., Kim, S. H., Wulff, T., Feist, A. M., Herrgard, M. & Palsson, B., 2020, In : ACS Synthetic Biology. 9, 3, p. 494-499

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Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

Gutierrez, J. M., Feizi, A., Li, S., Kallehauge, T. B., Hefzi, H., Grav, L. M., Ley, D., Baycin Hizal, D., Betenbaugh, M. J., Voldborg, B. G., Kildegaard, H. F., Min Lee, G., Palsson, B. O., Nielsen, J. & Lewis, N. E., 2020, In : Nature Communications. 11, 1, 68.

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Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus

Lee, N., Kim, W., Chung, J., Lee, Y., Cho, S., Jang, K-S., Kim, S. C., Palsson, B. & Cho, B-K., 2020, In : ISME Journal. 14, p. 1111–1124

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Metabolic and genetic basis for auxotrophies in Gram-negative species

Seif, Y., Choudhary, K. S., Hefner, Y., Anand, A., Yang, L. & Palsson, B. O., 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 11, p. 6264-6273

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Multiplex secretome engineering enhances recombinant protein production and purity

Kol, S., Ley, D., Wulff, T., Decker, M., Arnsdorf, J., Schoffelen, S., Hansen, A. H., Jensen, T. L., Gutierrez, J. M., Chiang, A. W. T., Masson, H. O., Palsson, B. O., Voldborg, B. G., Pedersen, L. E., Kildegaard, H. F., Min Lee, G. & Lewis, N. E., 2020, In : Nature Communications. 11, 1, 10 p.

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Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters

Lee, N., Kim, W., Hwang, S., Lee, Y., Cho, S., Palsson, B. & Cho, B. K., 2020, In : Scientific Data. 7, 55.

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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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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

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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

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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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Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses

Luo, H., Hansen, A. S. L., Yang, L., Schneider, K., Kristensen, M., Christensen, U., Christensen, H. B., Du, B., Özdemir, E., Feist, A. M., Keasling, J. D., Jensen, M. K., Herrgård, M. J. & Palsson, B. O., 2019, In : PLOS Biology. 17, 3, e2007050.

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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.

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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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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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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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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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Minimal cells, maximal knowledge

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

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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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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

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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.

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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.

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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.

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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

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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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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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

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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.

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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.

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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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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.

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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

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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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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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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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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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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.

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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.

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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

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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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