| Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion |
Gutierrez JM, Feizi A, Li S, Kallehauge TB, Hefzi H, Grav LM, Ley D, Baycin Hizal D, Betenbaugh MJ, Voldborg B, Faustrup Kildegaard H, Min Lee G, Palsson BO, Nielsen J, Lewis NE |
2020 |
| Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models |
Dahal S, Yurkovich JT, Xu H, Palsson BO |
2020 |
| iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning |
Rychel K, Decker K, Sastry AV, Phaneuf PV, Poudel S, Palsson BO |
2020 |
| Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli |
Luo H, Yang L, Kim SH, Wulff T, Feist AM, Herrgard M, Palsson BØ |
2020 |
| Redefining fundamental concepts of transcription initiation in bacteria |
Mejía-Almonte C, Busby SJW, Wade JT, et al. |
2020 |
| Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships |
Choudhary KS, Kleinmanns JA, Decker K, Sastry AV, Gao Y, Szubin R, Seif Y, Palsson BO |
2020 |
| Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus |
Salazar MJ, Machado H, Dillon NA, Tsunemoto H, Szubin R, Dahesh S, Pogliano J, Sakoulas G, Palsson BO, Nizet V, Feist AM |
2020 |
| Independent component analysis of E. coli's transcriptome reveals thecellular processes that respond to heterologous gene expression |
Tan, J., Sastry, A.V., Fremming, K.S., Bjørn, S.P., Hoffmeyer, A., Seo, S.,Voldborg, Bjø.G., Palsson, B.O. |
2020 |
| Scalable computation of intracellular metabolite concentrations |
Akbari, A. and Palsson, B.O. |
2020 |
| STATR: A simple analysis pipeline of Ribo-Seq in bacteria |
Choe D, Palsson B, Cho BK. |
2020 |
| Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces |
Lee N, Hwang S, Kim J, Cho S, Palsson B, Cho BK |
2020 |
| High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies |
Broddrick Jared T., Szubin Richard, Norsigian Charles J., Monk Jonathan M., Palsson Bernhard O., Parenteau Mary N. |
2020 |
| An atlas of human metabolism |
Robinson JL, Kocabaş P, Wang H, Cholley PE, Cook D, Nilsson A, Anton M, Ferreira R, Domenzain I, Billa V, Limeta A, Hedin A, Gustafsson J, Kerkhoven EJ, Svensson LT, Palsson BO, Mardinoglu A, Hansson L, Uhlén M, Nielsen J. |
2020 |
| Impact of insertion sequences on convergent evolution of Shigella species |
Hawkey J, Monk JM, Billman-Jacobe H, Palsson B, Holt KE |
2020 |
| Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome |
Rychel, K., Sastry, A.V. & Palsson, B.O. |
2020 |
| Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen |
Jensen CS, Norsigian CJ, Fang X, Nielsen XC, Christensen JJ, Palsson BO, Monk JM. |
2020 |
| Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity |
Phaneuf PV, Yurkovich JT, Heckmann D, et al. |
2020 |
| The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale |
Zielinski, D.C.; Patel, A.; Palsson, B.O. |
2020 |
| Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis |
Minasov G, Lam MR, Rosas Lemus M, Sławek J, Woinska M, Shabalin IG, Shuvalova L, Palsson BØ, Godzik A, Minor W, Satchell KJF |
2020 |
| Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes |
Sandberg TE, Szubin R, Phaneuf PV, Palsson BO |
2020 |
| DeepTFactor: A deep learning-based tool for the prediction of transcription factors |
Kim, G.B., Gao, Y., Palsson, B.O., Lee, S.Y. |
2020 |
| Genome Sequence Comparison of Staphylococcus aureus TX0117 and a Beta-Lactamase-Cured Derivative Shows Increased Cationic Peptide Resistance Accompanying Mutations in relA and mnaA |
Sales MJ, Sakoulas G, Szubin R, Palsson B, Arias C, Singh KV, Murray BE, Monk JM |
2020 |
| System-level understanding of gene expression and regulation for engineering secondary metabolite production in Streptomyces |
Lee Y, Lee N, Hwang S, et al. |
2020 |
| A biochemically-interpretable machine learning classifier for microbial GWAS |
Kavvas ES, Yang L, Monk JM, Heckmann D, Palsson BO |
2020 |
| SBML Level 3: an extensible format for the exchange and reuse of biological models |
Keating SM, Waltemath D, König M, et al. |
2020 |
| Transcriptome and translatome profiles of Streptomyces species in different growth phases. |
Kim W, Hwang S, Lee N, Lee Y, Cho S, Palsson B, Cho BK. |
2020 |
| Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers |
Heckmann D, Campeau A, Lloyd CJ, et al. |
2020 |
| Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis |
Hwang S, Lee N, Cho S, Palsson B, Cho BK
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2020 |
| Reconstructing organisms in silico: genome-scale models and their emerging applications |
Fang X, Lloyd CJ, Palsson BO |
2020 |
| Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus |
Lee N, Kim W, Chung J, Lee Y, Cho S, Jang KS, Kim SC, Palsson B, Cho BK |
2020 |