| Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus |
Wilken SE, Monk JM, Leggieri PA, Lawson CE, Lankiewicz TS, Seppälä S, Daum CG, Jenkins J, Lipzen AM, Mondo SJ, Barry KW, Grigoriev IV, Henske JK, Theodorou MK, Palsson BO, Petzold LR, O'Malley MA. |
2021 |
| proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms |
Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan SM, Kim D, Cho BK, Palsson BO |
2021 |
| MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics |
Haiman ZB, Zielinski DC, Koike Y, Yurkovich JT, Palsson BO |
2021 |
| Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data |
Phaneuf PV, Zielinski DC, Yurkovich JT, Johnsen J, Szubin R, Yang L, Kim SH, Schulz S, Wu M, Dalldorf C, Ozdemir E, Lennen RM, Palsson BO, Feist AM |
2021 |
| Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications |
Anand A, Olson CA, Sastry AV, Patel A, Szubin R, Yang L, Feist AM, Palsson BO |
2021 |
| Optimal dimensionality selection for independent component analysis of transcriptomic data |
McConn JL, Lamoureux CR, Poudel S, Palsson BO, Sastry AV |
2021 |
| Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture |
Kim JH, Lee N, Hwang S, Kim W, Lee Y, Cho S, Palsson BO, Cho BK |
2021 |
| Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome. |
Hwang S, Lee N, Choe D, Lee Y, Kim W, Jeong Y, Cho S, Palsson BO, Cho BK |
2021 |
| Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters |
Lee N, Choi M, Kim W, Hwang S, Lee Y, Kim JH, Kim G, Kim H, Cho S, Kim SC, Palsson B, Jang KS, Cho BK |
2021 |
| The quantitative metabolome is shaped by abiotic constraints |
Akbari A, Yurkovich JT, Zielinski DC, Palsson BO |
2021 |
| Streptomyces as Microbial Chassis for Heterologous Protein Expression |
Hwang S, Lee Y, Kim JH, Kim G, Kim H, Kim W, Cho S, Palsson BO, Cho BK |
2021 |
| Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus |
Machado H, Seif Y, Sakoulas G, Olson CA, Hefner Y, Anand A, Jones YZ, Szubin R, Palsson BO, Nizet V, Feist AM |
2021 |
| 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 |