| 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
|
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 |
| Multiplex secretome engineering enhances recombinant protein production and purity |
Kol S, Ley D, Wulff T, et al. |
2020 |
| The Bitome: digitized genomic features reveal fundamental genome organization |
Lamoureux CR, Choudhary KS, King ZA, Sandberg TE, Gao Y, Sastry AV, Phaneuf PV, Choe D, Cho BK, Palsson BO. |
2020 |
| 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 BK |
2020 |
| Adaptations of Escherichia Coli Strains to Oxidative Stress Are Reflected in Properties of Their Structural Proteomes |
Mih N, Monk JM, Fang X, et al. |
2020 |
| Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution |
Lim, H.G., Fong, B., Alacon, G., Magrudeniya, H.D., Eng, T., Szubin, R., Olson, C.A., Palsson, B.O., Gladden, J.M., Simmons, B.A., Mukhopadhyay, Singer, S.W., Feist, A.M., |
2020 |
| Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens |
Hyun JC, Kavvas ES, Monk JM, Palsson BO |
2020 |
| Microbial Synthesis of Human-Hormone Melatonin at Gram Scales |
Luo H, Schneider K, Christensen U, Lei Y, Herrgard M, Palsson BØ |
2020 |