| 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 |
| A defined minimal medium for systems analyses of Staphylococcus aureus reveals strain-specific metabolic requirements |
Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM. |
2019 |
| Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection |
Yan J, Estanbouli H, Liao C, Kim W, Monk JM, Rahman R, Kamboj M, Palsson BO, Qiu W, Xavier JB |
2019 |
| DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression |
Yang L, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO |
2019 |
| Inactivation of a Mismatch-Repair System Diversifies Genotypic Landscape of Escherichia coli During Adaptive Laboratory Evolution |
Kang M, Kim K, Choe D, Cho S, Kim SC, Palsson B, Cho BK |
2019 |
| A workflow for generating multi-strain genome-scale metabolic models of prokaryotes |
Norsigian CJ, Fang X, Seif Y, Monk JM, Palsson BO |
2019 |
| Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses |
Luo H, Hansen ASL, Yang L, Schneider K, Kristensen M, Christensen U,
Christensen HB, Du B, Özdemir E, Feist AM, Keasling JD, Jensen MK, Herrgård MJ,
Palsson BO |
2019 |
| The Transcription Unit Architecture of Streptomyces lividans TK24 |
Lee Y, Lee N, Jeong Y, Hwang S, Kim W, Cho S, Palsson BO, Cho BK |
2019 |
| Enzyme promiscuity shapes adaptation to novel growth substrates |
Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA,
Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM |
2019 |
| The genetic basis for adaptation of model-designed syntrophic co-cultures |
Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O'Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R, Feist AM |
2019 |
| Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum |
Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y,
Dupont CL, Mitchell BG, Palsson BO, Allen AE |
2019 |
| Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom |
Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, Nikoloski Z, Palsson BO, Allen AE |
2019 |
| Adaptive laboratory evolution of a genome-reduced Escherichia coli |
D. Choe; J.Hyoung Lee; M. Yoo; S. Hwang; B.Hyun Sung; S. Cho; B. Palsson; S.Chang Kim; B.K. Cho |
2019 |