| Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence |
Norsigian, C.J., Danhof, H.A., Brand, C.K. et al. |
2020 |
| 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 |
| A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. |
Y. Seif; J.M. Monk; N. Mih; H. Tsunemoto; S. Poudel; C. Zuniga; J. Broddrick; K. Zengler; B.O. Palsson |
2019 |
| Cellular responses to reactive oxygen species are predicted from molecular mechanisms |
Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ,
Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, Chen K,
Heckmann D, Szubin R, Hefner Y, Feist AM, Palsson BO. |
2019 |
| 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 CJ, Fang X, Palsson BO |
2019 |
| Metabolic Systems Analysis of Shock-Induced Endotheliopathy (SHINE) in Trauma: A New Research Paradigm |
Henriksen HH, McGarrity S, SigurÐardóttir RS, Nemkov T, D'Alessandro A, Palsson BO, Stensballe J, Wade CE, Rolfsson Ó, Johansson PI |
2019 |
| BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree |
Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z |
2019 |
| Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates |
Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ, Aziz RK, Monk JM |
2019 |
| Minimal cells, maximal knowledge |
Lachance JC, Rodrigue S, Palsson BO |
2019 |
| The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology |
Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM |
2019 |
| Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment |
Rosas-Lemus M, Minasov G, Shuvalova L, Wawrzak Z, Kiryukhina O, Mih N, Jaroszewski L, Palsson B, Godzik A, Satchell KJF |
2019 |
| Systems Biology and Pangenome of Salmonella O-Antigens |
Seif Y, Monk JM, Machado H, Palsson BO. |
2019 |
| 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 CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Nizet V, Palsson BO, Feist AM, Pogliano J. |
2019 |
| 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 |