| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| 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 |
| 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, |
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, |
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, |
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 |
| A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action | Yang, J.H., Wright, S.N., Hamblin, M., McCloskey, D., Alcantar, M.A., Schrubbers, L., Lopatkin, A.J., Satish, S., Nili, A., Palsson, B.O., Walker, G.C., Collins, J.J |
2019 |
| Adaptive laboratory evolution of Escherichia coli under acid stress | Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Hefner Y, Feist AM, Palsson BO |
2019 |
| Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. | L. Heirendt; S. Arreckx; T. Pfau; S.N. Mendoza; A. Richelle; A. Heinken; H.S. Haraldsdóttir; J. Wachowiak; S.M. Keating; V. Vlasov; S. Magnusdóttir; C.Yu Ng; G. Preciat; A. Žagare; S.H.J. Chan; M.K. Aurich; C.M. Clancy; J. Modamio; J.T. Sauls; A. Noronha; A. Bordbar; B. Cousins; D.C.El Assal; L.V. Valcarcel; I. Apaolaza; S. Ghaderi; M. Ahookhosh; M. Ben Guebila; A. Kostromins; N. Sompairac; H.M. Le; D. Ma; Y. Sun; L. Wang; J.T. Yurkovich; M.A.P. Oliveira; P.T. Vuong; L.P.El Assal; I. Kuperstein; A. Zinovyev; S. Hinton; W.A. Bryant; F.J.Aragón Artacho; F.J. Planes; E. Stalidzans; A. Maass; S. Vempala; M. Hucka; M.A. Saunders; C.D. Maranas; N.E. Lewis; T. Sauter; B.Ø. Palsson; I. Thiele; R.M.T. Fleming |
2019 |
| Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media | Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon |
2019 |
| OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states | Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO |
2019 |
| BOFdata: Generating biomass objective functions for genome-scale metabolic models from experimental data | Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, |
2019 |