| 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 |
| 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 |
| Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient |
X. Fang; J.M. Monk; S. Nurk; M. Akseshina; Q. Zhu; C. Gemmell; C. Gianetto-Hill; N. Leung; R. Szubin; J. Sanders; P.L. Beck; W. Li; W.J. Sandborn; S.D. Gray-Owen; R. Knight; E. Allen-Vercoe; B.O. Palsson; L. Smarr |
2018 |
| COBRAme: A computational framework for genome-scale models of metabolism and gene expression. |
C.J. Lloyd; A. Ebrahim; L. Yang; Z.A. King; E. Catoiu; E.J. O'Brien; J.K. Liu; B.O. Palsson |
2018 |
| Quantitative -omic data empowers bottom-up systems biology |
J.T. Yurkovich; B.O. Palsson |
2018 |
| Estimating Metabolic Equilibrium Constants: Progress and Future Challenges |
B. Du; D.C. Zielinski; B.O. Palsson |
2018 |
| Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. |
D. McCloskey; S. Xu; T.E. Sandberg; E. Brunk; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2018 |
| Modeling the multi-scale mechanisms of macromolecular resource allocation |
L. Yang; J.T. Yurkovich; Z.A. King; B.O. Palsson |
2018 |
| Identification of growth-coupled production strains considering protein costs and kinetic variability |
H.V. Dinh; Z.A. King; B.O. Palsson; A.M. Feist |
2018 |
| Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. |
X. Fang; J.M. Monk; N. Mih; B. Du; A.V. Sastry; E. Kavvas; Y. Seif; L. Smarr; B.O. Palsson |
2018 |
| Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. |
A.M. Abdel-Haleem; H. Hefzi; K. Mineta; X. Gao; T. Gojobori; B.O. Palsson; N.E. Lewis; N. Jamshidi |
2018 |
| Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance |
E.S. Kavvas; E. Catoiu; N. Mih; J.T. Yurkovich; Y. Seif; N. Dillon; D. Heckmann; A. Anand; L. Yang; V. Nizet; J.M. Monk; B.O. Palsson |
2018 |
| Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. |
D. McCloskey; S. Xu; T.E. Sandberg; E. Brunk; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2018 |
| Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing. |
J.Seong Lee; J.Hyoung Park; T.Kwang Ha; M. Samoudi; N.E. Lewis; B.O. Palsson; H.Faustrup Kildegaard; G.M. Lee |
2018 |
| Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow |
E. Brunk; R.L. Chang; J. Xia; H. Hefzi; J.T. Yurkovich; D. Kim; E. Buckmiller; H.H. Wang; B.K. Cho; C. Yang; B.O. Palsson; G.M. Church; N.E. Lewis |
2018 |
| Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method. |
B. Du; Z. Zhang; S. Grubner; J.T. Yurkovich; B.O. Palsson; D.C. Zielinski |
2018 |
| Dataset on economic analysis of mass production of algae in LED-based photobioreactors. |
W. Fu; S. Gudmundsson; K. Wichuk; S. Palsson; B.O. Palsson; K. Salehi-Ashtiani; S. Brynjólfsson |
2018 |
| Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice |
B. Du; D.C. Zielinski; J.M. Monk; B.O. Palsson |
2018 |
| The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures |
K.S. Choudhary; N. Mih; J. Monk; E. Kavvas; J.T. Yurkovich; G. Sakoulas; B.O. Palsson |
2018 |
| Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution. |
F. Johannsson; S. Guðmundsson; G. Paglia; S. Guðmundsson; B. Palsson; O.E. Sigurjónsson; O. Rolfsson |
2018 |
| ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. |
H. Latif; S. Federowicz; A. Ebrahim; J. Tarasova; R. Szubin; J. Utrilla; K. Zengler; B.O. Palsson |
2018 |