| The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function |
S. Ghatak; Z.A. King; A. Sastry; B.O. Palsson |
2019 |
| Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism |
Cheng C, O'Brien EJ, McCloskey D, Utrilla J, Olson C, LaCroix RA, Sandberg TE, Feist AM, Palsson BO, King ZA |
2019 |
| Expanding the uses of genome‐scale models with protein structures |
Mih N and Palsson BO |
2019 |
| Pseudogene repair driven by selection pressure applied in experimental evolution. |
A. Anand; C.A. Olson; L. Yang; A.V. Sastry; E. Catoiu; K.Sonal Choudhary; P.V. Phaneuf; T.E. Sandberg; S. Xu; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2019 |
| Synthetic Biology Tools for Novel Secondary Metabolite Discovery in Streptomyces |
Lee N, Hwang S, Lee Y, Cho S, Palsson B, Cho BK |
2019 |
| The Escherichia coli transcriptome mostly consists of independently regulated modules |
Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO |
2019 |
| 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 |
| Sugar-stimulated CO2 sequestration by the green microalga Chlorella vulgaris |
W. Fu; S. Gudmundsson; K. Wichuk; S. Palsson; B.O. Palsson; K. Salehi-Ashtiani; ður ólfsson |
2018 |
| Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome |
D. McCloskey; S. Xu; T.E. Sandberg; E. Brunk; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2018 |
| Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance. |
D. Choe; R. Szubin; S. Dahesh; S. Cho; V. Nizet; B. Palsson; B.K. Cho |
2018 |
| 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 |