| 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 |
| Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models |
D. Heckmann; C.J. Lloyd; N. Mih; Y. Ha; D.C. Zielinski; Z.B. Haiman; A.Amer Desouki; M.J. Lercher; B.O. Palsson |
2018 |
| Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. |
Y. Gao; J.T. Yurkovich; S.Woo Seo; I. Kabimoldayev; A. Dräger; K. Chen; A.V. Sastry; X. Fang; N. Mih; L. Yang; J. Eichner; B.K. Cho; D. Kim; B.O. Palsson |
2018 |
| Recon3D enables a three-dimensional view of gene variation in human metabolism. |
E. Brunk; S. Sahoo; D.C. Zielinski; A. Altunkaya; A. Dräger; N. Mih; F. Gatto; A. Nilsson; G.Andres Pre Gonzalez; M.Kathrin Aurich; A. Prlić; A. Sastry; A.D. Danielsdottir; A. Heinken; A. Noronha; P.W. Rose; S.K. Burley; R.M.T. Fleming; J. Nielsen; I. Thiele; B.O. Palsson |
2018 |
| Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology |
J.E. Pekar; P. Phaneuf; R. Szubin; B. Palsson; A. Feist; J.M. Monk |
2018 |
| Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. |
J.T. Yurkovich; M.A. Alcantar; Z.B. Haiman; B.O. Palsson |
2018 |
| ssbio: A Python Framework for Structural Systems Biology |
N. Mih; E. Brunk; K. Chen; E. Catoiu; A. Sastry; E. Kavvas; J.M. Monk; Z. Zhang; B.O. Palsson |
2018 |
| Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes. |
J.T. Broddrick; D.G. Welkie; D. Jallet; S.S. Golden; G. Peers; B.O. Palsson |
2018 |
| A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0 |
A. Santos-Zavaleta; M. Sánchez-Pérez; H. Salgado; D.A. Vázquez-Ramírez; S. Gama-Castro; V.H. Tierrafría; S.J.W. Busby; P. Aquino; X. Fang; B.O. Palsson; J.E. Galagan; J. Collado-Vides |
2018 |
| Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. |
D. Kim; S.Woo Seo; Y. Gao; H. Nam; G.I. Guzman; B.K. Cho; B.O. Palsson |
2018 |
| 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 |
| 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 |