| Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. |
E.S. Kavvas; Y. Seif; J.T. Yurkovich; C. Norsigian; S. Poudel; W.W. Greenwald; S. Ghatak; B.O. Palsson; J.M. Monk |
2018 |
| 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 |
| 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 |