| 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 |
| Escher-FBA: a web application for interactive flux balance analysis |
E. Rowe; B.O. Palsson; Z.A. King |
2018 |
| High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli. |
S. Cho; D. Choe; E. Lee; S.Chang Kim; B. Palsson; B.K. Cho |
2018 |
| Basics of genome-scale metabolic modeling and applications on C1-utilization. |
I. Kabimoldayev; A.Duc Nguyen; L. Yang; S. Park; E.Yeol Lee; D. Kim |
2018 |
| iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE |
C.J. Norsigian; E. Kavvas; Y. Seif; B.O. Palsson; J.M. Monk |
2018 |
| Reframing gene essentiality in terms of adaptive flexibility. |
G.I. Guzman; C.A. Olson; Y. Hefner; P.V. Phaneuf; E. Catoiu; L.B. Crepaldi; L.Goldschmid Micas; B.O. Palsson; A.M. Feist |
2018 |
| Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. |
Y. Seif; E. Kavvas; J.C. Lachance; J.T. Yurkovich; S.P. Nuccio; X. Fang; E. Catoiu; M. Raffatellu; B.O. Palsson; J.M. Monk |
2018 |
| Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae. |
T. Strucko; K. Zirngibl; F. Pereira; E. Kafkia; E.T. Mohamed; M. Rettel; F. Stein; A.M. Feist; P. Jouhten; K.Raosaheb Patil; J. Forster |
2018 |
| ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. |
P.V. Phaneuf; D. Gosting; B.O. Palsson; A.M. Feist |
2018 |
| Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. |
D. McCloskey; S. Xu; T.E. Sandberg; E. Brunk; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2018 |
| Systems biology as an emerging paradigm in transfusion medicine. |
J.T. Yurkovich; A. Bordbar; O.E. Sigurjónsson; B.O. Palsson |
2018 |
| Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates |
D. Heckmann; D.C. Zielinski; B.O. Palsson |
2018 |
| Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in knockout evolutions. |
D. McCloskey; S. Xu; T.E. Sandberg; E. Brunk; Y. Hefner; R. Szubin; A.M. Feist; B.O. Palsson |
2018 |
| 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 |