| 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 |
| Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function. |
J.H. Yang; P. Bhargava; D. McCloskey; N. Mao; B.O. Palsson; J.J. Collins |
2017 |
| Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. |
S.Woo Seo; Y. Gao; D. Kim; R. Szubin; J. Yang; B.K. Cho; B.O. Palsson |
2017 |
| Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. |
E.T. Mohamed; S. Wang; R.M. Lennen; M.J. Herrgard; B.A. Simmons; S.W. Singer; A.M. Feist |
2017 |
| Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. |
T.E. Sandberg; C.J. Lloyd; B.O. Palsson; A.M. Feist |
2017 |
| Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks. |
J.T. Yurkovich; D.C. Zielinski; L. Yang; G. Paglia; O. Rolfsson; O.E. Sigurjónsson; J.T. Broddrick; A. Bordbar; K. Wichuk; S. Brynjólfsson; S. Palsson; S. Gudmundsson; B.O. Palsson |
2017 |
| Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression. |
A. Sastry; J. Monk; H. Tegel; M. Uhlen; B.O. Palsson; J. Rockberg; E. Brunk |
2017 |
| iML1515, a knowledgebase that computes Escherichia coli traits. |
J.M. Monk; C.J. Lloyd; E. Brunk; N. Mih; A. Sastry; Z. King; R. Takeuchi; W. Nomura; Z. Zhang; H. Mori; A.M. Feist; B.O. Palsson |
2017 |
| Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism. |
Ó. Rolfsson; Ó.E. Sigurjonsson; M. Magnusdottir; F. Johannsson; G. Paglia; S. Guðmundsson; A. Bordbar; S. Palsson; S. Brynjólfsson; S. Guðmundsson; B. Palsson |
2017 |
| Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells |
J.T. Yurkovich; L. Yang; B.O. Palsson |
2017 |
| Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. |
A. Bordbar; J.T. Yurkovich; G. Paglia; O. Rolfsson; O.E. Sigurjónsson; B.O. Palsson |
2017 |
| Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation |
K. Chen; Y. Gao; N. Mih; E.J. ’ Brien; L. Yang; B.O. Palsson |
2017 |
| Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. |
J.T. Yurkovich; L. Yang; B.O. Palsson |
2017 |
| A Padawan Programmer’s Guide to Developing Software Libraries |
J.T. Yurkovich; B.J. Yurkovich; A. Draeger; B.O. Palsson; Z.A. King |
2017 |
| Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring. |
C.P. Long; J.E. Gonzalez; A.M. Feist; B.O. Palsson; M.R. Antoniewicz |
2017 |
| A Model for Designing Adaptive Laboratory Evolution Experiments. |
R.A. LaCroix; B.O. Palsson; A.M. Feist |
2017 |
| Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. |
X. Fang; A. Sastry; N. Mih; D. Kim; J. Tan; J.T. Yurkovich; C.J. Lloyd; Y. Gao; L. Yang; B.O. Palsson |
2017 |
| Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels. |
J. Levering; C.L. Dupont; A.E. Allen; B.O. Palsson; K. Zengler |
2017 |
| Underground metabolism: network-level perspective and biotechnological potential |
R.A. Notebaart; álint Kintses; A.M. Feist; ázs Papp |
2017 |