| Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. |
N.E. Lewis; K.K. Hixson; T.M. Conrad; J.A. Lerman; P. Charusanti; A.D. Polpitiya; J.N. Adkins; G. Schramm; S.O. Purvine; D. Lopez-Ferrer; K.K. Weitz; R. Eils; R. König; R.D. Smith; B.Ø. Palsson |
2010 |
| Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. |
V.A. Portnoy; D.A. Scott; N.E. Lewis; Y. Tarasova; A.L. Osterman; B.Ø. Palsson |
2010 |
| Drug off-target effects predicted using structural analysis in the context of a metabolic network model. |
R.L. Chang; L. Xie; L. Xie; P.E. Bourne; B.Ø. Palsson |
2010 |
| A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. |
M.I. Sigurdsson; N. Jamshidi; E. Steingrimsson; I. Thiele; B.Ø. Palsson |
2010 |
| A protocol for generating a high-quality genome-scale metabolic reconstruction. |
I. Thiele; B.Ø. Palsson |
2010 |
| Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. |
A. Bordbar; N.E. Lewis; J. Schellenberger; B.Ø. Palsson; N. Jamshidi |
2010 |
| Towards genome-scale signalling network reconstructions. |
D.R. Hyduke; B.Ø. Palsson |
2010 |
| RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. |
T.M. Conrad; M. Frazier; A.R. Joyce; B.K. Cho; E.M. Knight; N.E. Lewis; R. Landick; B.Ø. Palsson |
2010 |
| What is flux balance analysis? |
J.D. Orth; I. Thiele; B.Ø. Palsson |
2010 |
| Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene. |
P. Charusanti; T.M. Conrad; E.M. Knight; K. Venkataraman; N.L. Fong; B. Xie; Y. Gao; B.Ø. Palsson |
2010 |
| Production of pilus-like filaments in Geobacter sulfurreducens in the absence of the type IV pilin protein PilA. |
A. Klimes; A.E. Franks; R.H. Glaven; H. Tran; C.L. Barrett; Y. Qiu; K. Zengler; D.R. Lovley |
2010 |
| Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. |
N. Jamshidi; B.Ø. Palsson |
2010 |
| Microbiology. Topping off a multiscale balancing act. |
J.A. Lerman; B.Ø. Palsson |
2010 |
| Reconstruction annotation jamborees: a community approach to systems biology. |
I. Thiele; B.Ø. Palsson |
2010 |
| Large-scale in silico modeling of metabolic interactions between cell types in the human brain. |
N.E. Lewis; G. Schramm; A. Bordbar; J. Schellenberger; M.P. Andersen; J.K. Cheng; N. Patel; A. Yee; R.A. Lewis; R. Eils; R. König; B.Ø. Palsson |
2010 |
| Connecting extracellular metabolomic measurements to intracellular flux states in yeast. |
M.L. Mo; B.Ø. Palsson; M.J. Herrgard |
2009 |
| Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. |
N.E. Lewis; B.K. Cho; E.M. Knight; B.Ø. Palsson |
2009 |
| Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. |
N. Jamshidi; B.Ø. Palsson |
2009 |
| Functional states of the genome-scale Escherichia coli transcriptional regulatory system. |
E.P. Gianchandani; A.R. Joyce; B.Ø. Palsson; J.A. Papin |
2009 |
| Probing the basis for genotype-phenotype relationships. |
B.K. Cho; B.Ø. Palsson |
2009 |
| Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect. |
B.K. Cho; B.Ø. Palsson |
2009 |
| Flux-concentration duality in dynamic nonequilibrium biological networks. |
N. Jamshidi; B.Ø. Palsson |
2009 |
| Use of randomized sampling for analysis of metabolic networks. |
J. Schellenberger; B.Ø. Palsson |
2009 |
| Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. |
T.M. Conrad; A.R. Joyce; K.M. Applebee; C.L. Barrett; B. Xie; Y. Gao; B.Ø. Palsson |
2009 |
| The transcription unit architecture of the Escherichia coli genome. |
B.K. Cho; K. Zengler; Y. Qiu; Y.S. Park; E.M. Knight; C.L. Barrett; Y. Gao; B.Ø. Palsson |
2009 |
| Understanding human metabolic physiology: a genome-to-systems approach. |
M.L. Mo; B.Ø. Palsson |
2009 |
| Applications of genome-scale metabolic reconstructions. |
M.A. Oberhardt; B.Ø. Palsson; J.A. Papin |
2009 |
| Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. |
C.L. Barrett; M.J. Herrgard; B.Ø. Palsson |
2009 |
| Reconstruction of biochemical networks in microorganisms. |
A.M. Feist; M.J. Herrgard; I. Thiele; J.L. Reed; B.Ø. Palsson |
2009 |
| Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. |
A. Raghunathan; J.L. Reed; S. Shin; B.Ø. Palsson; S. Daefler |
2009 |