| Systematizing the generation of missing metabolic knowledge. |
J.D. Orth; B.Ø. Palsson |
2010 |
| Structural and operational complexity of the Geobacter sulfurreducens genome. |
Y. Qiu; B.K. Cho; Y.S. Park; D.R. Lovley; B.Ø. Palsson; K. Zengler |
2010 |
| Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. |
A.M. Feist; D.C. Zielinski; J.D. Orth; J. Schellenberger; M.J. Herrgard; B.Ø. Palsson |
2010 |
| 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 |
| 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 |
| Metabolic network analysis integrated with transcript verification for sequenced genomes. |
A. Manichaikul; L. Ghamsari; E.F.Y. Hom; C. Lin; R.R. Murray; R.L. Chang; S. Balaji; T. Hao; Y. Shen; A.K. Chavali; I. Thiele; X. Yang; C. Fan; E. Mello; D.E. Hill; M. Vidal; K. Salehi-Ashtiani; J.A. Papin |
2009 |
| Genome-scale network analysis of imprinted human metabolic genes. |
M.I. Sigurdsson; N. Jamshidi; J.J. Jonsson; B.Ø. Palsson |
2009 |
| Three-dimensional structural view of the central metabolic network of Thermotoga maritima. |
Y. Zhang; I. Thiele; D. Weekes; Z. Li; L. Jaroszewski; K. Ginalski; A.M. Deacon; J. Wooley; S.A. Lesley; I.A. Wilson; B.Ø. Palsson; A.L. Osterman; A. Godzik |
2009 |
| Identification of potential pathway mediation targets in Toll-like receptor signaling. |
F. Li; I. Thiele; N. Jamshidi; B.Ø. Palsson |
2009 |
| Metabolic systems biology. |
B.Ø. Palsson |
2009 |
| Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. |
I. Thiele; N. Jamshidi; R.M.T. Fleming; B.Ø. Palsson |
2009 |
| 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 |
| Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain. |
V.A. Portnoy; M.J. Herrgard; B.Ø. Palsson |
2008 |
| Three factors underlying incorrect in silico predictions of essential metabolic genes. |
S.A. Becker; B.Ø. Palsson |
2008 |
| Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. |
B.K. Cho; C.L. Barrett; E.M. Knight; Y.S. Park; B.Ø. Palsson |
2008 |
| Formulating genome-scale kinetic models in the post-genome era. |
N. Jamshidi; B.Ø. Palsson |
2008 |
| Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. |
B.K. Cho; E.M. Knight; C.L. Barrett; B.Ø. Palsson |
2008 |