| BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. |
J. Schellenberger; J.O. Park; T.M. Conrad; B.Ø. Palsson |
2010 |
| The biomass objective function. |
A.M. Feist; B.Ø. Palsson |
2010 |
| Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol. |
D.H. Lee; B.Ø. Palsson |
2010 |
| Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery. |
I. Thiele; R.M.T. Fleming; A. Bordbar; J. Schellenberger; B.Ø. Palsson |
2010 |
| De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. |
H. Nagarajan; J.E. Butler; A. Klimes; Y. Qiu; K. Zengler; J. Ward; N.D. Young; B.A. Methé; B.Ø. Palsson; D.R. Lovley; C.L. Barrett |
2010 |
| 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 |
| 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 |
| 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 |
| 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 |