| Elimination of thermodynamically infeasible loops in steady-state metabolic models. |
J. Schellenberger; N.E. Lewis; B.Ø. Palsson |
2011 |
| iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. |
A. Bordbar; N. Jamshidi; B.O. Palsson |
2011 |
| Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis. |
S.Y. Ahn; N. Jamshidi; M.L. Mo; W. Wu; S.A. Eraly; A. Dnyanmote; K.T. Bush; T.F. Gallegos; D.H. Sweet; B.Ø. Palsson; S.K. Nigam |
2011 |
| Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. |
J. Schellenberger; R. Que; R.M.T. Fleming; I. Thiele; J.D. Orth; A.M. Feist; D.C. Zielinski; A. Bordbar; N.E. Lewis; S. Rahmanian; J. Kang; D.R. Hyduke; B.Ø. Palsson |
2011 |
| The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. |
X. Xu; H. Nagarajan; N.E. Lewis; S. Pan; Z. Cai; X. Liu; W. Chen; M. Xie; W. Wang; S. Hammond; M.R. Andersen; N. Neff; B. Passarelli; W. Koh; C.H. Fan; J. Wang; Y. Gui; K.H. Lee; M.J. Betenbaugh; S.R. Quake; I. Famili; B.O. Palsson; J. Wang |
2011 |
| Deciphering the transcriptional regulatory logic of amino acid metabolism. |
B.K. Cho; S. Federowicz; Y.S. Park; K. Zengler; B.Ø. Palsson |
2011 |
| Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. |
R.L. Chang; L. Ghamsari; A. Manichaikul; E.F.Y. Hom; S. Balaji; W. Fu; Y. Shen; T. Hao; B.Ø. Palsson; K. Salehi-Ashtiani; J.A. Papin |
2011 |
| Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis. |
C.L. Barrett; B.K. Cho; B.O. Palsson |
2011 |
| An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. |
Y.C. Liao; T.W. Huang; F.C. Chen; P. Charusanti; J.S.J. Hong; H.Y. Chang; S.F. Tsai; B.O. Palsson; C.A. Hsiung |
2011 |
| Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli. |
K.M. Applebee; A.R. Joyce; T.M. Conrad; D.W. Pettigrew; B.Ø. Palsson |
2011 |
| The role of cellular objectives and selective pressures in metabolic pathway evolution. |
H. Nam; T.M. Conrad; N.E. Lewis |
2011 |
| The PurR regulon in Escherichia coli K-12 MG1655. |
B.K. Cho; S.A. Federowicz; M. Embree; Y.S. Park; D. Kim; B.Ø. Palsson |
2011 |
| The challenges of integrating multi-omic data sets. |
B.Ø. Palsson; K. Zengler |
2010 |
| 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 |
| 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 |