Publication Title Authors Publication Year
Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage.

I. Thiele; R.M.T. Fleming; R. Que; A. Bordbar; D. Diep; B.O. Palsson

 2012
Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence.

S.J. Ho Sui; R. Lo; A.R. Fernandes; M.D.G. Caulfield; J.A. Lerman; L. Xie; P.E. Bourne; D.L. Baillie; F.S.L. Brinkman

 2012
Network context and selection in the evolution to enzyme specificity.

H. Nam; N.E. Lewis; J.A. Lerman; D.H. Lee; R.L. Chang; D. Kim; B.O. Palsson

 2012
Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling.

J. Schellenberger; D.C. Zielinski; W. Choi; S. Madireddi; V. Portnoy; D.A. Scott; J.L. Reed; A.L. Osterman; B. Palsson

 2012
Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling.

D. Kim; J.S.J. Hong; Y. Qiu; H. Nagarajan; J.H. Seo; B.K. Cho; S.F. Tsai; B.Ø. Palsson

 2012
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation.

A. Bordbar; M.L. Mo; E.S. Nakayasu; A.C. Schrimpe-Rutledge; Y.M. Kim; T.O. Metz; M.B. Jones; B.C. Frank; R.D. Smith; S.N. Peterson; D.R. Hyduke; J.N. Adkins; B.O. Palsson

 2012
Adaptive Laboratory Evolution

B.Ø. Palsson

 2011
Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering.

V.A. Portnoy; D. Bezdan; K. Zengler

 2011
In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.

R. Mahadevan; B.Ø. Palsson; D.R. Lovley

 2011
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.

O. Rolfsson; B.Ø. Palsson; I. Thiele

 2011
A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.

P.L. Tremblay; Z.M. Summers; R.H. Glaven; K.P. Nevin; K. Zengler; C.L. Barrett; Y. Qiu; B.O. Palsson; D.R. Lovley

 2011
Microbial laboratory evolution in the era of genome-scale science.

T.M. Conrad; N.E. Lewis; B.Ø. Palsson

 2011
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.

P. Charusanti; S. Chauhan; K. McAteer; J.A. Lerman; D.R. Hyduke; V.L. Motin; C. Ansong; J.N. Adkins; B.O. Palsson

 2011
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

J.D. Orth; T.M. Conrad; J. Na; J.A. Lerman; H. Nam; A.M. Feist; B.Ø. Palsson

 2011
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology.

A. Bordbar; A.M. Feist; R. Usaite-Black; J. Woodcock; B.O. Palsson; I. Famili

 2011
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.

I. Thiele; D.R. Hyduke; B. Steeb; G. Fankam; D.K. Allen; S. Bazzani; P. Charusanti; F.C. Chen; R.M.T. Fleming; C.A. Hsiung; S.C.J. De Keersmaecker; Y.C. Liao; K. Marchal; M.L. Mo; E. Özdemir; A. Raghunathan; J.L. Reed; Sil Shin; S. Sigurbjörnsdóttir; J. Steinmann; S. Sudarsan; N. Swainston; I.M. Thijs; K. Zengler; B.O. Palsson; J.N. Adkins; D. Bumann

 2011
Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.

D.H. Lee; A.M. Feist; C.L. Barrett; B.Ø. Palsson

 2011
Technologies and approaches to elucidate and model the virulence program of salmonella.

J.E. McDermott; H. Yoon; E.S. Nakayasu; T.O. Metz; D.R. Hyduke; A.S. Kidwai; B.O. Palsson; J.N. Adkins; F. Heffron

 2011
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