Publication Title Authors Publication Year Sort ascending
Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features.

J.H. Seo; J.S.J. Hong; D. Kim; B.K. Cho; T.W. Huang; S.F. Tsai; B.O. Palsson; P. Charusanti

2012
A road map for the development of community systems (CoSy) biology.

K. Zengler; B.O. Palsson

2012
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
Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor.

W. Fu; O. Gudmundsson; A.M. Feist; G. Herjolfsson; S. Brynjolfsson; B.O. Palsson

2012
Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies.

G. Paglia; M. Magnúsdóttir; S. Thorlacius; O.E. Sigurjónsson; S. Guðmundsson; B.Ø. Palsson; I. Thiele

2012
A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.

R.M.T. Fleming; C.M. Maes; M.A. Saunders; Y. Ye; B.Ø. Palsson

2012
In silico method for modelling metabolism and gene product expression at genome scale

J.A. Lerman; D.R. Hyduke; H. Latif; V.A. Portnoy; N.E. Lewis; J.D. Orth; A.C. Schrimpe-Rutledge; R.D. Smith; J.N. Adkins; K. Zengler; B.O. Palsson

2012
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions.

J.D. Orth; B.O. Palsson

2012
Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.

P. Charusanti; N.L. Fong; H. Nagarajan; A.R. Pereira; H.J. Li; E.A. Abate; Y. Su; W.H. Gerwick; B.O. Palsson

2012
Systems biology of stored blood cells: can it help to extend the expiration date?

G. Paglia; B.Ø. Palsson; O.E. Sigurjonsson

2012
Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.

J. Nogales; S. Gudmundsson; E.M. Knight; B.O. Palsson; I. Thiele

2012
Proteomic analysis of Chinese hamster ovary cells.

D. Baycin-Hizal; D.L. Tabb; R. Chaerkady; L. Chen; N.E. Lewis; H. Nagarajan; V. Sarkaria; A. Kumar; D. Wolozny; J. Colao; E. Jacobson; Y. Tian; R.N. O'Meally; S.S. Krag; R.N. Cole; B.O. Palsson; H. Zhang; M. Betenbaugh

2012
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.

N.E. Lewis; H. Nagarajan; B.O. Palsson

2012
Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).

G. Paglia; S. Hrafnsdóttir; M. Magnúsdóttir; R.M.T. Fleming; S. Thorlacius; B.Ø. Palsson; I. Thiele

2012
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
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