| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| The systems biology simulation core algorithm. | R. Keller; A. Dörr; A. Tabira; A. Funahashi; M.J. Ziller; R. Adams; N. Rodriguez; N. Le Novère; N. Hiroi; H. Planatscher; A. Zell; A. Dräger |
2013 |
| Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima. | D.A. Rodionov; I.A. Rodionova; X. Li; D.A. Ravcheev; Y. Tarasova; V.A. Portnoy; K. Zengler; A.L. Osterman |
2013 |
| The microbiome extends to subepidermal compartments of normal skin. | T. Nakatsuji; H.I. Chiang; S.B. Jiang; H. Nagarajan; K. Zengler; R.L. Gallo |
2013 |
| 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 |
| MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH. | J.E. McDermott; P. Braun; R. Bonneau; D.R. Hyduke |
2012 |
| Anaerobic utilization of toluene by marine alpha- and gammaproteobacteria reducing nitrate. | K. Alain; J. Harder; F. Widdel; K. Zengler |
2012 |
| Using the reconstructed genome-scale human metabolic network to study physiology and pathology. | A. Bordbar; B.O. Palsson |
2012 |
| UPLC-UV-MS(E) analysis for quantification and identification of major carotenoid and chlorophyll species in algae. | W. Fu; M. Magnúsdóttir; S. Brynjólfson; B.O. Palsson; G. Paglia |
2012 |
| Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. | D.A. Ravcheev; X. Li; H. Latif; K. Zengler; S.A. Leyn; Y.D. Korostelev; A.E. Kazakov; P.S. Novichkov; A.L. Osterman; D.A. Rodionov |
2012 |
| 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 |
| 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 |