| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| 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 |
| TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors. | J. Eichner; F. Topf; A. Dräger; C. Wrzodek; D. Wanke; A. Zell |
2013 |
| Optimizing Cofactor Specificity of Oxidoreductase Enzymes for the Generation of Microbial Production Strains—OptSwap | Z.A. King; A.M. Feist |
2013 |
| SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. | C. Chaouiya; D. Bérenguier; S.M. Keating; A. Naldi; M.P. van Iersel; N. Rodriguez; A. Dräger; F. Büchel; T. Cokelaer; B. Kowal; B. Wicks; E. Gonçalves; J. Dorier; M. Page; P.T. Monteiro; A. von Kamp; I. Xenarios; H. de Jong; M. Hucka; S. Klamt; D. Thieffry; N. Le Novère; J. Saez-Rodriguez; T. Helikar |
2013 |
| The COMBREX project: design, methodology, and initial results. | B.P. Anton; Y.C. Chang; P. Brown; H.P. Choi; L.L. Faller; J. Guleria; Z. Hu; N. Klitgord; A. Levy-Moonshine; A. Maksad; V. Mazumdar; M. McGettrick; L. Osmani; R. Pokrzywa; J. Rachlin; R. Swaminathan; B. Allen; G. Housman; C. Monahan; K. Rochussen; K. Tao; A.S. Bhagwat; S.E. Brenner; L. Columbus; V. de Crécy-Lagard; D. Ferguson; A. Fomenkov; G. Gadda; R.D. Morgan; A.L. Osterman; D.A. Rodionov; I.A. Rodionova; K.E. Rudd; D. Söll; J. Spain; S.Y. Xu; A. Bateman; R.M. Blumenthal; M. Bollinger; W.S. Chang; M. Ferrer; I. Friedberg; M.Y. Galperin; J. Gobeill; D. Haft; J. Hunt; P. Karp; W. Klimke; C. Krebs; D. Macelis; R. Madupu; M.J. Martin; J.H. Miller; C. O'Donovan; B. Palsson; P. Ruch; A. Setterdahl; G. Sutton; J. Tate; A. Yakunin; D. Tchigvintsev; G. Plata; J. Hu; R. Greiner; D. Horn; K. Sjölander; S.L. Salzberg; D. Vitkup; S. Letovsky; D. Segrè; C. DeLisi; R.J. Roberts; M. Steffen; S. Kasif |
2013 |
| The genome organization of Thermotoga maritima reflects its lifestyle. | H. Latif; J.A. Lerman; V.A. Portnoy; Y. Tarasova; H. Nagarajan; A.C. Schrimpe-Rutledge; R.D. Smith; J.N. Adkins; D.H. Lee; Y. Qiu; K. Zengler |
2013 |
| Path2Models: large-scale generation of computational models from biochemical pathway maps. | F. Büchel; N. Rodriguez; N. Swainston; C. Wrzodek; T. Czauderna; R. Keller; F. Mittag; M. Schubert; M. Glont; M. Golebiewski; M. van Iersel; S. Keating; M. Rall; M. Wybrow; H. Hermjakob; M. Hucka; D.B. Kell; W. Müller; P. Mendes; A. Zell; C. Chaouiya; J. Saez-Rodriguez; F. Schreiber; C. Laibe; A. Dräger; N. Le Novère |
2013 |
| Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant. | N.L. Fong; J.A. Lerman; I. Lam; B.O. Palsson; P. Charusanti |
2013 |
| Sulfide-driven microbial electrosynthesis. | Y. Gong; A. Ebrahim; A.M. Feist; M. Embree; T. Zhang; D. Lovley; K. Zengler |
2013 |
| 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 |