| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| 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 |
| Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein. | F. Büchel; S. Saliger; A. Dräger; S. Hoffmann; C. Wrzodek; A. Zell; P.J. Kahle |
2013 |
| Multispecific Drug Transporter Oat3 (Slc22a8) Regulates Multiple Metabolic Pathways. | W. Wu; N. Jamshidi; S.A. Eraly; H.C. Liu; K.T. Bush; B.O. Palsson; S.K. Nigam |
2013 |
| Analysis of omics data with genome-scale models of metabolism. | D.R. Hyduke; N.E. Lewis; B.Ø. Palsson |
2013 |
| COBRApy: COnstraints-Based Reconstruction and Analysis for Python. | A. Ebrahim; J.A. Lerman; B.O. Palsson; D.R. Hyduke |
2013 |
| Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity. | O. Rolfsson; G. Paglia; M. Magnusdóttir; B.Ø. Palsson; I. Thiele |
2013 |
| Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. | H. Nagarajan; M. Embree; A.E. Rotaru; P.M. Shrestha; A.M. Feist; B.Ø. Palsson; D.R. Lovley; K. Zengler |
2013 |
| Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. | N.E. Lewis; X. Liu; Y. Li; H. Nagarajan; G. Yerganian; E. O'Brien; A. Bordbar; A.M. Roth; J. Rosenbloom; C. Bian; M. Xie; W. Chen; N. Li; D. Baycin-Hizal; H. Latif; J. Forster; M.J. Betenbaugh; I. Famili; X. Xu; J. Wang; B.O. Palsson |
2013 |
| Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. | H. Nagarajan; M. Sahin; J. Nogales; H. Latif; D.R. Lovley; A. Ebrahim; K. Zengler |
2013 |
| MS/MS networking guided analysis of molecule and gene cluster families. | D.D. Nguyen; C.H. Wu; W.J. Moree; A. Lamsa; M.H. Medema; X. Zhao; R.G. Gavilan; M. Aparicio; L. Atencio; C. Jackson; J. Ballesteros; J. Sanchez; J.D. Watrous; V.V. Phelan; C. Wiel; R.D. Kersten; S. Mehnaz; R. De Mot; E.A. Shank; P. Charusanti; H. Nagarajan; B.M. Duggan; B.S. Moore; N. Bandeira; B.Ø. Palsson; K. Pogliano; M. Gutiérrez; P.C. Dorrestein |
2013 |
| A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent. | D. McCloskey; J.A. Gangoiti; Z.A. King; R.K. Naviaux; B.A. Barshop; B.O. Palsson; A.M. Feist |
2013 |
| Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. | R.L. Chang; K. Andrews; D. Kim; Z. Li; A. Godzik; B.O. Palsson |
2013 |
| Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. | J.M. Monk; P. Charusanti; R.K. Aziz; J.A. Lerman; N. Premyodhin; J.D. Orth; A.M. Feist; B.Ø. Palsson |
2013 |
| Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. | D. McCloskey; B.Ø. Palsson; A.M. Feist |
2013 |
| Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites. | K.S. Hwang; H.U. Kim; P. Charusanti; B.Ø. Palsson; S.Y. Lee |
2013 |
| Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling. | C. Ansong; B.L. Deatherage; D. Hyduke; B. Schmidt; J.E. McDermott; M.B. Jones; S. Chauhan; P. Charusanti; Y.M. Kim; E.S. Nakayasu; J. Li; A. Kidwai; G. Niemann; R.N. Brown; T.O. Metz; K. McAteer; F. Heffron; S.N. Peterson; V. Motin; B.O. Palsson; R.D. Smith; J.N. Adkins |
2013 |
| GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. | B.J. Schmidt; A. Ebrahim; T.O. Metz; J.N. Adkins; B.Ø. Palsson; D.R. Hyduke |
2013 |
| Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks. | Y. Qiu; H. Nagarajan; M. Embree; W. Shieu; E. Abate; K. Juárez; B.K. Cho; J.G. Elkins; K.P. Nevin; C.L. Barrett; D.R. Lovley; B.O. Palsson; K. Zengler |
2013 |
| Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community. | M. Embree; H. Nagarajan; N. Movahedi; H. Chitsaz; K. Zengler |
2013 |
| Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. | Y.M. Kim; B.J. Schmidt; A.S. Kidwai; M.B. Jones; B.L. Deatherage Kaiser; H.M. Brewer; H.D. Mitchell; B.O. Palsson; J.E. McDermott; F. Heffron; R.D. Smith; S.N. Peterson; C. Ansong; D.R. Hyduke; T.O. Metz; J.N. Adkins |
2013 |
| Antibacterial mechanisms identified through structural systems pharmacology. | R.L. Chang; L. Xie; P.E. Bourne; B.O. Palsson |
2013 |
| Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution. | W. Fu; O. Guðmundsson; G. Paglia; G. Herjólfsson; O.S. Andrésson; B.O. Palsson; S. Brynjólfsson |
2013 |
| 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 |