| Publication Title | Authors | Publication Year Sort ascending |
|---|---|---|
| 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 |
| The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models. | S. Palsson; T.P. Hickling; E.L. Bradshaw-Pierce; M. Zager; K. Jooss; P.J.O. Brien; M.E. Spilker; B.O. Palsson; P. Vicini |
2013 |
| A community-driven global reconstruction of human metabolism. | I. Thiele; N. Swainston; R.M.T. Fleming; A. Hoppe; S. Sahoo; M.K. Aurich; H. Haraldsdottir; M.L. Mo; O. Rolfsson; M.D. Stobbe; S.G. Thorleifsson; R. Agren; C. Bölling; S. Bordel; A.K. Chavali; P. Dobson; W.B. Dunn; L. Endler; D. Hala; M. Hucka; D. Hull; D. Jameson; N. Jamshidi; J.J. Jonsson; N. Juty; S. Keating; I. Nookaew; N. Le Novère; N. Malys; A. Mazein; J.A. Papin; N.D. Price; E. Selkov; M.I. Sigurdsson; E. Simeonidis; N. Sonnenschein; K. Smallbone; A. Sorokin; J.H.G.M. Beek; D. Weichart; I. Goryanin; J. Nielsen; H.V. Westerhoff; D.B. Kell; P. Mendes; B.Ø. Palsson |
2013 |
| Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. | E.J. O'Brien; J.A. Lerman; R.L. Chang; D.R. Hyduke; B.Ø. Palsson |
2013 |
| Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. | M.C. Gonnerman; M.N. Benedict; A.M. Feist; W.W. Metcalf; N.D. Price |
2013 |
| 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 |
| 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 |
| 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 |