A metabolic network approach for the identification and prioritization of antimicrobial drug targets.

[1]  B. Palsson,et al.  Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. , 1993, Journal of theoretical biology.

[2]  B. Palsson,et al.  Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 , 1994, Applied and environmental microbiology.

[3]  J. Edwards,et al.  Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype* , 1999, The Journal of Biological Chemistry.

[4]  B. Palsson,et al.  The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[5]  B. Palsson,et al.  Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. , 2000, Journal of theoretical biology.

[6]  J. Edwards,et al.  Robustness Analysis of the Escherichiacoli Metabolic Network , 2000, Biotechnology progress.

[7]  G. Church,et al.  Genome-Scale Metabolic Model of Helicobacter pylori 26695 , 2002, Journal of bacteriology.

[8]  G. Church,et al.  Analysis of optimality in natural and perturbed metabolic networks , 2002 .

[9]  B. Palsson,et al.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) , 2003, Genome Biology.

[10]  R. Mahadevan,et al.  The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.

[11]  B. Palsson,et al.  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. , 2003, Genome research.

[12]  B. Palsson,et al.  Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.

[13]  Jose L. Segovia-Juarez,et al.  Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model. , 2004, Journal of theoretical biology.

[14]  Bernhard O Palsson,et al.  Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. , 2004, Trends in biochemical sciences.

[15]  B. Palsson,et al.  Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation , 2005, BMC Microbiology.

[16]  M. Aoki,et al.  Host sphingolipid biosynthesis as a target for hepatitis C virus therapy , 2005, Nature chemical biology.

[17]  U. Sauer,et al.  Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast , 2005, Genome Biology.

[18]  B. Palsson,et al.  Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an In Silico Genome-Scale Characterization of Single- and Double-Deletion Mutants , 2005, Journal of bacteriology.

[19]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[20]  J. Sauer,et al.  The phagosomal transporter A couples threonine acquisition to differentiation and replication of Legionella pneumophila in macrophages. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Anne Kümmel,et al.  In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. , 2005, Biotechnology and bioengineering.

[22]  S. Handley,et al.  Histamine signaling through the H(2) receptor in the Peyer's patch is important for controlling Yersinia enterocolitica infection. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Erwin P. Gianchandani,et al.  Flux balance analysis in the era of metabolomics , 2006, Briefings Bioinform..

[24]  T. Chakraborty,et al.  Host gene expression profiling in pathogen-host interactions. , 2006, Current opinion in immunology.

[25]  Johannes Tramper,et al.  Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes , 2007, Genome Biology.

[26]  D. Stahl,et al.  Molecular Systems Biology 3; Article number 92; doi:10.1038/msb4100131 Citation: Molecular Systems Biology 3:92 , 2022 .

[27]  Adam M. Feist,et al.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.

[28]  C. Chong,et al.  New uses for old drugs , 2007, Nature.

[29]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[30]  S. Klamt,et al.  GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism , 2007, Genome Biology.

[31]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[32]  Bernhard O. Palsson,et al.  Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets , 2007 .

[33]  A. Barabasi,et al.  Drug—target network , 2007, Nature Biotechnology.

[34]  Eleanor C. Saunders,et al.  Living in a phagolysosome; metabolism of Leishmania amastigotes. , 2007, Trends in parasitology.

[35]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[36]  Jason A. Papin,et al.  Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major , 2008, Molecular systems biology.

[37]  Gregory A. Buck,et al.  Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi , 2009, BMC Systems Biology.

[38]  Bernhard O. Palsson,et al.  Context-Specific Metabolic Networks Are Consistent with Experiments , 2008, PLoS Comput. Biol..

[39]  F. Brombacher,et al.  Host-Directed Drug Targeting of Factors Hijacked by Pathogens , 2008, Science Signaling.

[40]  Jason A. Papin,et al.  * Corresponding authors , 2006 .

[41]  Markus J. Herrgård,et al.  Network-based prediction of human tissue-specific metabolism , 2008, Nature Biotechnology.

[42]  A. Hopkins.  Network pharmacology: the next paradigm in drug discovery. , 2008, Nature chemical biology.

[43]  Bernhard O. Palsson,et al.  Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction , 2009, BMC Systems Biology.

[44]  Jason A. Papin,et al.  Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology , 2008, PLoS Comput. Biol..

[45]  John A. Morgan,et al.  BMC Systems Biology BioMed Central Research article , 2009 .

[46]  M. Whiteley,et al.  Revisiting the host as a growth medium , 2008, Nature Reviews Microbiology.

[47]  Kalidas Yeturu,et al.  targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis , 2008, BMC Systems Biology.

[48]  Jason A. Papin,et al.  Applications of genome-scale metabolic reconstructions , 2009, Molecular systems biology.

[49]  Andreas Hoppe,et al.  Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis , 2010, BMC Systems Biology.

[50]  Simon Daefler,et al.  Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis , 2010, BMC Systems Biology.

[51]  Carla P. Guimarães,et al.  Haploid Genetic Screens in Human Cells Identify Host Factors Used by Pathogens , 2009, Science.

[52]  D. Kell,et al.  'Metabolite-likeness' as a criterion in the design and selection of pharmaceutical drug libraries. , 2009, Drug discovery today.

[53]  A. Barabasi,et al.  Targets Drug Genomes Identify Novel Antimicrobial Staphylococcus Aureus of Multiple Reconstruction and Flux Balance Analysis Comparative Genome-scale Metabolic Supplemental Material , 2009 .

[54]  Manal AbuOun,et al.  Genome Scale Reconstruction of a Salmonella Metabolic Model , 2009, The Journal of Biological Chemistry.

[55]  Leopold Parts,et al.  Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. , 2009, Genome research.

[56]  Ali Navid,et al.  Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001. , 2009, Molecular bioSystems.

[57]  V. Schachter,et al.  Genome-scale models of bacterial metabolism: reconstruction and applications , 2008, FEMS microbiology reviews.

[58]  Salomon Amar,et al.  Metabolic Network Model of a Human Oral Pathogen , 2008, Journal of bacteriology.

[59]  B. Palsson,et al.  A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .

[60]  Jaques Reifman,et al.  Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis , 2010, BMC Systems Biology.

[61]  Qibin Zhang,et al.  Temporal Proteome and Lipidome Profiles Reveal Hepatitis C Virus-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics , 2010, PLoS pathogens.

[62]  Stephen S Fong,et al.  A Genome‐Scale Metabolic Model of Cryptosporidium hominis , 2010, Chemistry & biodiversity.

[63]  A. Barabasi,et al.  Blueprint for antimicrobial hit discovery targeting metabolic networks , 2010, Proceedings of the National Academy of Sciences.

[64]  Suhua Chang,et al.  Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction , 2011, BMC Systems Biology.

[65]  S. Lee,et al.  Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE. , 2010, Molecular bioSystems.

[66]  Erwin P. Gianchandani,et al.  The application of flux balance analysis in systems biology , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

[67]  Jason A. Papin,et al.  Metabolic Network Analysis of Pseudomonas aeruginosa during Chronic Cystic Fibrosis Lung Infection , 2010, Journal of bacteriology.

[68]  Rick L. Stevens,et al.  High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.

[69]  Kathleen Marchal,et al.  A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 , 2011, BMC Systems Biology.

[70]  Kellen L. Olszewski,et al.  Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network , 2010, Molecular systems biology.

[71]  U. Sauer,et al.  Automatic policing of biochemical annotations using genomic correlations , 2009, Nature chemical biology.

[72]  Adam M. Feist,et al.  The biomass objective function. , 2010, Current opinion in microbiology.

[73]  Bernhard O. Palsson,et al.  An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228 , 2011, Journal of bacteriology.

[74]  Jason A. Papin,et al.  Functional integration of a metabolic network model and expression data without arbitrary thresholding , 2011, Bioinform..

[75]  Chen Qian,et al.  Comparative study of computational methods to detect the correlated reaction sets in biochemical networks , 2011, Briefings Bioinform..

[76]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[77]  Jason A. Papin,et al.  Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis , 2011, PLoS Comput. Biol..

[78]  S. Oliver,et al.  An integrated approach to characterize genetic interaction networks in yeast metabolism , 2011, Nature Genetics.

[79]  S. Lee,et al.  Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery , 2011, Molecular systems biology.

[80]  J. Reed,et al.  Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli. , 2011, Metabolic engineering.