Metabolic network modeling and simulation for drug targeting and discovery

targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

(2012) Karthik Raman et al.   BMC Systems Biology

Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

(2011) Kechi Fang et al.   BMC Systems Biology

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans

(2011) Vinay Satish Kumar et al.   BMC Systems Biology

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228

(2011) Y.-C. Liao et al.   JOURNAL OF BACTERIOLOGY

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA

(2011) Peng Xu et al.   METABOLIC ENGINEERING

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

(2011) H. U. Kim et al.   Molecular Systems Biology

Fix the antibiotics pipeline

(2011) Matthew A. Cooper et al.   NATURE

OncoTrack tests drugs in virtual people

(2011) Markus Elsner   NATURE BIOTECHNOLOGY

Will Computers Crash Genomics?

(2011) E. Pennisi   SCIENCE

Prospects for systems biology and modeling of the gut microbiome

(2011) Fredrik H. Karlsson et al.   TRENDS IN BIOTECHNOLOGY

Essential Metabolites of Mycobacterium tuberculosis and Their Mimics

(2011) G. Lamichhane et al.   mBio

A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

(2011) A. Aderem et al.   mBio

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

(2011) Matthew A. Oberhardt et al.   PLoS Computational Biology

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis

(2010) Carola Huthmacher et al.   BMC Systems Biology

Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis

(2010) Anu Raghunathan et al.   BMC Systems Biology

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

(2010) Xin Fang et al.   BMC Systems Biology

A Genome-Scale Metabolic Model of Cryptosporidium hominis

(2010) Niti Vanee et al.   CHEMISTRY & BIODIVERSITY

Data integration and analysis of biological networks

(2010) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genome-scale network analysis of imprinted human metabolic genes

(2010) Martin Sigurdsson et al.   Epigenetics

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Metabolic control analysis indicates a change of strategy in the treatment of cancer

(2010) Rafael Moreno-Sánchez et al.   MITOCHONDRION

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

(2010) Christoph Gille et al.   Molecular Systems Biology

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network

(2010) Germán Plata et al.   Molecular Systems Biology

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

The antibiotics market

(2010) Bashar Hamad   NATURE REVIEWS DRUG DISCOVERY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Modeling Core Metabolism in Cancer Cells: Surveying the Topology Underlying the Warburg Effect

(2010) Osbaldo Resendis-Antonio et al.   PLoS One

Blueprint for antimicrobial hit discovery targeting metabolic networks

(2010) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Reaction-Diffusion Model of Human Brain Development

(2010) Julien Lefèvre et al.   PLoS Computational Biology

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

Constraints-based genome-scale metabolic simulation for systems metabolic engineering

(2009) Jong Myoung Park et al.   BIOTECHNOLOGY ADVANCES

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

(2009) Anu Raghunathan et al.   BMC Systems Biology

Comparative Genome-Scale Metabolic Reconstruction and Flux Balance Analysis of Multiple Staphylococcus aureus Genomes Identify Novel Antimicrobial Drug Targets

(2009) D.-S. Lee et al.   JOURNAL OF BACTERIOLOGY

Genome Scale Reconstruction of a Salmonella Metabolic Model

(2009) Manal AbuOun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic Profiling of Human Lung Cancer Tissue by1H High Resolution Magic Angle Spinning (HRMAS) NMR Spectroscopy

(2009) Cláudia M. Rocha et al.   JOURNAL OF PROTEOME RESEARCH

Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks

(2009) Tae Yong Kim et al.   METABOLIC ENGINEERING

Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis

(2009) Karthik Raman et al.   Molecular BioSystems

Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001

(2009) Ali Navid et al.   Molecular BioSystems

Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE

(2009) Hyun Uk Kim et al.   Molecular BioSystems

Predicting metabolic biomarkers of human inborn errors of metabolism

(2009) Tomer Shlomi et al.   Molecular Systems Biology

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Synergistic drug combinations tend to improve therapeutically relevant selectivity

(2009) Joseph Lehár et al.   NATURE BIOTECHNOLOGY

Benzothiazinones Kill Mycobacterium tuberculosis by Blocking Arabinan Synthesis

(2009) V. Makarov et al.   SCIENCE

Antibiotics for Emerging Pathogens

(2009) M. A. Fischbach et al.   SCIENCE

Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

(2009) M. G. Vander Heiden et al.   SCIENCE

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

(2009) Patrick F. Suthers et al.   PLoS Computational Biology

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Impact of the solvent capacity constraint on E. coli metabolism

(2008) Alexei Vazquez et al.   BMC Systems Biology

‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries

(2008) Paul D. Dobson et al.   DRUG DISCOVERY TODAY

Metabolic Network Model of a Human Oral Pathogen

(2008) V. Mazumdar et al.   JOURNAL OF BACTERIOLOGY

Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

(2008) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY

Models from experiments: combinatorial drug perturbations of cancer cells

(2008) Sven Nelander et al.   Molecular Systems Biology

Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

(2008) Arvind K Chavali et al.   Molecular Systems Biology

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

The implications of human metabolic network topology for disease comorbidity

(2008) D.- S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Inhibitor of FtsZ with Potent and Selective Anti-Staphylococcal Activity

(2008) D. J. Haydon et al.   SCIENCE

Novel paradigms for drug discovery: computational multitarget screening

(2008) E JENWITHEESUK et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology