Genome scale metabolic models as tools for drug design and personalized medicine

Could drugs inhibiting the mevalonate pathway also target cancer stem cells?

(2016) Wirginia Likus et al.   DRUG RESISTANCE UPDATES

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

BioModels: ten-year anniversary

(2014) Vijayalakshmi Chelliah et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells

(2014) Blanca E. Himes et al.   PLoS One

Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer

(2014) Keren Yizhak et al.   eLife

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Latest developments in molecular docking: 2010-2011 in review

(2013) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

(2013) A. Mardinoglu et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Experimental evidence suggests the existence of evolutionary conserved global operation principles governing microbial metabolism

(2013) Sergio Bordel   Scientific Reports

Metabolic and protein interaction sub-networks controlling the proliferation rate of cancer cells and their impact on patient survival

(2013) Amir Feizi et al.   Scientific Reports

Pharmacogenomics Knowledge for Personalized Medicine

(2012) M Whirl-Carrillo et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design

(2012) Hui Sun Lee et al.   Journal of Chemical Information and Modeling

Metabolite Profiling Identifies a Key Role for Glycine in Rapid Cancer Cell Proliferation

(2012) M. Jain et al.   SCIENCE

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

Old friends in new guise: repositioning of known drugs with structural bioinformatics

(2011) V. J. Haupt et al.   BRIEFINGS IN BIOINFORMATICS

Predicting selective drug targets in cancer through metabolic networks

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

Caffeine inhibits cell proliferation and regulates PKA/GSK3β pathways in U87MG human glioma cells

(2011) Bo Mi Ku et al.   MOLECULES AND CELLS

Targeting cancer metabolism: a therapeutic window opens

(2011) Matthew G. Vander Heiden   NATURE REVIEWS DRUG DISCOVERY

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling

(2009) Michal Brylinski 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