Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions

L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH

(2017) Andrew M Intlekofer et al.   Nature Chemical Biology

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

(2017) Edik M. Blais et al.   Nature Communications

Analysing Algorithms and Data Sources for the Tissue-Specific Reconstruction of Liver Healthy and Cancer Cells

(2017) Jorge Ferreira et al.   Interdisciplinary Sciences-Computational Life Sciences

Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism

(2017) Daniel C. Zielinski et al.   Scientific Reports

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

(2016) A. J. Aguirre et al.   Cancer Discovery

Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms

(2016) Maria P. Pacheco et al.   Frontiers in Physiology

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

(2016) Hooman Hefzi et al.   Cell Systems

Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method

(2016) Luis Tobalina et al.   PLoS One

An algorithm for the reduction of genome-scale metabolic network models to meaningful core models

(2015) Philipp Erdrich et al.   BMC Systems Biology

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism

(2015) Francesco Gatto et al.   Scientific Reports

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Reducing Recon 2 for steady-state flux analysis of HEK cell culture

(2014) Lake-Ee Quek et al.   JOURNAL OF BIOTECHNOLOGY

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

(2014) R. Agren et al.   Molecular Systems Biology

A comprehensive transcriptional portrait of human cancer cell lines

(2014) Christiaan Klijn et al.   NATURE BIOTECHNOLOGY

Coordination of microbial metabolism

(2014) Victor Chubukov et al.   NATURE REVIEWS MICROBIOLOGY

Multi-Tissue Computational Modeling Analyzes Pathophysiology of Type 2 Diabetes in MKR Mice

(2014) Amit Kumar et al.   PLoS One

Towards a new science of secondary metabolism

(2013) Arryn Craney et al.   JOURNAL OF ANTIBIOTICS

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

(2012) Aarash Bordbar et al.   Molecular Systems Biology

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

From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants

(2011) Hoi Yee Chu et al.   PLANT JOURNAL

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

(2010) Martin I Sigurdsson et al.   BMC Systems Biology

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis 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

Cancer-associated IDH1 mutations produce 2-hydroxyglutarate

(2009) Lenny Dang et al.   NATURE

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

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