An analysis of a ‘community-driven’ reconstruction of the human metabolic network

MyCompoundID: Using an Evidence-Based Metabolome Library for Metabolite Identification

(2013) Liang Li et al.   ANALYTICAL CHEMISTRY

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology

(2013) Richard Adams et al.   BIOINFORMATICS

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

(2013) Makoto Miwa et al.   BIOINFORMATICS

Trimethylamine-N-Oxide, a Metabolite Associated with Atherosclerosis, Exhibits Complex Genetic and Dietary Regulation

(2013) Brian J. Bennett et al.   Cell Metabolism

The emerging CHO systems biology era: harnessing the ‘omics revolution for biotechnology

(2013) Helene Faustrup Kildegaard et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values

(2012) Nozomu Sakurai et al.   BIOINFORMATICS

Extracting semantically enriched events from biomedical literature

(2012) Makoto Miwa et al.   BMC BIOINFORMATICS

Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast

(2012) Karin Lanthaler et al.   BMC BIOLOGY

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

(2012) Benjamin D Heavner et al.   BMC Systems Biology

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

(2012) Yuliang Wang et al.   BMC Systems Biology

The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so

(2012) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

The core control system of intracellular iron homeostasis: A mathematical model

(2012) J. Chifman et al.   JOURNAL OF THEORETICAL BIOLOGY

MetaboLights: towards a new COSMOS of metabolomics data management

(2012) Christoph Steinbeck et al.   Metabolomics

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Metabolomics: A tool for early detection of toxicological effects and an opportunity for biology based grouping of chemicals—From QSAR to QBAR

(2012) B. van Ravenzwaay et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

An accelerated workflow for untargeted metabolomics using the METLIN database

(2012) Ralf Tautenhahn et al.   NATURE BIOTECHNOLOGY

Systems metabolic engineering of microorganisms for natural and non-natural chemicals

(2012) Jeong Wook Lee et al.   Nature Chemical Biology

Genetics and iron in the systems biology of Parkinson’s disease and some related disorders

(2012) Claudia Funke et al.   NEUROCHEMISTRY INTERNATIONAL

A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory

(2012) Leroy Hood et al.   New Biotechnology

ECMDB: The E. coli Metabolome Database

(2012) An Chi Guo et al.   NUCLEIC ACIDS RESEARCH

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

(2012) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

(2012) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database

(2012) Yuji Sawada et al.   PHYTOCHEMISTRY

MetaboSearch: Tool for Mass-Based Metabolite Identification Using Multiple Databases

(2012) Bin Zhou et al.   PLoS One

Reproducibility and robustness of metabolome analysis in rat plasma of 28-day repeated dose toxicity studies

(2012) H. Kamp et al.   TOXICOLOGY LETTERS

Chapter 3: Small Molecules and Disease

(2012) David S. Wishart   PLoS Computational Biology

Drug Transporters in Drug Efficacy and Toxicity

(2011) M.K. DeGorter et al.   Annual Review of Pharmacology and Toxicology

Metabolites as global regulators: A new view of protein regulation

(2011) Xiyan Li et al.   BIOESSAYS

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

Pharmaceutical drug transport: the issues and the implications that it is essentially carrier-mediated only

(2011) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Strategies for bringing drug delivery tools into discovery

(2011) Elizabeth Kwong et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

From zero to hero—Design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production

(2011) Judith Becker et al.   METABOLIC ENGINEERING

Controlled vocabularies and semantics in systems biology

(2011) M. Courtot et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

Open Babel: An open chemical toolbox

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

Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson’s, Huntington’s, Alzheimer’s, prions, bactericides, chemical toxicology and others as examples

(2010) Douglas B. Kell   ARCHIVES OF TOXICOLOGY

SBRML: a markup language for associating systems biology data with models

(2010) Joseph O. Dada et al.   BIOINFORMATICS

Utopia documents: linking scholarly literature with research data

(2010) T. K. Attwood 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

Further developments towards a genome-scale metabolic model of yeast

(2010) Paul D Dobson et al.   BMC Systems Biology

Towards a genome-scale kinetic model of cellular metabolism

(2010) Kieran Smallbone et al.   BMC Systems Biology

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

(2010) Xiyan Li et al.   CELL

Whole-body systems approaches for gut microbiota-targeted, preventive healthcare

(2010) Liping Zhao et al.   JOURNAL OF BIOTECHNOLOGY

Mining metabolites: extracting the yeast metabolome from the literature

(2010) Chikashi Nobata et al.   Metabolomics

Reconstruction annotation jamborees: a community approach to systems biology

(2010) Ines Thiele et al.   Molecular Systems Biology

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

(2010) Christoph Gille 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

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Metabolites do social networking

(2010) Douglas B Kell   Nature Chemical Biology

Membrane transporters in drug development

(2010)   NATURE REVIEWS DRUG DISCOVERY

Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses

(2010) J. M. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Event extraction for systems biology by text mining the literature

(2010) Sophia Ananiadou et al.   TRENDS IN BIOTECHNOLOGY

Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics

(2009) M. Brown et al.   ANALYST

Development and Performance of a Gas Chromatography−Time-of-Flight Mass Spectrometry Analysis for Large-Scale Nontargeted Metabolomic Studies of Human Serum

(2009) Paul Begley et al.   ANALYTICAL CHEMISTRY

Development of a Robust and Repeatable UPLC−MS Method for the Long-Term Metabolomic Study of Human Serum

(2009) Eva Zelena et al.   ANALYTICAL CHEMISTRY

Calling International Rescue: knowledge lost in literature and data landslide!

(2009) Teresa K. Attwood et al.   BIOCHEMICAL JOURNAL

libAnnotationSBML: a library for exploiting SBML annotations

(2009) N. Swainston et al.   BIOINFORMATICS

Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases

(2009) Douglas B Kell   BMC Medical Genomics

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Implications of the Dominant Role of Transporters in Drug Uptake by Cells (Supplementary Material)

(2009) Paul Dobson et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Flux balance analysis: A geometric perspective

(2009) Kieran Smallbone et al.   JOURNAL OF THEORETICAL BIOLOGY

A general map of iron metabolism and tissue-specific subnetworks

(2009) Valerie Hower et al.   Molecular BioSystems

Predicting metabolic biomarkers of human inborn errors of metabolism

(2009) Tomer Shlomi et al.   Molecular Systems Biology

Predicting promiscuity

(2009) Andrew L. Hopkins   NATURE

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

(2009) W. R. Wikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capillary Electrophoresis Time-of-Flight Mass Spectrometry for Comparative Metabolomics of Transgenic versus Conventional Maize

(2008) Tuuli Levandi et al.   ANALYTICAL CHEMISTRY

The State of Innovation in Drug Development

(2008) I Kola   CLINICAL PHARMACOLOGY & THERAPEUTICS

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

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

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule?

(2008) Paul D. Dobson et al.   NATURE REVIEWS DRUG DISCOVERY

Symbiotic gut microbes modulate human metabolic phenotypes

(2008) M. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The markup is the model: Reasoning about systems biology models in the Semantic Web era

(2007) Douglas B. Kell et al.   JOURNAL OF THEORETICAL BIOLOGY