Computational methods to identify metabolic sub-networks based on metabolomic profiles

Integrated pathway-based and network-based analysis of GC-MS rice metabolomics data under diazinon stress to infer affected biological pathways

(2016) Vahideh Mahdavi et al.   ANALYTICAL BIOCHEMISTRY

Metabolomic analysis reveals distinct profiles in the plasma and urine of rats fed a high-protein diet

(2015) Chunlong Mu et al.   AMINO ACIDS

Biological insights through nontargeted metabolomics

(2015) Daniel C Sévin et al.   CURRENT OPINION IN BIOTECHNOLOGY

ChEMBL web services: streamlining access to drug discovery data and utilities

(2015) Mark Davies et al.   NUCLEIC ACIDS RESEARCH

Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network

(2015) Taehyong Kim et al.   PLANT PHYSIOLOGY

ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics

(2014) Ricardo R. Silva et al.   BIOINFORMATICS

Optimal metabolic route search based on atom mappings

(2014) Mario Latendresse et al.   BIOINFORMATICS

BioModels linked dataset

(2014) Sarala M Wimalaratne et al.   BMC Systems Biology

Metabolite identification: are you sure? And how do your peers gauge your confidence?

(2014) Darren J. Creek et al.   Metabolomics

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

(2013) Paulo Vieira Milreu et al.   BIOINFORMATICS

SubNet: a Java application for subnetwork extraction

(2013) Quanwei Zhang et al.   BIOINFORMATICS

Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets

(2013) M. Kotera et al.   BIOINFORMATICS

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Positive Outcomes Influence the Rate and Time to Publication, but Not the Impact Factor of Publications of Clinical Trial Results

(2013) Pilar Suñé et al.   PLoS One

InChI - the worldwide chemical structure identifier standard

(2013) Stephen Heller et al.   Journal of Cheminformatics

Automatic reaction mapping and reaction center detection

(2013) William Lingran Chen et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity

(2012) Dinesh K Barupal et al.   BMC BIOINFORMATICS

Reconciliation of metabolites and biochemical reactions for metabolic networks

(2012) T. Bernard et al.   BRIEFINGS IN BIOINFORMATICS

Identification of potential drug targets in Yersinia pestis using metabolic pathway analysis: MurE ligase as a case study

(2012) Aditya Sharma et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets

(2012) Vicente Acuña et al.   THEORETICAL COMPUTER SCIENCE

Similarity methods in chemoinformatics

(2011) Peter Willett   ANNUAL REVIEW OF INFORMATION SCIENCE AND TECHNOLOGY

Prediction of metabolic pathways from genome-scale metabolic networks

(2011) Karoline Faust et al.   BIOSYSTEMS

Visualizing multi-omics data in metabolic networks with the software Omix—A case study

(2011) Peter Droste et al.   BIOSYSTEMS

Engineering antibiotic production and overcoming bacterial resistance

(2011) Anne-Gaëlle Planson et al.   Biotechnology Journal

The metabolic footprint of aging in mice

(2011) Riekelt H. Houtkooper et al.   Scientific Reports

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

Path finding methods accounting for stoichiometry in metabolic networks

(2011) Jon Pey et al.   GENOME BIOLOGY

Pathway discovery in metabolic networks by subgraph extraction

(2010) Karoline Faust et al.   BIOINFORMATICS

The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports

(2010) G. Wohlgemuth et al.   BIOINFORMATICS

MetPA: a web-based metabolomics tool for pathway analysis and visualization

(2010) J. Xia et al.   BIOINFORMATICS

Microbial 1-butanol production: Identification of non-native production routes andin silicoengineering interventions

(2010) Sridhar Ranganathan et al.   Biotechnology Journal

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

Centrality measure in graphs

(2010) D. J. Klein   JOURNAL OF MATHEMATICAL CHEMISTRY

Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining

(2010) Fabien Jourdan et al.   Metabolomics

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

(2010) Ines Thiele et al.   Nature Protocols

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

(2010) L. Cottret et al.   NUCLEIC ACIDS RESEARCH

PathPred: an enzyme-catalyzed metabolic pathway prediction server

(2010) Y. Moriya et al.   NUCLEIC ACIDS RESEARCH

MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data

(2010) J. Xia et al.   NUCLEIC ACIDS RESEARCH

Graph methods for the investigation of metabolic networks in parasitology

(2010) LUDOVIC COTTRET et al.   PARASITOLOGY

Pathway identification by network pruning in the metabolic network of Escherichia coli

(2009) P. Gerlee et al.   BIOINFORMATICS

Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison

(2009) Aziz Mithani et al.   BIOINFORMATICS

Inferring branching pathways in genome-scale metabolic networks

(2009) Esa Pitkänen et al.   BMC Systems Biology

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

Metabolic Pathfinding Using RPAIR Annotation

(2009) Karoline Faust et al.   JOURNAL OF MOLECULAR BIOLOGY

Model validation of simple-graph representations of metabolism

(2009) P. Holme   Journal of the Royal Society Interface

Applications of genome-scale metabolic reconstructions

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

Hypergraphs and Cellular Networks

(2009) Steffen Klamt et al.   PLoS Computational Biology

Probabilistic assignment of formulas to mass peaks in metabolomics experiments

(2008) Simon Rogers et al.   BIOINFORMATICS

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization

(2008) Torsten Blum et al.   BIOINFORMATICS

Chemical substructures that enrich for biological activity

(2008) Justin Klekota et al.   BIOINFORMATICS

A critical examination of stoichiometric and path-finding approaches to metabolic pathways

(2008) F. J. Planes et al.   BRIEFINGS IN BIOINFORMATICS

An Introduction to Metabolic Networks and Their Structural Analysis

(2008) V. Lacroix et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks

(2008) Torsten Blum et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The University of Minnesota pathway prediction system: predicting metabolic logic

(2008) Lynda B.M. Ellis et al.   NUCLEIC ACIDS RESEARCH

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

(2008) S. Brohee et al.   NUCLEIC ACIDS RESEARCH

Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium

(2008) Hagai Ginsburg   TRENDS IN PARASITOLOGY