Advances in network-based metabolic pathway analysis and gene expression data integration

Selection of human tissue-specific elementary flux modes using gene expression data

(2013) Alberto Rezola et al.   BIOINFORMATICS

A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype

(2013) Jon Pey et al.   BMC Systems Biology

Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways

(2013) Jon Pey et al.   BMC Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans

(2011) Christoph Kaleta et al.   PLoS Computational Biology

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

Exploring metabolic pathways in genome-scale networks via generating flux modes

(2010) A. Rezola et al.   BIOINFORMATICS

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Estimating the proportion of microarray probes expressed in an RNA sample

(2010) Wei Shi et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

(2010) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

In response to ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’

(2009) Karoline Faust et al.   BIOINFORMATICS

Computing the shortest elementary flux modes in genome-scale metabolic networks

(2009) Luis F. de Figueiredo et al.   BIOINFORMATICS

A note on the complexity of finding and enumerating elementary modes

(2009) Vicente Acuña et al.   BIOSYSTEMS

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns

(2009) C. Kaleta et al.   GENOME RESEARCH

SubpathwayMiner: a software package for flexible identification of pathways

(2009) C. Li et al.   NUCLEIC ACIDS RESEARCH

Can sugars be produced from fatty acids? A test case for pathway analysis tools

(2008) L. F. de Figueiredo et al.   BIOINFORMATICS

Large-scale computation of elementary flux modes with bit pattern trees

(2008) Marco Terzer et al.   BIOINFORMATICS

Modes and cuts in metabolic networks: Complexity and algorithms

(2008) Vicente Acuña et al.   BIOSYSTEMS

The Systems Biology Research Tool: evolvable open-source software

(2008) Jeremiah Wright et al.   BMC Systems Biology

Path finding approaches and metabolic pathways

(2008) F.J. Planes et al.   DISCRETE APPLIED MATHEMATICS

A new constraint-based description of the steady-state flux cone of metabolic networks

(2008) Abdelhalim Larhlimi et al.   DISCRETE APPLIED MATHEMATICS

Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico

(2008) Segun Fatumo et al.   INFECTION GENETICS AND EVOLUTION

Stoichiometric modelling of cell metabolism

(2008) Francisco Llaneras et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

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

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network

(2008) Alexey V Antonov et al.   GENOME BIOLOGY