Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration

Metabolomic Markers of Altered Nucleotide Metabolism in Early Stage Adenocarcinoma

(2015) W. R. Wikoff et al.   Cancer Prevention Research

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Text Mining Infrastructure inR

(2015) Ingo Feinerer et al.   Journal of Statistical Software

Mapping eQTL Networks with Mixed Graphical Markov Models

(2014) Inma Tur et al.   GENETICS

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

O-GlcNAc in cancer biology

(2013) Zhiyuan Ma et al.   AMINO ACIDS

3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data

(2013) Tien-Chueh Kuo et al.   BMC Systems Biology

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

(2013) Leif Väremo et al.   NUCLEIC ACIDS RESEARCH

Batch Normalizer: A Fast Total Abundance Regression Calibration Method to Simultaneously Adjust Batch and Injection Order Effects in Liquid Chromatography/Time-of-Flight Mass Spectrometry-Based Metabolomics Data and Comparison with Current Calibration Methods

(2012) San-Yuan Wang et al.   ANALYTICAL CHEMISTRY

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

MYC on the Path to Cancer

(2012) Chi V. Dang   CELL

Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression

(2012) S. A. Selamat et al.   GENOME RESEARCH

Metabolomics: the apogee of the omics trilogy

(2012) Gary J. Patti et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis

(2012) J. Xia et al.   NUCLEIC ACIDS RESEARCH

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Cross Talk Between O-GlcNAcylation and Phosphorylation: Roles in Signaling, Transcription, and Chronic Disease

(2011) Gerald W. Hart et al.   Annual Review of Biochemistry

Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA

(2011) Atanas Kamburov et al.   BIOINFORMATICS

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data

(2011) Alla Karnovsky et al.   BIOINFORMATICS

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

(2011) Warwick B Dunn et al.   Nature Protocols

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

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

BioNet: an R-Package for the functional analysis of biological networks

(2010) D. Beisser et al.   BIOINFORMATICS

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

(2010) J. Xia et al.   BIOINFORMATICS

Reverse Engineering Molecular Regulatory Networks from Microarray Data with qp-Graphs

(2009) Robert Castelo et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

MetaboAnalyst: a web server for metabolomic data analysis and interpretation

(2009) J. Xia et al.   NUCLEIC ACIDS RESEARCH

Identifying functional modules in protein-protein interaction networks: an integrated exact approach

(2008) M. T. Dittrich et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

(2008) Ana Oliveira et al.   BMC Systems Biology