NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

Data integration in the era of omics: current and future challenges

(2014) David Gomez-Cabrero et al.   BMC Systems Biology

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Epiviz: interactive visual analytics for functional genomics data

(2014) Florin Chelaru et al.   NATURE METHODS

MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae

(2014) Judith A. H. Wodke et al.   NUCLEIC ACIDS RESEARCH

NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration

(2014) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

An Endotoxin Tolerance Signature Predicts Sepsis and Organ Dysfunction at Initial Clinical Presentation

(2014) Olga M. Pena et al.   EBioMedicine

INVEX—a web-based tool for integrative visualization of expression data

(2013) Jianguo Xia et al.   BIOINFORMATICS

Integration of Metabolomics and Transcriptomics Revealed a Fatty Acid Network Exerting Growth Inhibitory Effects in Human Pancreatic Cancer

(2013) G. Zhang et al.   CLINICAL CANCER RESEARCH

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

(2013) Shuzhao Li et al.   NATURE IMMUNOLOGY

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

INMEX—a web-based tool for integrative meta-analysis of expression data

(2013) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

Disturbed protein-protein interaction networks in metastatic melanoma are associated with worse prognosis and increased functional mutation burden

(2013) Sarah-Jane Schramm et al.   Pigment Cell & Melanoma Research

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases

(2012) Yu Liu et al.   BMC Systems Biology

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

(2012) Sandra Orchard et al.   NATURE METHODS

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

Comprehensive literature review and statistical considerations for microarray meta-analysis

(2012) George C. Tseng et al.   NUCLEIC ACIDS RESEARCH

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis

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

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Endotoxin Tolerance Represents a Distinctive State of Alternative Polarization (M2) in Human Mononuclear Cells

(2011) O. M. Pena et al.   JOURNAL OF IMMUNOLOGY

Interaction databases on the same page

(2011) Andrei L Turinsky et al.   NATURE BIOTECHNOLOGY

Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst

(2011) Jianguo Xia et al.   Nature Protocols

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

(2011) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps

(2011) Christian Perez-Llamas et al.   PLoS One

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

(2010) D. Beisser et al.   BIOINFORMATICS

Visualizing biological data—now and in the future

(2010) Seán I O'Donoghue et al.   NATURE METHODS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

State of the nation in data integration for bioinformatics

(2008) Carole Goble et al.   JOURNAL OF BIOMEDICAL INFORMATICS

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

(2008) David J Lynn et al.   Molecular Systems Biology

GEPAS, a web-based tool for microarray data analysis and interpretation

(2008) J. Tarraga et al.   NUCLEIC ACIDS RESEARCH

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum

(2008) Christian Gieger et al.   PLoS Genetics

Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets

(2008) Adaikalavan Ramasamy et al.   PLOS MEDICINE