Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression

The role of mitochondria in neurodegenerative diseases

(2011) Massimiliano Filosto et al.   JOURNAL OF NEUROLOGY

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

(2010) J. Montojo et al.   BIOINFORMATICS

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

(2010) Bruno M Tesson et al.   BMC BIOINFORMATICS

An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis

(2010) Matthew P. R. Berry et al.   NATURE

Initiation and propagation of neurodegeneration

(2010) Christian Haass   NATURE MEDICINE

Expander: from expression microarrays to networks and functions

(2010) Igor Ulitsky et al.   Nature Protocols

Towards computational prediction of microRNA function and activity

(2010) Igor Ulitsky et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases

(2010) Alberto de la Fuente   TRENDS IN GENETICS

Genetic Control of Human Brain Transcript Expression in Alzheimer Disease

(2009) Jennifer A. Webster et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

(2009) Galina V. Glazko et al.   BIOINFORMATICS

Statistical methods for gene set co-expression analysis

(2009) YounJeong Choi et al.   BIOINFORMATICS

Identifying set-wise differential co-expression in gene expression microarray data

(2009) Sung Cho et al.   BMC BIOINFORMATICS

Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor

(2009) Wieslawa I Mentzen et al.   BMC GENOMICS

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

The role of cytochrome c oxidase deficiency in ROS and amyloid plaque formation

(2009) Alicia M. Pickrell et al.   JOURNAL OF BIOENERGETICS AND BIOMEMBRANES

Allegro: Analyzing expression and sequence in concert to discover regulatory programs

(2009) Yonit Halperin et al.   NUCLEIC ACIDS RESEARCH

BioMart Central Portal—unified access to biological data

(2009) Syed Haider et al.   NUCLEIC ACIDS RESEARCH

A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation

(2009) Nicholas J. Hudson et al.   PLoS Computational Biology

Aging Mice Show a Decreasing Correlation of Gene Expression within Genetic Modules

(2009) Lucinda K. Southworth et al.   PLoS Genetics

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

miR2Disease: a manually curated database for microRNA deregulation in human disease

(2008) Q. Jiang et al.   NUCLEIC ACIDS RESEARCH

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY