Beyond differential expression: the quest for causal mutations and effector molecules

Activin signaling as an emerging target for therapeutic interventions

(2012) Kunihiro Tsuchida et al.   Cell Communication and Signaling

A multiple network learning approach to capture system-wide condition-specific responses

(2011) S. Roy et al.   BIOINFORMATICS

DDN: a caBIG® analytical tool for differential network analysis

(2011) Bai Zhang et al.   BIOINFORMATICS

A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer

(2011) Shivashankar H Nagaraj et al.   BMC Systems Biology

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genetic variability in SNCA and Parkinson’s disease

(2011) Lasse Pihlstrøm et al.   NEUROGENETICS

Chronic exposure to anabolic steroids induces the muscle expression of oxytocin and a more than fiftyfold increase in circulating oxytocin in cattle

(2011) Nadia De Jager et al.   PHYSIOLOGICAL GENOMICS

Average Rank-Based Score to Measure Deregulation of Molecular Pathway Gene Sets

(2011) Huan Yang et al.   PLoS One

Role of SPI-1 Secreted Effectors in Acute Bovine Response to Salmonella enterica Serovar Typhimurium: A Systems Biology Analysis Approach

(2011) Sara D. Lawhon et al.   PLoS One

Immune Response and Mitochondrial Metabolism Are Commonly Deregulated in DMD and Aging Skeletal Muscle

(2011) Daniel Baron et al.   PLoS One

Introduction to Statistical Methods for Analyzing Large Data Sets: Gene-Set Enrichment Analysis

(2011) N. R. Clark et al.   Science Signaling

Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data

(2010) Antonio Reverter et al.   BIOINFORMATICS

PC4/Tis7/IFRD1Stimulates Skeletal Muscle Regeneration and Is Involved in Myoblast Differentiation as a Regulator of MyoD and NF-κB

(2010) Laura Micheli et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2010) Alberto de la Fuente   TRENDS IN GENETICS

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Comparison of next generation sequencing technologies for transcriptome characterization

(2009) P Kerr Wall et al.   BMC GENOMICS

Structure, expression, and biological function of INSM1 transcription factor in neuroendocrine differentiation

(2009) Michael S. Lan et al.   FASEB JOURNAL

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Sequences and consequences

(2009) S. Brenner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Inferring the Transcriptional Landscape of Bovine Skeletal Muscle by Integrating Co-Expression Networks

(2009) Nicholas J. Hudson et al.   PLoS One

Recovering time-varying networks of dependencies in social and biological studies

(2009) A. Ahmed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

SIRENE: supervised inference of regulatory networks

(2008) F. Mordelet et al.   BIOINFORMATICS

Differential dependency network analysis to identify condition-specific topological changes in biological networks

(2008) Bai Zhang et al.   BIOINFORMATICS

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

(2008) Antonio Reverter et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

CARM1 Regulates Estrogen-Stimulated Breast Cancer Growth through Up-regulation of E2F1

(2008) S. Frietze et al.   CANCER RESEARCH

Myostatin promotes the terminal differentiation of embryonic muscle progenitors

(2008) M. Manceau et al.   GENES & DEVELOPMENT

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

CDK8 is a colorectal cancer oncogene that regulates β-catenin activity

(2008) Ron Firestein et al.   NATURE

Human Gene Coexpression Landscape: Confident Network Derived from Tissue Transcriptomic Profiles

(2008) Carlos Prieto et al.   PLoS One

Defining diversity, specialization, and gene specificity in transcriptomes through information theory

(2008) O. Martinez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA