Rigorous assessment of gene set enrichment tests

TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information

(2011) Qi Liu et al.   BMC BIOINFORMATICS

MicroRNAs Differentially Expressed in Postnatal Aortic Development Downregulate Elastin via 3′ UTR and Coding-Sequence Binding Sites

(2011) Claus Eric Ott et al.   PLoS One

MIRTFnet: Analysis of miRNA Regulated Transcription Factors

(2011) Haroon Naeem et al.   PLoS One

miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature

(2010) Haroon Naeem et al.   BMC BIOINFORMATICS

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets

(2010) Daniel M Gatti et al.   BMC GENOMICS

An efficient algorithm to identify coordinately activated transcription factors

(2010) Haiyan Hu   GENOMICS

A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks

(2010) Varun Narendra et al.   GENOMICS

GOing Bayesian: model-based gene set analysis of genome-scale data

(2010) Sebastian Bauer et al.   NUCLEIC ACIDS RESEARCH

Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

(2010) Ahmed Essaghir et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

The interplay between transcription factors and microRNAs in genome-scale regulatory networks

(2009) Natalia J. Martinez et al.   BIOESSAYS

A general modular framework for gene set enrichment analysis

(2009) Marit Ackermann et al.   BMC BIOINFORMATICS

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function

(2009) Petri Törönen et al.   BMC BIOINFORMATICS

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

(2009) Tom Michoel et al.   BMC Systems Biology

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Predicting microRNA targets and functions: traps for the unwary

(2009) William Ritchie et al.   NATURE METHODS

Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms

(2009) Kang Tu et al.   NUCLEIC ACIDS RESEARCH

mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer

(2009) Chao Cheng et al.   GENOME BIOLOGY

A statistical framework for testing functional categories in microarray data

(2008) William T. Barry et al.   Annals of Applied Statistics

Gene-set approach for expression pattern analysis

(2008) D. Nam et al.   BRIEFINGS IN BIOINFORMATICS

Coordinated Regulation of Cell Cycle Transcripts by p53-Inducible microRNAs, miR-192 and miR-215

(2008) S. A. Georges et al.   CANCER RESEARCH

Most mammalian mRNAs are conserved targets of microRNAs

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

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

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

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

The database of experimentally supported targets: a functional update of TarBase

(2008) G. L. Papadopoulos et al.   NUCLEIC ACIDS RESEARCH

miRecords: an integrated resource for microRNA-target interactions

(2008) F. Xiao et al.   NUCLEIC ACIDS RESEARCH

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

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

Inferring Condition-Specific Modulation of Transcription Factor Activity in Yeast through Regulon-Based Analysis of Genomewide Expression

(2008) André Boorsma et al.   PLoS One

Gene Regulation by Transcription Factors and MicroRNAs

(2008) O. Hobert   SCIENCE