Combining multiple tools outperforms individual methods in gene set enrichment analyses

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

(2016) Ludwig Geistlinger et al.   BMC BIOINFORMATICS

Comparative study on gene set and pathway topology-based enrichment methods

(2015) Michaela Bayerlová et al.   BMC BIOINFORMATICS

A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1

(2015) Julie M Sheridan et al.   BMC CANCER

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The role of IL-4 and IL-13 in cutaneous Leishmaniasis

(2014) Ramona Hurdayal et al.   IMMUNOLOGY LETTERS

Fast decorrelated neural network ensembles with random weights

(2014) Monther Alhamdoosh et al.   INFORMATION SCIENCES

Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns

(2014) Panagiotis Moulos 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

Production of a human neutralizing monoclonal antibody and its crystal structure in complex with ectodomain 3 of the interleukin-13 receptor α1

(2013) Nicholas T. Redpath et al.   BIOCHEMICAL JOURNAL

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Gene set analysis methods: statistical models and methodological differences

(2013) H. Maciejewski   BRIEFINGS IN BIOINFORMATICS

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

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

(2013) Adi L. Tarca et al.   PLoS One

Down-weighting overlapping genes improves gene set analysis

(2012) Adi Tarca et al.   BMC BIOINFORMATICS

IL-13 in asthma and allergic disease: Asthma phenotypes and targeted therapies

(2012) Jennifer L. Ingram et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis

(2012) Hiromitsu Araki et al.   FEBS Open Bio

Staphylococcus Aureus Increases Cytokine and Matrix Metalloproteinase Expression in Nasal Mucosae of Patients with Chronic Rhinosinusitis and Nasal Polyps

(2010) Jong Hwan Wang et al.   American Journal of Rhinology & Allergy

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Interleukin-13 Protects Against Experimental Autoimmune Myocarditis by Regulating Macrophage Differentiation

(2008) Daniela Cihakova et al.   AMERICAN JOURNAL OF PATHOLOGY

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology