Gene set analysis methods: a systematic comparison

Network-based pathway enrichment analysis with incomplete network information

(2016) Jing Ma et al.   BIOINFORMATICS

Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster

(2016) Lucie Kučerová et al.   BMC GENOMICS

Phenotypic differentiation does not affect tumorigenicity of primary human colon cancer initiating cells

(2016) Taronish D. Dubash et al.   CANCER LETTERS

The RSPO–LGR4/5–ZNRF3/RNF43 module controls liver zonation and size

(2016) Lara Planas-Paz et al.   NATURE CELL BIOLOGY

Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk

(2016) Sara Sdelci et al.   Nature Chemical Biology

Metabolomics and transcriptomics identify pathway differences between visceral and subcutaneous adipose tissue in colorectal cancer patients: the ColoCare study

(2015) David B Liesenfeld et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

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

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

Association of Prostate Cancer Risk Variants with Gene Expression in Normal and Tumor Tissue

(2014) K. L. Penney et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

REST and stress resistance in ageing and Alzheimer’s disease

(2014) Tao Lu et al.   NATURE

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 MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

More power via graph-structured tests for differential expression of gene networks

(2012) Laurent Jacob et al.   Annals of Applied Statistics

TTC7B Emerges as a Novel Risk Factor for Ischemic Stroke Through the Convergence of Several Genome-Wide Approaches

(2012) Tiago Krug et al.   JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Pathway analysis of genomic data: concepts, methods, and prospects for future development

(2012) Vijay K. Ramanan et al.   TRENDS IN GENETICS

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Gene set enrichment analysis: performance evaluation and usage guidelines

(2011) J.-H. Hung et al.   BRIEFINGS IN BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Regulated functional alternative splicing in Drosophila

(2011) J. P. Venables et al.   NUCLEIC ACIDS RESEARCH

A framework for oligonucleotide microarray preprocessing

(2010) Benilton S. Carvalho et al.   BIOINFORMATICS

A general modular framework for gene set enrichment analysis

(2009) Marit Ackermann et al.   BMC BIOINFORMATICS

MDM2-Dependent Downregulation of p21 and hnRNP K Provides a Switch between Apoptosis and Growth Arrest Induced by Pharmacologically Activated p53

(2009) Martin Enge et al.   CANCER CELL

A statistical framework for testing functional categories in microarray data

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

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Microarray background correction: maximum likelihood estimation for the normal-exponential convolution

(2008) J. D. Silver et al.   BIOSTATISTICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS