KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

The clinical promise of biomarkers of synapse damage or loss in Alzheimer’s disease

(2020) Martí Colom-Cadena et al.   Alzheimers Research & Therapy

GeneTrail 3: advanced high-throughput enrichment analysis

(2020) Nico Gerstner et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

(2020) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

(2019) Maxim V Kuleshov et al.   NUCLEIC ACIDS RESEARCH

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update

(2018) Jia Ye et al.   NUCLEIC ACIDS RESEARCH

CGPS: A machine learning-based approach integrating multiple gene set analysis tools for better prioritization of biologically relevant pathways

(2018) Chen Ai et al.   Journal of Genetics and Genomics

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

GOplot: an R package for visually combining expression data with functional analysis: Fig. 1.

(2015) Wencke Walter et al.   BIOINFORMATICS

Neuroinflammation in Alzheimer's disease

(2015) Michael T Heneka et al.   LANCET NEUROLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

CePa: an R package for finding significant pathways weighted by multiple network centralities

(2013) Zuguang Gu et al.   BIOINFORMATICS

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Down-weighting overlapping genes improves gene set analysis

(2012) Adi Tarca et al.   BMC BIOINFORMATICS

MicroRNA-143 (miR-143) Regulates Cancer Glycolysis via Targeting Hexokinase 2 Gene

(2012) Rong Fang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

A network-based gene-weighting approach for pathway analysis

(2011) Zhaoyuan Fang et al.   CELL RESEARCH

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

SPICi: a fast clustering algorithm for large biological networks

(2010) Peng Jiang et al.   BIOINFORMATICS

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

(2010) Sebastian Bauer et al.   NUCLEIC ACIDS RESEARCH

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

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

(2009) Eran Eden et al.   BMC BIOINFORMATICS

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Understanding biological functions through molecular networks

(2008) Jing-Dong Jackie Han   CELL RESEARCH

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

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

Maps of random walks on complex networks reveal community structure

(2008) M. Rosvall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA