eVITTA: a web-based visualization and inference toolbox for transcriptome analysis

Smell and taste disorders in COVID-19: From pathogenesis to clinical features and outcomes

(2021) Andrea Mastrangelo et al.   NEUROSCIENCE LETTERS

Integrative pathway enrichment analysis of multivariate omics data

(2020) Marta Paczkowska et al.   Nature Communications

Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution

(2020) Kenji Fukushima et al.   Nature Communications

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age

(2020) Nicole A. P. Lieberman et al.   PLOS BIOLOGY

Caenorhabditis elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor

(2020) Gabrielle E Giese et al.   eLife

WikiPathways: connecting communities

(2020) Marvin Martens 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

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

(2019) Uku Raudvere 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

GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data

(2019) Naim Al Mahi et al.   Scientific Reports

A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

(2019) Stanislav A. Listopad et al.   BMC BIOINFORMATICS

WormCat: An Online Tool for Annotation and Visualization of Caenorhabditis elegans Genome-Scale Data

(2019) Amy D. Holdorf et al.   GENETICS

Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine

(2018) Wei Ding et al.   PLoS Genetics

VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams

(2016) Felix Lam et al.   BMC BIOINFORMATICS

Impact of outdated gene annotations on pathway enrichment analysis

(2016) Lina Wadi et al.   NATURE METHODS

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

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

GRACOMICS: software for graphical comparison of multiple results with omics data

(2015) Minseok Seo et al.   BMC GENOMICS

s-Adenosylmethionine Levels Govern Innate Immunity through Distinct Methylation-Dependent Pathways

(2015) Wei Ding et al.   Cell Metabolism

Toll-like Receptor Signaling Promotes Development and Function of Sensory Neurons Required for a C. elegans Pathogen-Avoidance Behavior

(2015) Julia P. Brandt et al.   CURRENT BIOLOGY

Pathway and network analysis of cancer genomes

(2015)   NATURE METHODS

Babelomics 5.0: functional interpretation for new generations of genomic data

(2015) Roberto Alonso et al.   NUCLEIC ACIDS RESEARCH

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

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

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

A Conserved SREBP-1/Phosphatidylcholine Feedback Circuit Regulates Lipogenesis in Metazoans

(2011) Amy K. Walker et al.   CELL

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

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures

(2010) Seema B. Plaisier et al.   NUCLEIC ACIDS RESEARCH

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

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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS