reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization

liputils: a Python module to manage individual fatty acid moieties from complex lipids

(2020) Stefano Manzini et al.   Scientific Reports

Aortic Gene Expression Profiles Show How ApoA-I Levels Modulate Inflammation, Lysosomal Activity, and Sphingolipid Metabolism in Murine Atherosclerosis

(2020) Marco Busnelli et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

(2020) Damian Szklarczyk 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

Toward understanding the origin and evolution of cellular organisms

(2019) Minoru Kanehisa   PROTEIN SCIENCE

Fenretinide treatment accelerates atherosclerosis development in apoE‐deficient mice in spite of beneficial metabolic effects

(2019) Marco Busnelli et al.   BRITISH JOURNAL OF PHARMACOLOGY

The reactome pathway knowledgebase

(2019) Bijay Jassal et al.   NUCLEIC ACIDS RESEARCH

Gene set analysis methods: a systematic comparison

(2018) Ravi Mathur et al.   BioData Mining

Comparison of iTRAQ and SWATH in a clinical study with multiple time points

(2018) Antti Jylhä et al.   Clinical Proteomics

Topiramate protects apoE-deficient mice from kidney damage without affecting plasma lipids

(2018) Stefano Manzini et al.   PHARMACOLOGICAL RESEARCH

Effect of Dietary Components from Antarctic Krill on Atherosclerosis in apoE-Deficient Mice

(2017) Cinzia Parolini et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Liver-specific deletion of the Plpp3 gene alters plasma lipid composition and worsens atherosclerosis in apoE−/− mice

(2017) Marco Busnelli et al.   Scientific Reports

Role of omics techniques in the toxicity testing of nanoparticles

(2017) Eleonore Fröhlich   JOURNAL OF NANOBIOTECHNOLOGY

Advancements in Next-Generation Sequencing

(2016) Shawn E. Levy et al.   Annual Review of Genomics and Human Genetics

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

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

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

High-density lipoprotein deficiency in genetically modified mice deeply affects skin morphology: A structural and ultrastructural study

(2015) Francesca Arnaboldi et al.   EXPERIMENTAL CELL RESEARCH

Beta2-adrenergic activity modulates vascular tone regulation in lecithin:cholesterol acyltransferase knockout mice

(2015) S. Manzini et al.   VASCULAR PHARMACOLOGY

A Salmon Protein Hydrolysate Exerts Lipid-Independent Anti-Atherosclerotic Activity in ApoE-Deficient Mice

(2014) Cinzia Parolini et al.   PLoS One

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Reduced biliary sterol output with no change in total faecal excretion in mice expressing a human apolipoprotein A-I variant

(2012) Cinzia Parolini et al.   LIVER INTERNATIONAL

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Rosuvastatin does not affect human apolipoprotein A-I expression in genetically modified mice: a clue to the disputed effect of statins on HDL

(2011) Marta Marchesi et al.   BRITISH JOURNAL OF PHARMACOLOGY

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Improving Bioscience Research Reporting: The ARRIVE Guidelines for Reporting Animal Research

(2010) Carol Kilkenny et al.   PLOS BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

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