Interpreting omics data with pathway enrichment analysis

K Zhao, SY Rhee - Trends in Genetics, 2023 - cell.com
Pathway enrichment analysis is indispensable for interpreting omics datasets and
generating hypotheses. However, the foundations of enrichment analysis remain elusive to …

A brief survey of tools for genomic regions enrichment analysis

D Chicco, G Jurman - Frontiers in bioinformatics, 2022 - frontiersin.org
Functional enrichment analysis or pathway enrichment analysis (PEA) is a bioinformatics
technique which identifies the most over-represented biological pathways in a list of genes …

Eleven quick tips for data cleaning and feature engineering

D Chicco, L Oneto, E Tavazzi - PLOS Computational Biology, 2022 - journals.plos.org
Applying computational statistics or machine learning methods to data is a key component of
many scientific studies, in any field, but alone might not be sufficient to generate robust and …

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses

D Chicco, F Cumbo, C Angione - PLOS Computational Biology, 2023 - journals.plos.org
Data are the most important elements of bioinformatics: Computational analysis of
bioinformatics data, in fact, can help researchers infer new knowledge about biology …

Ten quick tips for computational analysis of medical images

D Chicco, R Shiradkar - PLoS computational biology, 2023 - journals.plos.org
Medical imaging is a great asset for modern medicine, since it allows physicians to spatially
interrogate a disease site, resulting in precise intervention for diagnosis and treatment, and …

Eight quick tips for biologically and medically informed machine learning

L Oneto, D Chicco - PLOS Computational Biology, 2025 - journals.plos.org
Machine learning has become a powerful tool for computational analysis in the biomedical
sciences, with its effectiveness significantly enhanced by integrating domain-specific …

Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment

D Chicco, U Ferraro Petrillo… - PLOS Computational …, 2023 - journals.plos.org
Some scientific studies involve huge amounts of bioinformatics data that cannot be analyzed
on personal computers usually employed by researchers for day-to-day activities but rather …

Seven quick tips for gene-focused computational pangenomic analysis

V Bonnici, D Chicco - BioData Mining, 2024 - Springer
Pangenomics is a relatively new scientific field which investigates the union of all the
genomes of a clade. The word pan means everything in ancient Greek; the term …

Combined inhibition of EZH2 and CDK4/6 perturbs endoplasmic reticulum-mitochondrial homeostasis and increases antitumor activity against glioblastoma

T Freitag, P Kaps, J Ramtke, S Bertels, E Zunke… - NPJ Precision …, 2024 - nature.com
Here, we show that combined use of the EZH2 inhibitor GSK126 and the CDK4/6 inhibitor
abemaciclib synergistically enhances antitumoral effects in preclinical GBM models. Dual …

Chronic inflammation degrades CD4 T cell immunity to prior vaccines in treated HIV infection

M Kießling, JJ Cole, S Kübel, P Klein, K Korn… - Nature …, 2024 - nature.com
To date, our understanding of how HIV infection impacts vaccine-induced cellular immunity
is limited. Here, we investigate inflammation, immune activation and antigen-specific T cell …