AUTHOR=Leer Marina , Soultoukis George A. , Jähnert Markus , Oveisi Masoome , Walther Dirk , Schulz Tim J. 

TITLE=pubCounteR: an R package for interrogating published literature for experimentally-derived gene lists within a user-defined biological context

JOURNAL=Frontiers in Bioinformatics

VOLUME=Volume 5 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1523184

DOI=10.3389/fbinf.2025.1523184

ISSN=2673-7647

ABSTRACT=Basic and clinical biomedical research relies heavily on modern large-scale datasets that include genomics, transcriptomics, epigenomics, metabolomics, and proteomics, among other “Omics”. These research tools very often generate lists of candidate genes that are hypothesized or shown to be responsible for the biological effect in question. To aid the biological interpretation of experimentally-obtained gene lists, we developed pubCounteR, an R-package and web-based interface that screens publications by a user-defined set of keywords representing a specific biological context for experimentally-derived gene lists.