BRIEF RESEARCH REPORT article
Front. Bioinform.
Sec. Data Visualization
Volume 5 - 2025 | doi: 10.3389/fbinf.2025.1523184
pubCounteR: an R package for interrogating published literature for experimentally-derived gene lists within a user-defined biological context
Provisionally accepted
- 1German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Potsdam, Germany
- 2Max Planck Institute of Molecular Plant Physiology, Potsdam, Brandenburg, Germany
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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.
Keywords: text mining, Literature search, Publication activity, gene list, information retrieval
Received: 05 Nov 2024; Accepted: 18 Apr 2025.
Copyright: © 2025 Leer, Soultoukis, Jähnert, Oveisi, Walther and Schulz. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Marina Leer, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Potsdam, Germany
Tim J. Schulz, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Potsdam, Germany
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