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GenePioneer: a comprehensive Python package for identification of essential genes and modules in cancer
Stockholm Univ, Dept Comp & Syst Sci, S-16455 Stockholm, Sweden.
KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-2741-0355
2025 (English)In: BIOINFORMATICS ADVANCES, ISSN 2635-0041, Vol. 5, no 1, article id vbaf094Article in journal (Refereed) Published
Abstract [en]

We propose a network-based unsupervised learning model to identify essential cancer genes and modules for 12 different cancer types, supported by a Python package for practical application. The model constructs a gene network from frequently mutated genes and biological processes, ranks genes using topological features, and detects critical modules. Evaluation across cancer types confirms its effectiveness in prioritizing cancer-related genes and uncovering relevant modules. The Python package allows users to input gene lists, retrieve rankings, and identify associated modules. This work provides a robust method for gene prioritization and module detection, along with a user-friendly package to support research and clinical decision-making in cancer genomics. Availability and implementation:GenePioneer is released as an open-source software under the MIT license. The source code is available on GitHub at https://github.com/Golnazthr/ModuleDetection.

Place, publisher, year, edition, pages
Oxford University Press (OUP) , 2025. Vol. 5, no 1, article id vbaf094
National Category
Bioinformatics and Computational Biology
Identifiers
URN: urn:nbn:se:kth:diva-366161DOI: 10.1093/bioadv/vbaf094ISI: 001492858700001PubMedID: 40417653Scopus ID: 2-s2.0-105006519499OAI: oai:DiVA.org:kth-366161DiVA, id: diva2:1981548
Note

QC 20250704

Available from: 2025-07-04 Created: 2025-07-04 Last updated: 2025-07-04Bibliographically approved

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Taheri, Golnaz

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CiteExportLink to record
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