{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:58Z","timestamp":1753875898340,"version":"3.41.2"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,6,11]],"date-time":"2025-06-11T00:00:00Z","timestamp":1749600000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Tecnol\u00f3gico de Monterrey and Consejo Nacional de Humanidades Ciencia y Tecnolog\u00eda"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), still claims around 1.25 million lives each year. The growing threat of drug resistance\u2014often driven by single\u2011nucleotide polymorphisms (SNPs) in Mtb genomes underscores the need for high\u2011quality genomic data and powerful bioinformatics tools. We present FuNTB, a python\u2011based pipeline that detects non\u2011synonymous SNPs in Mtb and builds functional network clusters to reveal genotype\u2013phenotype relationships.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>FuNTB profiles non\u2011synonymous SNPs at the gene level across user\u2011defined phenotypes, pinpointing both shared and unique mutations. It ingests annotated Variant Call Format (VCF) files or MTBseq outputs and merges them with clinical metadata to produce network\u2011XML files compatible with Cytoscape and Gephi. When applied to the CRyPTIC Mtb collection, FuNTB rapidly recovered established resistance genes and surfaced novel candidates, validating its utility for mapping genotype\u2013phenotype associations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>FuNTB is implemented in Python 3.8+ and is freely available under the MIT license at https:\/\/doi.org\/10.5281\/zenodo.15399917.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf341","type":"journal-article","created":{"date-parts":[[2025,6,11]],"date-time":"2025-06-11T11:56:25Z","timestamp":1749642985000},"source":"Crossref","is-referenced-by-count":0,"title":["FuNTB: a functional network clustering tool for the analysis of genome-wide genetic variants in <i>Mycobacterium tuberculosis<\/i>"],"prefix":"10.1093","volume":"41","author":[{"given":"Axel A","family":"Ramos-Garc\u00eda","sequence":"first","affiliation":[{"name":"Escuela de Ingenier\u00eda y Ciencias, Tecnol\u00f3gico de Monterrey, Monterrey, Nuevo Le\u00f3n, 64700, M\u00e9xico"}]},{"given":"Paulina M","family":"Mej\u00eda-Ponce","sequence":"additional","affiliation":[{"name":"Centro de Biotecnolog\u00eda FEMSA, Escuela de Ingenier\u00eda y Ciencias, Tecnol\u00f3gico de Monterrey, Monterrey, Nuevo Le\u00f3n, 64700, M\u00e9xico"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1697-3862","authenticated-orcid":false,"given":"Nelly","family":"S\u00e9lem-Mojica","sequence":"additional","affiliation":[{"name":"Centro de Ciencias Matem\u00e1ticas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Residencial San Jos\u00e9 de la Huerta, Morelia, Michoac\u00e1n, 58089, M\u00e9xico"}]},{"given":"Alejandro","family":"Santos-D\u00edaz","sequence":"additional","affiliation":[{"name":"Escuela de Ingenier\u00eda y Ciencias, Tecnol\u00f3gico de Monterrey, Monterrey, Nuevo Le\u00f3n, 64700, M\u00e9xico"}]},{"given":"Emmanuel","family":"Mart\u00ednez-Ledesma","sequence":"additional","affiliation":[{"name":"Unidad de Biolog\u00eda Integrativa, The Institute for Obesity Research, Tecnol\u00f3gico de Monterrey, Monterrey, Nuevo Le\u00f3n, 64700, M\u00e9xico"},{"name":"Escuela de Medicina y Ciencias de la Salud, Tecnol\u00f3gico de Monterrey, Monterrey, Nuevo Le\u00f3n, 64700, M\u00e9xico"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0360-3945","authenticated-orcid":false,"given":"Cuauht\u00e9moc","family":"Licona-Cassani","sequence":"additional","affiliation":[{"name":"Centro de Biotecnolog\u00eda FEMSA, Escuela de Ingenier\u00eda y Ciencias, Tecnol\u00f3gico de Monterrey, Monterrey, Nuevo Le\u00f3n, 64700, M\u00e9xico"},{"name":"Unidad de Biolog\u00eda Integrativa, The Institute for Obesity Research, Tecnol\u00f3gico de Monterrey, Monterrey, Nuevo Le\u00f3n, 64700, M\u00e9xico"},{"name":"Instituto de Biotecnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, 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