{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T01:52:28Z","timestamp":1768787548041,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1206,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights ) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations.<\/jats:p><jats:p>Results: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2% versus 56.5%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5%).<\/jats:p><jats:p>Availability: AdvISER-PYRO is implemented in an R package (http:\/\/sites.uclouvain.be\/md-ctma\/index.php\/softwares) and can be used in broad range of clinical applications including multiplex pyrosequencing and oncogene re-sequencing in heterogeneous tumor cell samples.<\/jats:p><jats:p>Contact: \u00a0jerome.ambroise@uclouvain.be or jean-luc.gala@uclouvain.be<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt339","type":"journal-article","created":{"date-parts":[[2013,6,15]],"date-time":"2013-06-15T02:25:10Z","timestamp":1371263110000},"page":"1963-1969","source":"Crossref","is-referenced-by-count":9,"title":["AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal"],"prefix":"10.1093","volume":"29","author":[{"given":"J\u00e9r\u00f4me","family":"Ambroise","sequence":"first","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Anne-Sophie","family":"Piette","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"},{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Cathy","family":"Delcorps","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"},{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Leen","family":"Rigouts","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Bouke C.","family":"de Jong","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Leonid","family":"Irenge","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"},{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Annie","family":"Robert","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"}]},{"given":"Jean-Luc","family":"Gala","sequence":"additional","affiliation":[{"name":"1 Center for Applied Molecular Technologies (CTMA), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium, 2Defence Laboratories Department, Belgian Armed Forces, Brussels, Belgium, 3Biomedical Sciences, Mycobacteriology unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2018 Antwerpen, Belgium and 4Epidemiology and Biostatistics Department (EPID), Institut de Recherche Exp\u00e9rimentale et Clinique (IREC), Universit\u00e9 catholique de Louvain, Clos Chapelle-aux-Champs 30, 1200 Bruxelles, Belgium"},{"name":"1 Center for 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