{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T01:16:11Z","timestamp":1779930971587,"version":"3.53.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,10,3]],"date-time":"2019-10-03T00:00:00Z","timestamp":1570060800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["638553-TB-ACCELERATE"],"award-info":[{"award-number":["638553-TB-ACCELERATE"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["SAF2013-43521-R"],"award-info":[{"award-number":["SAF2013-43521-R"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["SAF2016-77346-R"],"award-info":[{"award-number":["SAF2016-77346-R"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["SAF2017\u201392345\u2013EXP"],"award-info":[{"award-number":["SAF2017\u201392345\u2013EXP"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["BES-2014-071066"],"award-info":[{"award-number":["BES-2014-071066"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["FPU 13\/00913"],"award-info":[{"award-number":["FPU 13\/00913"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281\/zenodo.3374377.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz729","type":"journal-article","created":{"date-parts":[[2019,9,26]],"date-time":"2019-09-26T07:28:48Z","timestamp":1569482928000},"page":"985-989","source":"Crossref","is-referenced-by-count":20,"title":["Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4136-6610","authenticated-orcid":false,"given":"Galo A","family":"Goig","sequence":"first","affiliation":[{"name":"Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC) , Valencia 46010, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuela","family":"Torres-Puente","sequence":"additional","affiliation":[{"name":"Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC) , Valencia 46010, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carla","family":"Mariner-Llicer","sequence":"additional","affiliation":[{"name":"Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC) , Valencia 46010, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis M","family":"Villamayor","sequence":"additional","affiliation":[{"name":"Genomics and Health Unit, FISABIO Public Health (CSISP) , Valencia 46035, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c1lvaro","family":"Chiner-Oms","sequence":"additional","affiliation":[{"name":"Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC) , Valencia 46010, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Gil-Brusola","sequence":"additional","affiliation":[{"name":"Microbiology Service, La Fe University and Polytechnic Hospital , Valencia 46026, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"Borr\u00e1s","sequence":"additional","affiliation":[{"name":"Microbiology Service, University Clinic Hospital , Valencia 46010, Spain"},{"name":"Microbiology Department, School of Medicine, University of Valencia , Valencia 46010, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5504-9408","authenticated-orcid":false,"given":"I\u00f1aki","family":"Comas Espadas","sequence":"additional","affiliation":[{"name":"Tuberculosis Genomics Unit, Institute of Biomedicine of Valencia (CSIC) , Valencia 46010, Spain"},{"name":"CIBER in Epidemiology and Public Health , Madrid 28029, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,10,3]]},"reference":[{"key":"2023013110151608200_btz729-B1","doi-asserted-by":"crossref","first-page":"1180","DOI":"10.1074\/mcp.M112.018846","article-title":"Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems","volume":"12","author":"Albrethsen","year":"2013","journal-title":"Mol. 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