{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T06:14:46Z","timestamp":1790662486015,"version":"4.1.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2017,5,11]],"date-time":"2017-05-11T00:00:00Z","timestamp":1494460800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"publisher","award":["R01-AI110724"],"award-info":[{"award-number":["R01-AI110724"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"publisher","award":["R21-AI117247"],"award-info":[{"award-number":["R21-AI117247"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"publisher","award":["U01-AI124302"],"award-info":[{"award-number":["U01-AI124302"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Transposon insertion sequencing (Tn-Seq) is a microbial systems-level tool, that can determine on a genome-wide scale and in high-throughput, whether a gene, or a specific genomic region, is important for fitness under a specific experimental condition.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present MAGenTA, a suite of analysis tools which accurately calculate the growth rate for each disrupted gene in the genome to enable the discovery of: (i) new leads for gene function, (ii) non-coding RNAs; (iii) genes, pathways and ncRNAs that are involved in tolerating drugs or induce disease; (iv) higher order genome organization; and (v) host-factors that affect bacterial host susceptibility. MAGenTA is a complete Tn-Seq analysis pipeline making sensitive genome-wide fitness (i.e. growth rate) analysis available for most transposons and Tn-Seq associated approaches (e.g. TraDis, HiTS, IN-Seq) and includes fitness (growth rate) calculations, sliding window analysis, bottleneck calculations and corrections, statistics to compare experiments and strains and genome-wide fitness visualization.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MAGenTA is available at the Galaxy public ToolShed repository and all source code can be found and are freely available at https:\/\/vanopijnenlab.github.io\/MAGenTA\/.<\/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\/btx320","type":"journal-article","created":{"date-parts":[[2017,5,10]],"date-time":"2017-05-10T19:12:05Z","timestamp":1494443525000},"page":"2781-2783","source":"Crossref","is-referenced-by-count":43,"title":["MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization"],"prefix":"10.1093","volume":"33","author":[{"given":"Katherine Maia","family":"McCoy","sequence":"first","affiliation":[{"name":"Biology Department, Boston College, Chestnut Hill, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret L","family":"Antonio","sequence":"additional","affiliation":[{"name":"Biology Department, Boston College, Chestnut Hill, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"van Opijnen","sequence":"additional","affiliation":[{"name":"Biology Department, Boston College, Chestnut Hill, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,5,11]]},"reference":[{"key":"2023020206273204400_btx320-B1","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1016\/j.chom.2014.04.005","article-title":"Genomic analyses of pneumococci from children with sickle cell disease expose host-specific bacterial adaptations and deficits in current interventions","volume":"15","author":"Carter","year":"2014","journal-title":"Cell Host Microbe"},{"key":"2023020206273204400_btx320-B2","doi-asserted-by":"crossref","first-page":"9033","DOI":"10.1093\/nar\/gkt654","article-title":"High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data","volume":"41","author":"Chao","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020206273204400_btx320-B3","doi-asserted-by":"crossref","first-page":"16422","DOI":"10.1073\/pnas.0906627106","article-title":"Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung","volume":"106","author":"Gawronski","year":"2009","journal-title":"Proc. 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