{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T20:56:26Z","timestamp":1769374586149,"version":"3.49.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>MicrobeTrace is a free, secure, browser-based bioinformatics tool to integrate and visualize epidemiologic, laboratory, and molecular data for outbreak investigations, with over 14,000 users from 127 countries. Regular testing, user feedback, and comparison with other bioinformatics tools identified areas for improvement, prompting major architectural and functional upgrades. In MicrobeTrace 2.0, we refactored the codebase using Angular to improve scalability, performance, and usability. We also replaced the D3.js visualization engine with Cytoscape.js for faster, more efficient rendering of large networks. The update adds enhanced visualizations, new analytical tools, and expanded functionality within existing views. It also supports seamless integration with external phylogenetic platforms, such as Nextstrain and UShER (Ultrafast Sample Placement on Existing Trees), enabling users to import phylogenetic trees, visualize them as genetic networks, and securely enrich them with epidemiological and demographic metadata. These enhancements position MicrobeTrace as a next-generation, interoperable tool for genomic epidemiology and data-driven public health response.<\/jats:p>","DOI":"10.1093\/molbev\/msaf334","type":"journal-article","created":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T12:52:01Z","timestamp":1767185521000},"source":"Crossref","is-referenced-by-count":0,"title":["MicrobeTrace 2.0: the enhanced visualization multitool for molecular epidemiology and bioinformatics"],"prefix":"10.1093","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4453-818X","authenticated-orcid":false,"given":"Anupama","family":"Shankar","sequence":"first","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30329 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1132-8964","authenticated-orcid":false,"given":"Evan","family":"Moscoso","sequence":"additional","affiliation":[{"name":"General Dynamics Information Technology , Atlanta, GA 30329 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4501-8437","authenticated-orcid":false,"given":"David","family":"Cowan","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30329 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5063-0655","authenticated-orcid":false,"given":"Reagan","family":"Kelly","sequence":"additional","affiliation":[{"name":"General Dynamics Information Technology , Atlanta, GA 30329 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0765-1186","authenticated-orcid":false,"given":"Roxana","family":"Cintron","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30329 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-8798-2114","authenticated-orcid":false,"given":"Omar Ali","family":"Al-Naimi","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30329 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4591-8731","authenticated-orcid":false,"given":"William M","family":"Switzer","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30329 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,1,2]]},"reference":[{"key":"2026012303421322600_msaf334-B1","doi-asserted-by":"publisher","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D(3): data-driven documents","volume":"17","author":"Bostock","year":"2011","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"2026012303421322600_msaf334-B2","doi-asserted-by":"publisher","first-page":"e1009300","DOI":"10.1371\/journal.pcbi.1009300","article-title":"MicrobeTrace: retooling molecular epidemiology for rapid public health response","volume":"17","author":"Campbell","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2026012303421322600_msaf334-B3","volume-title":"Effective data visualization: the right chart for the right data","author":"Evergreen","year":"2019"},{"key":"2026012303421322600_msaf334-B4","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1017\/dmp.2018.157","article-title":"Addressing disease-related stigma during infectious disease outbreaks","volume":"13","author":"Fischer","year":"2019","journal-title":"Disaster Med Public Health Prep"},{"key":"2026012303421322600_msaf334-B5","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1093\/bioinformatics\/btv557","article-title":"Cytoscape.js: a graph theory library for visualisation and analysis","volume":"32","author":"Franz","year":"2016","journal-title":"Bioinformatics"},{"key":"2026012303421322600_msaf334-B6","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1093\/bioinformatics\/btad031","article-title":"Cytoscape.js 2023 update: a graph theory library for visualization and analysis","volume":"39","author":"Franz","year":"2023","journal-title":"Bioinformatics"},{"key":"2026012303421322600_msaf334-B7","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"2026012303421322600_msaf334-B8","doi-asserted-by":"publisher","first-page":"5","DOI":"10.2202\/1948-4690.1038","article-title":"Prediction of an epidemic curve: a supervised classification approach","volume":"3","author":"Nsoesie","year":"2011","journal-title":"Stat Commun Infect Dis"},{"key":"2026012303421322600_msaf334-B9","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1038\/s41588-021-00862-7","article-title":"Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic","volume":"53","author":"Turakhia","year":"2021","journal-title":"Nat Genet"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msaf334\/66192130\/msaf334.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/43\/1\/msaf334\/66192130\/msaf334.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/43\/1\/msaf334\/66192130\/msaf334.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T08:42:25Z","timestamp":1769157745000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/doi\/10.1093\/molbev\/msaf334\/8408170"}},"subtitle":[],"editor":[{"given":"Nicolas","family":"Rodrigue","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":9,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,3]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msaf334","relation":{},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,1]]},"published":{"date-parts":[[2026,1]]},"article-number":"msaf334"}}