{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T09:55:26Z","timestamp":1773741326296,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,2,23]],"date-time":"2018-02-23T00:00:00Z","timestamp":1519344000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Union\u2019s Horizon 2020","award":["686070"],"award-info":[{"award-number":["686070"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Metabolite analogues (MAs) mimic the structure of native metabolites, can competitively inhibit their utilization in enzymatic reactions, and are commonly used as selection tools for isolating desirable mutants of industrial microorganisms. Genome-scale metabolic models representing all biochemical reactions in an organism can be used to predict effects of MAs on cellular phenotypes. Here, we present the metabolite analogues for rational strain improvement (MARSI) framework. MARSI provides a rational approach to strain improvement by searching for metabolites as targets instead of genes or reactions. The designs found by MARSI can be implemented by supplying MAs in the culture media, enabling metabolic rewiring without the use of recombinant DNA technologies that cannot always be used due to regulations. To facilitate experimental implementation, MARSI provides tools to identify candidate MAs to a target metabolite from a database of known drugs and analogues.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code is freely available at https:\/\/github.com\/biosustain\/marsi under the Apache License V2. MARSI is implemented in Python.<\/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\/bty108","type":"journal-article","created":{"date-parts":[[2018,2,22]],"date-time":"2018-02-22T12:23:43Z","timestamp":1519302223000},"page":"2319-2321","source":"Crossref","is-referenced-by-count":9,"title":["MARSI: metabolite analogues for rational strain improvement"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8173-2673","authenticated-orcid":false,"given":"Jo\u00e3o G R","family":"Cardoso","sequence":"first","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9984-5625","authenticated-orcid":false,"given":"Ahmad A","family":"Zeidan","sequence":"additional","affiliation":[{"name":"Discovery, Chr. Hansen A\/S, H\u00f8rsholm, Denmark"}]},{"given":"Kristian","family":"Jensen","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark"}]},{"given":"Nikolaus","family":"Sonnenschein","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark"}]},{"given":"Ana Rute","family":"Neves","sequence":"additional","affiliation":[{"name":"Discovery, Chr. Hansen A\/S, H\u00f8rsholm, Denmark"}]},{"given":"Markus J","family":"Herrg\u00e5rd","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2018,2,23]]},"reference":[{"key":"2023051604203572600_bty108-B1","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1002\/msb.145122","article-title":"Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling","volume":"10","author":"Agren","year":"2014","journal-title":"Mol. Syst. Biol"},{"key":"2023051604203572600_bty108-B2","doi-asserted-by":"crossref","DOI":"10.1186\/1475-2859-13-S1-S5","article-title":"The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology","volume":"13","author":"Derkx","year":"2014","journal-title":"Microb. Cell. Fact."},{"key":"2023051604203572600_bty108-B3","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.copbio.2016.11.018","article-title":"Systems biology solutions for biochemical production challenges","volume":"45","author":"Hansen","year":"2017","journal-title":"Curr. Opin. Biotechnol"},{"key":"2023051604203572600_bty108-B4","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.ymben.2016.05.008","article-title":"Model-based metabolic engineering enables high yield itaconic acid production by Escherichia coli","volume":"38","author":"Harder","year":"2016","journal-title":"Metab. Eng"},{"key":"2023051604203572600_bty108-B5","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1038\/msb.2010.115","article-title":"Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery","volume":"7","author":"Kim","year":"2014","journal-title":"Mol. Syst. 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Microbiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/13\/2319\/50315783\/bioinformatics_34_13_2319.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/13\/2319\/50315783\/bioinformatics_34_13_2319.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T04:21:05Z","timestamp":1684210865000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/13\/2319\/4904267"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,2,23]]},"references-count":11,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2018,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty108","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,7,1]]},"published":{"date-parts":[[2018,2,23]]}}}