{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T11:32:08Z","timestamp":1767007928951,"version":"3.37.3"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,1]],"date-time":"2019-02-01T00:00:00Z","timestamp":1548979200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Edmond J. Safra Center for Bioinformatics at Tel-Aviv University"},{"DOI":"10.13039\/501100001738","name":"Israeli Ministry of Science, Technology and Space","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001738","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Manna Center for Plant Biosciences"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Regulation of the amount of protein that is synthesized from genes has proved to be a serious challenge in terms of analysis and prediction, and in terms of engineering and optimization, due to the large diversity in expression machinery across species.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>To address this challenge, we developed a methodology and a software tool (ChimeraUGEM) for predicting gene expression as well as adapting the coding sequence of a target gene to any host organism. We demonstrate these methods by predicting protein levels in seven organisms, in seven human tissues, and by increasing in vivo the expression of a synthetic gene up to 26-fold in the single-cell green alga Chlamydomonas reinhardtii. The underlying model is designed to capture sequence patterns and regulatory signals with minimal prior knowledge on the host organism and can be applied to a multitude of species and applications.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Source code (MATLAB, C) and binaries are freely available for download for non-commercial use at http:\/\/www.cs.tau.ac.il\/~tamirtul\/ChimeraUGEM\/, and supported on macOS, Linux and Windows.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz080","type":"journal-article","created":{"date-parts":[[2019,1,30]],"date-time":"2019-01-30T21:20:03Z","timestamp":1548883203000},"page":"3365-3371","source":"Crossref","is-referenced-by-count":12,"title":["ChimeraUGEM: unsupervised gene expression modeling in any given organism"],"prefix":"10.1093","volume":"35","author":[{"given":"Alon","family":"Diament","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel"}]},{"given":"Iddo","family":"Weiner","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel"},{"name":"School of Plant Sciences and Food Security, The George S. 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Wise Faculty of Life Sciences , Tel Aviv, Israel"}]},{"given":"Shimshi","family":"Atar","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel"}]},{"given":"Meital","family":"Avitan","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv, Israel"},{"name":"School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel"}]},{"given":"Shira","family":"Schweitzer","sequence":"additional","affiliation":[{"name":"School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences , Tel Aviv, Israel"}]},{"given":"Iftach","family":"Yacoby","sequence":"additional","affiliation":[{"name":"School of Plant Sciences and Food Security, The George S. 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