{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T14:37:31Z","timestamp":1762353451503,"version":"3.41.2"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,1,31]],"date-time":"2024-01-31T00:00:00Z","timestamp":1706659200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["355\/23"],"award-info":[{"award-number":["355\/23"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>GeNLP is a web application that enables exploring microbial gene \u201csemantics\u201d and predictions of uncharacterized gene families based on their genomic context. It utilizes a pre-trained language model to uncover gene relationships and allows users to access and utilize the data as well as make their own predictions through an interactive interface.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The web application is accessible from all browsers at: http:\/\/gnlp.bursteinlab.org\/. All source codes are freely available from GitHub under the MIT license here: https:\/\/github.com\/burstein-lab\/genomic-nlp-server.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae034","type":"journal-article","created":{"date-parts":[[2024,1,31]],"date-time":"2024-01-31T08:13:07Z","timestamp":1706688787000},"source":"Crossref","is-referenced-by-count":3,"title":["GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3039-4376","authenticated-orcid":false,"given":"Danielle","family":"Miller","sequence":"first","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University , Tel-Aviv 6997801, Israel"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-3133-4769","authenticated-orcid":false,"given":"Ofir","family":"Arias","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University , Tel-Aviv 6997801, Israel"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6219-1880","authenticated-orcid":false,"given":"David","family":"Burstein","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University , Tel-Aviv 6997801, Israel"}]}],"member":"286","published-online":{"date-parts":[[2024,1,30]]},"reference":[{"key":"2024020805382331300_btae034-B1","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1016\/j.cels.2021.05.017","article-title":"Learning the protein language: evolution, structure, and function","volume":"12","author":"Bepler","year":"2021","journal-title":"Cell Syst"},{"key":"2024020805382331300_btae034-B2","doi-asserted-by":"crossref","first-page":"2102","DOI":"10.1093\/bioinformatics\/btac020","article-title":"ProteinBERT: a universal deep-learning model of protein sequence and function","volume":"38","author":"Brandes","year":"2022","journal-title":"Bioinformatics"},{"key":"2024020805382331300_btae034-B3","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"2024020805382331300_btae034-B4","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2024020805382331300_btae034-B5","doi-asserted-by":"crossref","first-page":"1947","DOI":"10.1002\/pro.3715","article-title":"Toward understanding the origin and evolution of cellular organisms","volume":"28","author":"Kanehisa","year":"2019","journal-title":"Protein Sci"},{"key":"2024020805382331300_btae034-B6","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1126\/science.ade2574","article-title":"Evolutionary-scale prediction of atomic-level protein structure with a language model","volume":"379","author":"Lin","year":"2023","journal-title":"Science"},{"key":"2024020805382331300_btae034-B7","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1038\/s41587-022-01618-2","article-title":"Large language models generate functional protein sequences across diverse families","volume":"41","author":"Madani","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2024020805382331300_btae034-B8","doi-asserted-by":"crossref","first-page":"861","DOI":"10.21105\/joss.00861","article-title":"UMAP: Uniform manifold approximation and projection","volume":"3","author":"McInnes","year":"2018","journal-title":"JOSS"},{"year":"2013","author":"Mikolov","key":"2024020805382331300_btae034-B9"},{"key":"2024020805382331300_btae034-B10","doi-asserted-by":"crossref","first-page":"5731","DOI":"10.1038\/s41467-022-33397-4","article-title":"Deciphering microbial gene function using natural language processing","volume":"13","author":"Miller","year":"2022","journal-title":"Nat Commun"},{"key":"2024020805382331300_btae034-B11","first-page":"D570","article-title":"MGnify: the microbiome analysis resource in 2020","volume":"48","author":"Mitchell","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024020805382331300_btae034-B12","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1073\/pnas.96.6.2896","article-title":"The use of gene clusters to infer functional coupling","volume":"96","author":"Overbeek","year":"1999","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024020805382331300_btae034-B13","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkaa1023","article-title":"GenBank","volume":"49","author":"Sayers","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024020805382331300_btae034-B14","doi-asserted-by":"crossref","first-page":"E5307","DOI":"10.1073\/pnas.1803440115","article-title":"Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis","volume":"115","author":"Shmakov","year":"2018","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae034\/56486799\/btae034.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/2\/btae034\/56619422\/btae034.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/2\/btae034\/56619422\/btae034.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T06:03:25Z","timestamp":1707372205000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae034\/7593804"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,1,30]]},"references-count":14,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae034","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2024,2,1]]},"published":{"date-parts":[[2024,1,30]]},"article-number":"btae034"}}