{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:07:16Z","timestamp":1775606836850,"version":"3.50.1"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"12","license":[{"start":{"date-parts":[[2021,12,9]],"date-time":"2021-12-09T00:00:00Z","timestamp":1639008000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2021,12,9]],"date-time":"2021-12-09T00:00:00Z","timestamp":1639008000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Mach Intell"],"DOI":"10.1038\/s42256-021-00419-7","type":"journal-article","created":{"date-parts":[[2021,12,9]],"date-time":"2021-12-09T17:02:55Z","timestamp":1639069375000},"page":"1050-1060","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Protein function prediction for newly sequenced organisms"],"prefix":"10.1038","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9796-1742","authenticated-orcid":false,"given":"Mateo","family":"Torres","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8724-4192","authenticated-orcid":false,"given":"Haixuan","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8855-5569","authenticated-orcid":false,"given":"Alfonso E.","family":"Romero","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8059-1346","authenticated-orcid":false,"given":"Alberto","family":"Paccanaro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,12,9]]},"reference":[{"key":"419_CR1","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1007\/978-1-4939-7231-9_5","volume":"1654","author":"LM Cruz","year":"2017","unstructured":"Cruz, L. M., Trefflich, S., Weiss, V. A. & Castro, M. A. A. Protein function prediction. Methods Mol. Biol. 1654, 55\u201375 (2017).","journal-title":"Methods Mol. Biol."},{"key":"419_CR2","doi-asserted-by":"publisher","unstructured":"Shehu, A., Barbar\u00e1, D. & Molloy, K. in Big Data Analytics in Genomics (ed. Wong, K.-C.) 225\u2013298 (Springer, 2016); https:\/\/doi.org\/10.1007\/978-3-319-41279-5_7","DOI":"10.1007\/978-3-319-41279-5_7"},{"key":"419_CR3","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-1037-6","volume":"17","author":"Y Jiang","year":"2016","unstructured":"Jiang, Y. et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 17, 184 (2016).","journal-title":"Genome Biol."},{"key":"419_CR4","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner, M. et al. Gene Ontology: tool for the unification of biology. Nat. Genet. 25, 25\u201329 (2000).","journal-title":"Nat. Genet."},{"key":"419_CR5","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/nrg.2017.38","volume":"18","author":"L Cowen","year":"2017","unstructured":"Cowen, L., Ideker, T., Raphael, B. J. & Sharan, R. Network propagation: a universal amplifier of genetic associations. Nat. Rev. Genet. 18, 551\u2013562 (2017).","journal-title":"Nat. Rev. Genet."},{"key":"419_CR6","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1835-8","volume":"20","author":"N Zhou","year":"2019","unstructured":"Zhou, N. et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 20, 244 (2019).","journal-title":"Genome Biol."},{"key":"419_CR7","first-page":"832","volume":"8","author":"G Valentini","year":"2011","unstructured":"Valentini, G. True path rule hierarchical ensembles for genome-wide gene function prediction. IEEE\/ACM Trans. Comput. Biol. Bioinform. 8, 832\u2013847 (2011).","journal-title":"IEEE"},{"key":"419_CR8","doi-asserted-by":"publisher","unstructured":"Friedberg, I. & Radivojac, P. in The Gene Ontology Handbook (eds Dessimoz, C. & \u0160kunca, N.) 133\u2013146 (Springer, 2017); https:\/\/doi.org\/10.1007\/978-1-4939-3743-1_10","DOI":"10.1007\/978-1-4939-3743-1_10"},{"key":"419_CR9","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-s1-s6","volume":"9","author":"G Obozinski","year":"2008","unstructured":"Obozinski, G., Lanckriet, G., Grant, C., Jordan, M. I. & Noble, W. S. Consistent probabilistic outputs for protein function prediction. Genome Biol. 9, S6 (2008).","journal-title":"Genome Biol."},{"key":"419_CR10","doi-asserted-by":"publisher","first-page":"D351","DOI":"10.1093\/nar\/gky1100","volume":"47","author":"AL Mitchell","year":"2019","unstructured":"Mitchell, A. L. et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47, D351\u2013D360 (2019).","journal-title":"Nucleic Acids Res."},{"key":"419_CR11","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1126\/science.287.5450.116","volume":"287","author":"AJ Walhout","year":"2000","unstructured":"Walhout, A. J. et al. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287, 116\u2013122 (2000).","journal-title":"Science"},{"key":"419_CR12","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1101\/gr.1774904","volume":"14","author":"H Yu","year":"2004","unstructured":"Yu, H. et al. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 14, 1107\u20131118 (2004).","journal-title":"Genome Res."},{"key":"419_CR13","doi-asserted-by":"publisher","first-page":"i38","DOI":"10.1093\/bioinformatics\/bti1016","volume":"21","author":"A Ben-Hur","year":"2005","unstructured":"Ben-Hur, A. & Noble, W. S. Kernel methods for predicting protein-protein interactions. Bioinformatics 21, i38\u2013i46 (2005).","journal-title":"Bioinformatics"},{"key":"419_CR14","doi-asserted-by":"publisher","first-page":"1974","DOI":"10.1073\/pnas.0409522102","volume":"102","author":"R Sharan","year":"2005","unstructured":"Sharan, R. et al. Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA 102, 1974\u20131979 (2005).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"419_CR15","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gky1131","volume":"47","author":"D Szklarczyk","year":"2019","unstructured":"Szklarczyk, D. et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607\u2013D613 (2019).","journal-title":"Nucleic Acids Res."},{"key":"419_CR16","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-s1-s4","volume":"9","author":"S Mostafavi","year":"2008","unstructured":"Mostafavi, S., Ray, D., Warde-Farley, D., Grouios, C. & Morris, Q. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol. 9, S4 (2008).","journal-title":"Genome Biol."},{"key":"419_CR17","doi-asserted-by":"publisher","first-page":"D1057","DOI":"10.1093\/nar\/gku1113","volume":"43","author":"RP Huntley","year":"2015","unstructured":"Huntley, R. P. et al. The GOA database: gene ontology annotation updates for 2015. Nucleic Acids Res. 43, D1057\u2013D1063 (2015).","journal-title":"Nucleic Acids Res."},{"key":"419_CR18","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.ymeth.2015.08.021","volume":"93","author":"E Lavezzo","year":"2016","unstructured":"Lavezzo, E., Falda, M., Fontana, P., Bianco, L. & Toppo, S. Enhancing protein function prediction with taxonomic constraints\u2014the Argot2.5 web server. Methods 93, 15\u201323 (2016).","journal-title":"Methods"},{"key":"419_CR19","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1093\/bioinformatics\/btz595","volume":"36","author":"M Kulmanov","year":"2020","unstructured":"Kulmanov, M. & Hoehndorf, R. DeepGOPlus: improved protein function prediction from sequence. Bioinformatics 36, 422\u2013429 (2020).","journal-title":"Bioinformatics"},{"key":"419_CR20","doi-asserted-by":"publisher","first-page":"2465","DOI":"10.1093\/bioinformatics\/bty130","volume":"34","author":"R You","year":"2018","unstructured":"You, R. et al. GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank. Bioinformatics 34, 2465\u20132473 (2018).","journal-title":"Bioinformatics"},{"key":"419_CR21","doi-asserted-by":"publisher","first-page":"W379","DOI":"10.1093\/nar\/gkz388","volume":"47","author":"R You","year":"2019","unstructured":"You, R. et al. NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Res. 47, W379\u2013W387 (2019).","journal-title":"Nucleic Acids Res."},{"key":"419_CR22","doi-asserted-by":"publisher","first-page":"1264","DOI":"10.3390\/genes11111264","volume":"11","author":"S Makrodimitris","year":"2020","unstructured":"Makrodimitris, S., van Ham, R. C. H. J. & Reinders, M. J. T. Automatic gene function prediction in the 2020s. Genes 11, 1264 (2020).","journal-title":"Genes"},{"key":"419_CR23","doi-asserted-by":"publisher","first-page":"e76339","DOI":"10.1371\/journal.pone.0076339","volume":"8","author":"M Cao","year":"2013","unstructured":"Cao, M. et al. Going the distance for protein function prediction: a new distance metric for protein interaction networks. PLoS ONE 8, e76339 (2013).","journal-title":"PLoS ONE"},{"key":"419_CR24","unstructured":"Zhou, D., Bousquet, O., Lal, T. N., Weston, J. & Sch\u00f6lkopf, B. Learning with local and global consistency. In Proc. 16th International Conference on Neural Information Processing Systems (eds Thrun, S. et al.) 321\u2013328 (MIT, 2004)."},{"key":"419_CR25","doi-asserted-by":"publisher","unstructured":"Torres, M., Yang, H., Romero, A. E. & Paccanaro, A. Input data for 'Protein function prediction for newly sequenced organisms'. Zenodo https:\/\/doi.org\/10.5281\/ZENODO.5514323 (2021).","DOI":"10.5281\/ZENODO.5514323"},{"key":"419_CR26","doi-asserted-by":"publisher","unstructured":"Torres, M., Yang, H., Romero, A. E. & Paccanaro, A. Source code for 'Protein function prediction for newly sequenced organisms'. Zenodo https:\/\/doi.org\/10.5281\/ZENODO.5513071 (2021).","DOI":"10.5281\/ZENODO.5513071"},{"key":"419_CR27","doi-asserted-by":"crossref","unstructured":"UniProt Consortium UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 47, D506\u2013D515 (2019).","DOI":"10.1093\/nar\/gky1049"}],"container-title":["Nature Machine Intelligence"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42256-021-00419-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42256-021-00419-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42256-021-00419-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,13]],"date-time":"2023-11-13T21:52:49Z","timestamp":1699912369000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42256-021-00419-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,9]]},"references-count":27,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2021,12]]}},"alternative-id":["419"],"URL":"https:\/\/doi.org\/10.1038\/s42256-021-00419-7","relation":{},"ISSN":["2522-5839"],"issn-type":[{"value":"2522-5839","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,12,9]]},"assertion":[{"value":"8 December 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 October 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 December 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}