{"id":457919,"date":"2026-03-04T23:46:09","date_gmt":"2026-03-04T23:46:09","guid":{"rendered":"https:\/\/www.newsbeep.com\/uk\/457919\/"},"modified":"2026-03-04T23:46:09","modified_gmt":"2026-03-04T23:46:09","slug":"genome-modelling-and-design-across-all-domains-of-life-with-evo-2","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/uk\/457919\/","title":{"rendered":"Genome modelling and design across all domains of life with Evo 2"},"content":{"rendered":"<p class=\"c-article-references__text\" id=\"ref-CR1\">Nguyen, E. et al. Sequence modeling and design from molecular to genome scale with Evo. Science 386, eado9336 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1126\/science.ado9336\" data-track-item_id=\"10.1126\/science.ado9336\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1126%2Fscience.ado9336\" aria-label=\"Article reference 1\" data-doi=\"10.1126\/science.ado9336\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXisFarsb7K\" aria-label=\"CAS reference 1\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=39541441\" aria-label=\"PubMed reference 1\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC12057570\" aria-label=\"PubMed Central reference 1\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 1\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Sequence%20modeling%20and%20design%20from%20molecular%20to%20genome%20scale%20with%20Evo&amp;journal=Science&amp;doi=10.1126%2Fscience.ado9336&amp;volume=386&amp;publication_year=2024&amp;author=Nguyen%2CE\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR2\">Merchant, A. T., King, S. H., Nguyen, E. &amp; Hie, B. L. Semantic design of functional de novo genes from a genomic language model. Nature 649, 749\u2013758 (2026).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41586-025-09749-7\" data-track-item_id=\"10.1038\/s41586-025-09749-7\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41586-025-09749-7\" aria-label=\"Article reference 2\" data-doi=\"10.1038\/s41586-025-09749-7\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2MXivV2htbfK\" aria-label=\"CAS reference 2\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=41261132\" aria-label=\"PubMed reference 2\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 2\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Semantic%20design%20of%20functional%20de%20novo%20genes%20from%20a%20genomic%20language%20model&amp;journal=Nature&amp;doi=10.1038%2Fs41586-025-09749-7&amp;volume=649&amp;pages=749-758&amp;publication_year=2026&amp;author=Merchant%2CAT&amp;author=King%2CSH&amp;author=Nguyen%2CE&amp;author=Hie%2CBL\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR3\">Avsec, \u017d et al. Effective gene expression prediction from sequence by integrating long-range interactions. Nat. Methods 18, 1196\u20131203 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41592-021-01252-x\" data-track-item_id=\"10.1038\/s41592-021-01252-x\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41592-021-01252-x\" aria-label=\"Article reference 3\" data-doi=\"10.1038\/s41592-021-01252-x\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXitFOltLbP\" aria-label=\"CAS reference 3\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=34608324\" aria-label=\"PubMed reference 3\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC8490152\" aria-label=\"PubMed Central reference 3\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 3\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Effective%20gene%20expression%20prediction%20from%20sequence%20by%20integrating%20long-range%20interactions&amp;journal=Nat.%20Methods&amp;doi=10.1038%2Fs41592-021-01252-x&amp;volume=18&amp;pages=1196-1203&amp;publication_year=2021&amp;author=Avsec%2C%C5%BD\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR4\">Linder, J., Srivastava, D., Yuan, H., Agarwal, V. &amp; Kelley, D. R. Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation. Nat. Genet. 57, 949\u2013961 (2025).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41588-024-02053-6\" data-track-item_id=\"10.1038\/s41588-024-02053-6\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41588-024-02053-6\" aria-label=\"Article reference 4\" data-doi=\"10.1038\/s41588-024-02053-6\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2MXhtVWrsLs%3D\" aria-label=\"CAS reference 4\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=39779956\" aria-label=\"PubMed reference 4\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC11985352\" aria-label=\"PubMed Central reference 4\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 4\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Predicting%20RNA-seq%20coverage%20from%20DNA%20sequence%20as%20a%20unifying%20model%20of%20gene%20regulation&amp;journal=Nat.%20Genet.&amp;doi=10.1038%2Fs41588-024-02053-6&amp;volume=57&amp;pages=949-961&amp;publication_year=2025&amp;author=Linder%2CJ&amp;author=Srivastava%2CD&amp;author=Yuan%2CH&amp;author=Agarwal%2CV&amp;author=Kelley%2CDR\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR5\">Ku, J. et al. Systems and algorithms for convolutional multi-hybrid language models at scale. Preprint at <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2503.01868\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.48550\/arXiv.2503.01868\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.48550\/arXiv.2503.01868<\/a> (2025).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR6\">Vaswani, A. et al. Attention is all you need. In Adv. Neural Information Processing Systems Vol. 30 (eds Guyon, I. et al.) (NIPS, 2017).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR7\">Kaplan, J. et al. Scaling laws for neural language models. Preprint at <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2001.08361\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.48550\/arXiv.2001.08361\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.48550\/arXiv.2001.08361<\/a> (2020).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR8\">Radford, A. et al. Language models are unsupervised multitask learners. OpenAI Blog 1, 9 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 8\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Language%20models%20are%20unsupervised%20multitask%20learners&amp;journal=OpenAI%20Blog&amp;volume=1&amp;publication_year=2019&amp;author=Radford%2CA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR9\">Gao, T., Wettig, A., Yen, H. &amp; Chen, D. How to train long-context language models (effectively). In Proc. 63rd Annual Meeting of the Association for Computational Linguistics 1, 7376\u20137399 (ACL, 2025).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR10\">Dubey, A. et al. The Llama 3 herd of models. Preprint at <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2407.21783\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.48550\/arXiv.2407.21783\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.48550\/arXiv.2407.21783<\/a> (2024).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR11\">Liu, S. J. et al. In vivo perturb-seq of cancer and microenvironment cells dissects oncologic drivers and radiotherapy responses in glioblastoma. Genome Biol. 25, 256 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener nofollow\" data-track-label=\"10.1186\/s13059-024-03404-6\" data-track-item_id=\"10.1186\/s13059-024-03404-6\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/s13059-024-03404-6\" aria-label=\"Article reference 11\" data-doi=\"10.1186\/s13059-024-03404-6\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXitFGqtbjO\" aria-label=\"CAS reference 11\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=39375777\" aria-label=\"PubMed reference 11\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC11457336\" aria-label=\"PubMed Central reference 11\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 11\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=In%20vivo%20perturb-seq%20of%20cancer%20and%20microenvironment%20cells%20dissects%20oncologic%20drivers%20and%20radiotherapy%20responses%20in%20glioblastoma&amp;journal=Genome%20Biol.&amp;doi=10.1186%2Fs13059-024-03404-6&amp;volume=25&amp;publication_year=2024&amp;author=Liu%2CSJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR12\">Poli, M. et al. Hyena hierarchy: towards larger convolutional language models. In Proc. 40th International Conference on Machine Learning (eds Karuse, A. et al.) 28043\u201328078 (2023).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR13\">Poli, M. et al. Mechanistic design and scaling of hybrid architectures. In Proc. 41st International Conference on Machine Learning 235, 40908\u201340950 (2024); <a href=\"https:\/\/proceedings.mlr.press\/v235\/poli24a.html\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"https:\/\/proceedings.mlr.press\/v235\/poli24a.html\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/proceedings.mlr.press\/v235\/poli24a.html<\/a>.<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR14\">Meier, J. et al. Language models enable zero-shot prediction of the effects of mutations on protein function. Preprint at bioRxiv <a href=\"https:\/\/doi.org\/10.1101\/2021.07.09.450648\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.1101\/2021.07.09.450648\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.1101\/2021.07.09.450648<\/a> (2021).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR15\">Notin, P. et al. ProteinGym: large-scale benchmarks for protein design and fitness prediction. Adv. Neural Inf. Process. Syst. 36, 64331\u201364379 (2023).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR16\">Benegas, G., Albors, C., Aw, A. J., Ye, C. &amp; Song, Y. S. A DNA language model based on multispecies alignment predicts the effects of genome-wide variants. Nat. Biotechnol. 43, 1960\u20131965 (2025).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41587-024-02511-w\" data-track-item_id=\"10.1038\/s41587-024-02511-w\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41587-024-02511-w\" aria-label=\"Article reference 16\" data-doi=\"10.1038\/s41587-024-02511-w\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2MXksFalug%3D%3D\" aria-label=\"CAS reference 16\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=39747647\" aria-label=\"PubMed reference 16\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 16\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20DNA%20language%20model%20based%20on%20multispecies%20alignment%20predicts%20the%20effects%20of%20genome-wide%20variants&amp;journal=Nat.%20Biotechnol.&amp;doi=10.1038%2Fs41587-024-02511-w&amp;volume=43&amp;pages=1960-1965&amp;publication_year=2025&amp;author=Benegas%2CG&amp;author=Albors%2CC&amp;author=Aw%2CAJ&amp;author=Ye%2CC&amp;author=Song%2CYS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR17\">Shine, J. &amp; Dalgarno, L. The 3\u2032-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc. Natl Acad. Sci. USA 71, 1342\u20131346 (1974).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1073\/pnas.71.4.1342\" data-track-item_id=\"10.1073\/pnas.71.4.1342\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1073%2Fpnas.71.4.1342\" aria-label=\"Article reference 17\" data-doi=\"10.1073\/pnas.71.4.1342\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=1974PNAS...71.1342S\" aria-label=\"ADS reference 17\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DyaE2cXksVKmt70%3D\" aria-label=\"CAS reference 17\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=4598299\" aria-label=\"PubMed reference 17\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC388224\" aria-label=\"PubMed Central reference 17\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 17\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%203%E2%80%B2-terminal%20sequence%20of%20Escherichia%20coli%2016S%20ribosomal%20RNA%3A%20complementarity%20to%20nonsense%20triplets%20and%20ribosome%20binding%20sites&amp;journal=Proc.%20Natl%20Acad.%20Sci.%20USA&amp;doi=10.1073%2Fpnas.71.4.1342&amp;volume=71&amp;pages=1342-1346&amp;publication_year=1974&amp;author=Shine%2CJ&amp;author=Dalgarno%2CL\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR18\">Kozak, M. The scanning model for translation: an update. J. Cell Biol. 108, 229\u2013241 (1989).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1083\/jcb.108.2.229\" data-track-item_id=\"10.1083\/jcb.108.2.229\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1083%2Fjcb.108.2.229\" aria-label=\"Article reference 18\" data-doi=\"10.1083\/jcb.108.2.229\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=1989oscs.book.....K\" aria-label=\"ADS reference 18\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DyaL1MXhtlSmurY%3D\" aria-label=\"CAS reference 18\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=2645293\" aria-label=\"PubMed reference 18\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2115416\" aria-label=\"PubMed Central reference 18\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 18\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20scanning%20model%20for%20translation%3A%20an%20update&amp;journal=J.%20Cell%20Biol.&amp;doi=10.1083%2Fjcb.108.2.229&amp;volume=108&amp;pages=229-241&amp;publication_year=1989&amp;author=Kozak%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR19\">Nijkamp, E., Ruffolo, J. A., Weinstein, E. N., Naik, N. &amp; Madani, A. ProGen2: exploring the boundaries of protein language models. Cell Syst. 14, 968\u2013978 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cels.2023.10.002\" data-track-item_id=\"10.1016\/j.cels.2023.10.002\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cels.2023.10.002\" aria-label=\"Article reference 19\" data-doi=\"10.1016\/j.cels.2023.10.002\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 19\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=ProGen2%3A%20exploring%20the%20boundaries%20of%20protein%20language%20models&amp;journal=Cell%20Syst.&amp;doi=10.1016%2Fj.cels.2023.10.002&amp;volume=14&amp;pages=968-978&amp;publication_year=2022&amp;author=Nijkamp%2CE&amp;author=Ruffolo%2CJA&amp;author=Weinstein%2CEN&amp;author=Naik%2CN&amp;author=Madani%2CA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR20\">Li, F.-Z., Amini, A. P., Yue, Y., Yang, K. K. &amp; Lu, A. X. Feature reuse and scaling: understanding transfer learning with protein language models. In Proc. 41st International Conference on Machine Learning 235, 27351\u201327375 (2024).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR21\">Weinstein, E. N., Amin, A. N., Frazer, J. &amp; Marks, D. Non-identifiability and the blessings of misspecification in models of molecular fitness. In Adv. Neural Information Processing Systems <a href=\"https:\/\/proceedings.neurips.cc\/paper_files\/paper\/2022\/file\/247e592848391fe01f153f179c595090-Paper-Conference.pdf\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"https:\/\/proceedings.neurips.cc\/paper_files\/paper\/2022\/file\/247e592848391fe01f153f179c595090-Paper-Conference.pdf\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/proceedings.neurips.cc\/paper_files\/paper\/2022\/file\/247e592848391fe01f153f179c595090-Paper-Conference.pdf<\/a> (2022).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR22\">Dalla-torre, H. et al. Nucleotide Transformer: building and evaluating robust foundation models for human genomics. Nat. Methods 22, 287\u2013297 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41592-024-02523-z\" data-track-item_id=\"10.1038\/s41592-024-02523-z\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41592-024-02523-z\" aria-label=\"Article reference 22\" data-doi=\"10.1038\/s41592-024-02523-z\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=39609566\" aria-label=\"PubMed reference 22\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC11810778\" aria-label=\"PubMed Central reference 22\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 22\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Nucleotide%20Transformer%3A%20building%20and%20evaluating%20robust%20foundation%20models%20for%20human%20genomics&amp;journal=Nat.%20Methods&amp;doi=10.1038%2Fs41592-024-02523-z&amp;volume=22&amp;pages=287-297&amp;publication_year=2024&amp;author=Dalla-torre%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR23\">Stanke, M., Steinkamp, R., Waack, S. &amp; Morgenstern, B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 32, W309\u2013W312 (2004).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/gkh379\" data-track-item_id=\"10.1093\/nar\/gkh379\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2Fgkh379\" aria-label=\"Article reference 23\" data-doi=\"10.1093\/nar\/gkh379\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD2cXlvFKntLg%3D\" aria-label=\"CAS reference 23\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=15215400\" aria-label=\"PubMed reference 23\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC441517\" aria-label=\"PubMed Central reference 23\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 23\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=AUGUSTUS%3A%20a%20web%20server%20for%20gene%20finding%20in%20eukaryotes&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2Fgkh379&amp;volume=32&amp;pages=W309-W312&amp;publication_year=2004&amp;author=Stanke%2CM&amp;author=Steinkamp%2CR&amp;author=Waack%2CS&amp;author=Morgenstern%2CB\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR24\">de Almeida, B. P. et al. SegmentNT: annotating the genome at single-nucleotide resolution with DNA foundation models. Nat. Methods 22, 2301\u20132315 (2025).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR25\">Ji, Y., Zhou, Z., Liu, H. &amp; Davuluri, R. V. DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome. Bioinformatics 37, 2112\u20132120 (2021).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/bioinformatics\/btab083\" data-track-item_id=\"10.1093\/bioinformatics\/btab083\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fbioinformatics%2Fbtab083\" aria-label=\"Article reference 25\" data-doi=\"10.1093\/bioinformatics\/btab083\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3MXisFantbzM\" aria-label=\"CAS reference 25\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=33538820\" aria-label=\"PubMed reference 25\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC11025658\" aria-label=\"PubMed Central reference 25\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 25\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=DNABERT%3A%20pre-trained%20Bidirectional%20Encoder%20Representations%20from%20Transformers%20model%20for%20DNA-language%20in%20genome&amp;journal=Bioinformatics&amp;doi=10.1093%2Fbioinformatics%2Fbtab083&amp;volume=37&amp;pages=2112-2120&amp;publication_year=2021&amp;author=Ji%2CY&amp;author=Zhou%2CZ&amp;author=Liu%2CH&amp;author=Davuluri%2CRV\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR26\">Findlay, G. M. et al. Accurate classification of BRCA1 variants with saturation genome editing. Nature 562, 217\u2013222 (2018).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41586-018-0461-z\" data-track-item_id=\"10.1038\/s41586-018-0461-z\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41586-018-0461-z\" aria-label=\"Article reference 26\" data-doi=\"10.1038\/s41586-018-0461-z\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2018Natur.562..217F\" aria-label=\"ADS reference 26\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1cXhslSnu7bI\" aria-label=\"CAS reference 26\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30209399\" aria-label=\"PubMed reference 26\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6181777\" aria-label=\"PubMed Central reference 26\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 26\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Accurate%20classification%20of%20BRCA1%20variants%20with%20saturation%20genome%20editing&amp;journal=Nature&amp;doi=10.1038%2Fs41586-018-0461-z&amp;volume=562&amp;pages=217-222&amp;publication_year=2018&amp;author=Findlay%2CGM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR27\">Huang, H. et al. Functional evaluation and clinical classification of BRCA2 variants. Nature 638, 528\u2013537 (2025).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41586-024-08388-8\" data-track-item_id=\"10.1038\/s41586-024-08388-8\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41586-024-08388-8\" aria-label=\"Article reference 27\" data-doi=\"10.1038\/s41586-024-08388-8\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2025Natur.638..528H\" aria-label=\"ADS reference 27\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2MXhtVWrtL8%3D\" aria-label=\"CAS reference 27\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=39779857\" aria-label=\"PubMed reference 27\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC11821525\" aria-label=\"PubMed Central reference 27\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 27\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Functional%20evaluation%20and%20clinical%20classification%20of%20BRCA2%20variants&amp;journal=Nature&amp;doi=10.1038%2Fs41586-024-08388-8&amp;volume=638&amp;pages=528-537&amp;publication_year=2025&amp;author=Huang%2CH\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR28\">Patel, A. et al. DART-Eval: a comprehensive DNA language model evaluation benchmark on regulatory DNA. Neural Inf. Process. Syst. 37, 62024\u201362061 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 28\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=DART-Eval%3A%20a%20comprehensive%20DNA%20language%20model%20evaluation%20benchmark%20on%20regulatory%20DNA&amp;journal=Neural%20Inf.%20Process.%20Syst.&amp;volume=37&amp;pages=62024-62061&amp;publication_year=2024&amp;author=Patel%2CA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR29\">Cunningham, H., Ewart, A., Smith, L. R., Huben, R. &amp; Sharkey, L. Sparse autoencoders find highly interpretable features in language models. Preprint at <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2309.08600\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.48550\/arXiv.2309.08600\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.48550\/arXiv.2309.08600<\/a> (2023).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR30\">Bricken, T. et al. Towards monosemanticity: decomposing language models with dictionary learning. Transformer Circuits Thread <a href=\"https:\/\/transformer-circuits.pub\/2023\/monosemantic-features\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"https:\/\/transformer-circuits.pub\/2023\/monosemantic-features\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/transformer-circuits.pub\/2023\/monosemantic-features<\/a> (2023).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR31\">Templeton, A. et al. Scaling monosemanticity: extracting interpretable features from Claude 3 Sonnet. Transformer Circuits Thread <a href=\"https:\/\/transformer-circuits.pub\/2024\/scaling-monosemanticity\/\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"https:\/\/transformer-circuits.pub\/2024\/scaling-monosemanticity\/\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/transformer-circuits.pub\/2024\/scaling-monosemanticity\/<\/a> (2024).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR32\">Bussmann, B., Leask, P. &amp; Nanda, N. BatchTopK Sparse Autoencoders. Preprint at <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2412.06410\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.48550\/arXiv.2412.06410\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.48550\/arXiv.2412.06410<\/a> (2024).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR33\">Camargo, A. et al. Identification of mobile genetic elements with geNomad. Nat. Biotechnol. 42, 1303\u20131312 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41587-023-01953-y\" data-track-item_id=\"10.1038\/s41587-023-01953-y\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41587-023-01953-y\" aria-label=\"Article reference 33\" data-doi=\"10.1038\/s41587-023-01953-y\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2024NatBi..42.1303C\" aria-label=\"ADS reference 33\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=37735266\" aria-label=\"PubMed reference 33\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC11324519\" aria-label=\"PubMed Central reference 33\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 33\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Identification%20of%20mobile%20genetic%20elements%20with%20geNomad&amp;journal=Nat.%20Biotechnol.&amp;doi=10.1038%2Fs41587-023-01953-y&amp;volume=42&amp;pages=1303-1312&amp;publication_year=2023&amp;author=Camargo%2CA\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR34\">Vorontsov, I. E. et al. HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors. Nucleic Acids Res. 52, D154\u2013D163 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/gkad1077\" data-track-item_id=\"10.1093\/nar\/gkad1077\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2Fgkad1077\" aria-label=\"Article reference 34\" data-doi=\"10.1093\/nar\/gkad1077\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXivVamsLjN\" aria-label=\"CAS reference 34\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=37971293\" aria-label=\"PubMed reference 34\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC10767914\" aria-label=\"PubMed Central reference 34\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 34\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=HOCOMOCO%20in%202024%3A%20a%20rebuild%20of%20the%20curated%20collection%20of%20binding%20models%20for%20human%20and%20mouse%20transcription%20factors&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2Fgkad1077&amp;volume=52&amp;pages=D154-D163&amp;publication_year=2024&amp;author=Vorontsov%2CIE\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR35\">Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L. &amp; Noble, W. S. Quantifying similarity between motifs. Genome Biol. 8, R24 (2007).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener nofollow\" data-track-label=\"10.1186\/gb-2007-8-2-r24\" data-track-item_id=\"10.1186\/gb-2007-8-2-r24\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/gb-2007-8-2-r24\" aria-label=\"Article reference 35\" data-doi=\"10.1186\/gb-2007-8-2-r24\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=17324271\" aria-label=\"PubMed reference 35\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1852410\" aria-label=\"PubMed Central reference 35\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 35\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Quantifying%20similarity%20between%20motifs&amp;journal=Genome%20Biol.&amp;doi=10.1186%2Fgb-2007-8-2-r24&amp;volume=8&amp;publication_year=2007&amp;author=Gupta%2CS&amp;author=Stamatoyannopoulos%2CJA&amp;author=Bailey%2CTL&amp;author=Noble%2CWS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR36\">Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cells 38, 576\u2013589 (2010).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.molcel.2010.05.004\" data-track-item_id=\"10.1016\/j.molcel.2010.05.004\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.molcel.2010.05.004\" aria-label=\"Article reference 36\" data-doi=\"10.1016\/j.molcel.2010.05.004\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC3cXns1SlsLc%3D\" aria-label=\"CAS reference 36\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 36\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Simple%20combinations%20of%20lineage-determining%20transcription%20factors%20prime%20cis-regulatory%20elements%20required%20for%20macrophage%20and%20B%20cell%20identities&amp;journal=Mol.%20Cells&amp;doi=10.1016%2Fj.molcel.2010.05.004&amp;volume=38&amp;pages=576-589&amp;publication_year=2010&amp;author=Heinz%2CS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR37\">Sandoval-Velasco, M. et al. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell 187, 3541\u20133562.e51 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cell.2024.06.002\" data-track-item_id=\"10.1016\/j.cell.2024.06.002\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cell.2024.06.002\" aria-label=\"Article reference 37\" data-doi=\"10.1016\/j.cell.2024.06.002\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 37\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Three-dimensional%20genome%20architecture%20persists%20in%20a%2052%2C000-year-old%20woolly%20mammoth%20skin%20sample&amp;journal=Cell&amp;doi=10.1016%2Fj.cell.2024.06.002&amp;volume=187&amp;pages=3541-3562.e51&amp;publication_year=2023&amp;author=Sandoval-Velasco%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR38\">Meng, G., Li, Y., Yang, C. &amp; Liu, S. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res. 47, e63 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/gkz173\" data-track-item_id=\"10.1093\/nar\/gkz173\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2Fgkz173\" aria-label=\"Article reference 38\" data-doi=\"10.1093\/nar\/gkz173\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXisV2htL3M\" aria-label=\"CAS reference 38\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=30864657\" aria-label=\"PubMed reference 38\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6582343\" aria-label=\"PubMed Central reference 38\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 38\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=MitoZ%3A%20a%20toolkit%20for%20animal%20mitochondrial%20genome%20assembly%2C%20annotation%20and%20visualization&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2Fgkz173&amp;volume=47&amp;publication_year=2019&amp;author=Meng%2CG&amp;author=Li%2CY&amp;author=Yang%2CC&amp;author=Liu%2CS\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR39\">Gibson, D. G. et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215\u20131220 (2008).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1126\/science.1151721\" data-track-item_id=\"10.1126\/science.1151721\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1126%2Fscience.1151721\" aria-label=\"Article reference 39\" data-doi=\"10.1126\/science.1151721\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2008Sci...319.1215G\" aria-label=\"ADS reference 39\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BD1cXisVSksbs%3D\" aria-label=\"CAS reference 39\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=18218864\" aria-label=\"PubMed reference 39\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 39\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Complete%20chemical%20synthesis%2C%20assembly%2C%20and%20cloning%20of%20a%20Mycoplasma%20genitalium%20genome&amp;journal=Science&amp;doi=10.1126%2Fscience.1151721&amp;volume=319&amp;pages=1215-1220&amp;publication_year=2008&amp;author=Gibson%2CDG\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR40\">Karr, J. R. et al. A whole-cell computational model predicts phenotype from genotype. Cell 150, 389\u2013401 (2012).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1016\/j.cell.2012.05.044\" data-track-item_id=\"10.1016\/j.cell.2012.05.044\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1016%2Fj.cell.2012.05.044\" aria-label=\"Article reference 40\" data-doi=\"10.1016\/j.cell.2012.05.044\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2012Cell..150..389K\" aria-label=\"ADS reference 40\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC38XhtVymsr7L\" aria-label=\"CAS reference 40\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=22817898\" aria-label=\"PubMed reference 40\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC3413483\" aria-label=\"PubMed Central reference 40\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 40\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=A%20whole-cell%20computational%20model%20predicts%20phenotype%20from%20genotype&amp;journal=Cell&amp;doi=10.1016%2Fj.cell.2012.05.044&amp;volume=150&amp;pages=389-401&amp;publication_year=2012&amp;author=Karr%2CJR\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR41\">Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener nofollow\" data-track-label=\"10.1186\/1471-2105-11-119\" data-track-item_id=\"10.1186\/1471-2105-11-119\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/1471-2105-11-119\" aria-label=\"Article reference 41\" data-doi=\"10.1186\/1471-2105-11-119\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=20211023\" aria-label=\"PubMed reference 41\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2848648\" aria-label=\"PubMed Central reference 41\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 41\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Prodigal%3A%20prokaryotic%20gene%20recognition%20and%20translation%20initiation%20site%20identification&amp;journal=BMC%20Bioinformatics&amp;doi=10.1186%2F1471-2105-11-119&amp;volume=11&amp;publication_year=2010&amp;author=Hyatt%2CD\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR42\">Fredens, J. et al. Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514\u2013518 (2019).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41586-019-1192-5\" data-track-item_id=\"10.1038\/s41586-019-1192-5\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41586-019-1192-5\" aria-label=\"Article reference 42\" data-doi=\"10.1038\/s41586-019-1192-5\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2019Natur.569..514F\" aria-label=\"ADS reference 42\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC1MXpslGmurg%3D\" aria-label=\"CAS reference 42\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=31092918\" aria-label=\"PubMed reference 42\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC7039709\" aria-label=\"PubMed Central reference 42\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 42\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Total%20synthesis%20of%20Escherichia%20coli%20with%20a%20recoded%20genome&amp;journal=Nature&amp;doi=10.1038%2Fs41586-019-1192-5&amp;volume=569&amp;pages=514-518&amp;publication_year=2019&amp;author=Fredens%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR43\">Li, Y. et al. Competition-level code generation with AlphaCode. Science 378, 1092\u20131097 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1126\/science.abq1158\" data-track-item_id=\"10.1126\/science.abq1158\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1126%2Fscience.abq1158\" aria-label=\"Article reference 43\" data-doi=\"10.1126\/science.abq1158\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2022Sci...378.1092L\" aria-label=\"ADS reference 43\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38XjtVyhtrrJ\" aria-label=\"CAS reference 43\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=36480631\" aria-label=\"PubMed reference 43\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 43\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Competition-level%20code%20generation%20with%20AlphaCode&amp;journal=Science&amp;doi=10.1126%2Fscience.abq1158&amp;volume=378&amp;pages=1092-1097&amp;publication_year=2022&amp;author=Li%2CY\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR44\">Brown, B. et al. Large language monkeys: scaling inference compute with repeated sampling. Preprint at <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2407.21787\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.48550\/arXiv.2407.21787\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.48550\/arXiv.2407.21787<\/a> (2024).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR45\">Allis, C. D. &amp; Jenuwein, T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 17, 487\u2013500 (2016).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/nrg.2016.59\" data-track-item_id=\"10.1038\/nrg.2016.59\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fnrg.2016.59\" aria-label=\"Article reference 45\" data-doi=\"10.1038\/nrg.2016.59\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BC28XhtVGiur%2FJ\" aria-label=\"CAS reference 45\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=27346641\" aria-label=\"PubMed reference 45\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 45\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=The%20molecular%20hallmarks%20of%20epigenetic%20control&amp;journal=Nat.%20Rev.%20Genet.&amp;doi=10.1038%2Fnrg.2016.59&amp;volume=17&amp;pages=487-500&amp;publication_year=2016&amp;author=Allis%2CCD&amp;author=Jenuwein%2CT\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR46\">Schreiber, J., Lu, Y. Y. &amp; Noble, W. S. Ledidi: Designing genomic edits that induce functional activity. Preprint at bioRxiv <a href=\"https:\/\/doi.org\/10.1101\/2020.05.21.109686\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.1101\/2020.05.21.109686\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.1101\/2020.05.21.109686<\/a> (2020).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR47\">Linder, J. &amp; Seelig, G. Fast activation maximization for molecular sequence design. BMC Bioinformatics 22, 510 (2020).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"noopener nofollow\" data-track-label=\"10.1186\/s12859-021-04437-5\" data-track-item_id=\"10.1186\/s12859-021-04437-5\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/link.springer.com\/doi\/10.1186\/s12859-021-04437-5\" aria-label=\"Article reference 47\" data-doi=\"10.1186\/s12859-021-04437-5\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 47\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Fast%20activation%20maximization%20for%20molecular%20sequence%20design&amp;journal=BMC%20Bioinformatics&amp;doi=10.1186%2Fs12859-021-04437-5&amp;volume=22&amp;publication_year=2020&amp;author=Linder%2CJ&amp;author=Seelig%2CG\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR48\">Zrimec, J. et al. Controlling gene expression with deep generative design of regulatory DNA. Nat. Commun. 13, 5099 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41467-022-32818-8\" data-track-item_id=\"10.1038\/s41467-022-32818-8\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41467-022-32818-8\" aria-label=\"Article reference 48\" data-doi=\"10.1038\/s41467-022-32818-8\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2022NatCo..13.5099Z\" aria-label=\"ADS reference 48\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38XitlWisr%2FL\" aria-label=\"CAS reference 48\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=36042233\" aria-label=\"PubMed reference 48\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC9427793\" aria-label=\"PubMed Central reference 48\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 48\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Controlling%20gene%20expression%20with%20deep%20generative%20design%20of%20regulatory%20DNA&amp;journal=Nat.%20Commun.&amp;doi=10.1038%2Fs41467-022-32818-8&amp;volume=13&amp;publication_year=2022&amp;author=Zrimec%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR49\">de Almeida, B. P. et al. Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo. Nature 626, 207\u2013211 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1038\/s41586-023-06905-9\" data-track-item_id=\"10.1038\/s41586-023-06905-9\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1038%2Fs41586-023-06905-9\" aria-label=\"Article reference 49\" data-doi=\"10.1038\/s41586-023-06905-9\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=38086418\" aria-label=\"PubMed reference 49\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC10830412\" aria-label=\"PubMed Central reference 49\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 49\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Targeted%20design%20of%20synthetic%20enhancers%20for%20selected%20tissues%20in%20the%20Drosophila%20embryo&amp;journal=Nature&amp;doi=10.1038%2Fs41586-023-06905-9&amp;volume=626&amp;pages=207-211&amp;publication_year=2023&amp;author=Almeida%2CBP\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR50\">DaSilva, L. F. et al. DNA-diffusion: leveraging generative models for controlling chromatin accessibility and gene expression via synthetic regulatory elements. Nat. Genet. 58, 180\u2013194 (2026).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR51\">Sarkar, A. et al. Designing DNA with tunable regulatory activity using score-entropy discrete diffusion. Preprint at bioRxiv <a href=\"https:\/\/doi.org\/10.1101\/2024.05.23.595630\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.1101\/2024.05.23.595630\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.1101\/2024.05.23.595630<\/a> (2024).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR52\">Dauparas, J. et al. Robust deep learning-based protein sequence design using ProteinMPNN. Science 378, 49\u201356 (2022).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1126\/science.add2187\" data-track-item_id=\"10.1126\/science.add2187\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1126%2Fscience.add2187\" aria-label=\"Article reference 52\" data-doi=\"10.1126\/science.add2187\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2022Sci...378...49D\" aria-label=\"ADS reference 52\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB38Xis1amsrjF\" aria-label=\"CAS reference 52\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=36108050\" aria-label=\"PubMed reference 52\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC9997061\" aria-label=\"PubMed Central reference 52\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 52\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Robust%20deep%20learning-based%20protein%20sequence%20design%20using%20ProteinMPNN&amp;journal=Science&amp;doi=10.1126%2Fscience.add2187&amp;volume=378&amp;pages=49-56&amp;publication_year=2022&amp;author=Dauparas%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR53\">Verkuil, R. et al. Language models generalize beyond natural proteins. Preprint at bioRxiv <a href=\"https:\/\/doi.org\/10.1101\/2022.12.21.521521\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.1101\/2022.12.21.521521\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.1101\/2022.12.21.521521<\/a> (2022).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR54\">Bloomfield, D. et al. AI and biosecurity: The need for governance. Science 385, 831\u2013833 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1126\/science.adq1977\" data-track-item_id=\"10.1126\/science.adq1977\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1126%2Fscience.adq1977\" aria-label=\"Article reference 54\" data-doi=\"10.1126\/science.adq1977\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"ads reference\" data-track-action=\"ads reference\" href=\"http:\/\/adsabs.harvard.edu\/cgi-bin\/nph-data_query?link_type=ABSTRACT&amp;bibcode=2024Sci...385..831B\" aria-label=\"ADS reference 54\" target=\"_blank\">ADS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=39172825\" aria-label=\"PubMed reference 54\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC12158449\" aria-label=\"PubMed Central reference 54\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 54\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=AI%20and%20biosecurity%3A%20The%20need%20for%20governance&amp;journal=Science&amp;doi=10.1126%2Fscience.adq1977&amp;volume=385&amp;pages=831-833&amp;publication_year=2024&amp;author=Bloomfield%2CD\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR55\">Pathak, A. K. et al. Pervasive ancestry bias in variant effect predictors. Preprint at bioRxiv <a href=\"https:\/\/doi.org\/10.1101\/2024.05.20.594987\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.1101\/2024.05.20.594987\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.1101\/2024.05.20.594987<\/a> (2025).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR56\">Schubach, M., Maass, T., Nazaretyan, L., R\u00f6ner, S. &amp; Kircher, M. CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions. Nucleic Acids Res. 52, D1143\u2013D1154 (2024).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1093\/nar\/gkad989\" data-track-item_id=\"10.1093\/nar\/gkad989\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1093%2Fnar%2Fgkad989\" aria-label=\"Article reference 56\" data-doi=\"10.1093\/nar\/gkad989\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB2cXivVamt7%2FP\" aria-label=\"CAS reference 56\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=38183205\" aria-label=\"PubMed reference 56\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed central reference\" data-track-action=\"pubmed central reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC10767851\" aria-label=\"PubMed Central reference 56\" target=\"_blank\">PubMed Central<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 56\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=CADD%20v1.7%3A%20using%20protein%20language%20models%2C%20regulatory%20CNNs%20and%20other%20nucleotide-level%20scores%20to%20improve%20genome-wide%20variant%20predictions&amp;journal=Nucleic%20Acids%20Res.&amp;doi=10.1093%2Fnar%2Fgkad989&amp;volume=52&amp;pages=D1143-D1154&amp;publication_year=2024&amp;author=Schubach%2CM&amp;author=Maass%2CT&amp;author=Nazaretyan%2CL&amp;author=R%C3%B6ner%2CS&amp;author=Kircher%2CM\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR57\">Cheng, J. et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science 381, eadg7492 (2023).<\/p>\n<p class=\"c-article-references__links u-hide-print\"><a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"10.1126\/science.adg7492\" data-track-item_id=\"10.1126\/science.adg7492\" data-track-value=\"article reference\" data-track-action=\"article reference\" href=\"https:\/\/doi.org\/10.1126%2Fscience.adg7492\" aria-label=\"Article reference 57\" data-doi=\"10.1126\/science.adg7492\" target=\"_blank\">Article<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"cas reference\" data-track-action=\"cas reference\" href=\"https:\/\/www.nature.com\/articles\/cas-redirect\/1:CAS:528:DC%2BB3sXhvFyjtbfE\" aria-label=\"CAS reference 57\" target=\"_blank\">CAS<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" rel=\"nofollow noopener\" data-track-label=\"link\" data-track-item_id=\"link\" data-track-value=\"pubmed reference\" data-track-action=\"pubmed reference\" href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Abstract&amp;list_uids=37733863\" aria-label=\"PubMed reference 57\" target=\"_blank\">PubMed<\/a>\u00a0<br \/>\n    <a data-track=\"click_references\" data-track-action=\"google scholar reference\" data-track-value=\"google scholar reference\" data-track-label=\"link\" data-track-item_id=\"link\" rel=\"nofollow noopener\" aria-label=\"Google Scholar reference 57\" href=\"http:\/\/scholar.google.com\/scholar_lookup?&amp;title=Accurate%20proteome-wide%20missense%20variant%20effect%20prediction%20with%20AlphaMissense&amp;journal=Science&amp;doi=10.1126%2Fscience.adg7492&amp;volume=381&amp;publication_year=2023&amp;author=Cheng%2CJ\" target=\"_blank\"><br \/>\n                    Google Scholar<\/a>\u00a0\n                <\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR58\">Pampari, A. et al. ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants. Preprint at bioRxiv <a href=\"https:\/\/doi.org\/10.1101\/2024.12.25.630221\" data-track=\"click_references\" data-track-action=\"external reference\" data-track-value=\"external reference\" data-track-label=\"10.1101\/2024.12.25.630221\" rel=\"nofollow noopener\" target=\"_blank\">https:\/\/doi.org\/10.1101\/2024.12.25.630221<\/a> (2025).<\/p>\n<p class=\"c-article-references__text\" id=\"ref-CR59\">Durrant, M. G. et al. Bridge RNAs direct programmable recombination of target and donor DNA. Nature 630, 984\u2013993 (2024).<\/p>\n","protected":false},"excerpt":{"rendered":"Nguyen, E. et al. Sequence modeling and design from molecular to genome scale with Evo. Science 386, eado9336&hellip;\n","protected":false},"author":2,"featured_media":457920,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[6195,59,5459,4230,11376,4231,90,56,54,55],"class_list":{"0":"post-457919","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-evolutionary-biology","9":"tag-gb","10":"tag-genomics","11":"tag-humanities-and-social-sciences","12":"tag-machine-learning","13":"tag-multidisciplinary","14":"tag-science","15":"tag-uk","16":"tag-united-kingdom","17":"tag-unitedkingdom"},"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/posts\/457919","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/comments?post=457919"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/posts\/457919\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/media\/457920"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/media?parent=457919"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/categories?post=457919"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/uk\/wp-json\/wp\/v2\/tags?post=457919"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}