{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,7]],"date-time":"2026-11-07T14:27:34Z","timestamp":1794061654634,"version":"4.8.0"},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T00:00:00Z","timestamp":1776902400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T00:00:00Z","timestamp":1776902400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Hillblom\/BARI Graduate Student Fellowship"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Protoc"],"published-print":{"date-parts":[[2026,11]]},"DOI":"10.1038\/s41596-026-01364-8","type":"journal-article","created":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T14:35:29Z","timestamp":1776954929000},"page":"5009-5032","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Discovery of candidate therapeutic targets with Geneformer"],"prefix":"10.1038","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1017-0316","authenticated-orcid":false,"given":"Yujie","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madhavan S.","family":"Venkatesh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1658-1447","authenticated-orcid":false,"given":"Christina V.","family":"Theodoris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,4,23]]},"reference":[{"key":"1364_CR1","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1038\/s41586-023-06139-9","volume":"618","author":"CV Theodoris","year":"2023","unstructured":"Theodoris, C. V. et al. Transfer learning enables predictions in network biology. Nature 618, 616\u2013624 (2023).","journal-title":"Nature"},{"key":"1364_CR2","doi-asserted-by":"publisher","unstructured":"Vaswani, A. et al. Attention is all you need. Preprint at arXiv https:\/\/doi.org\/10.48550\/arXiv.1706.03762 (2017).","DOI":"10.48550\/arXiv.1706.03762"},{"key":"1364_CR3","doi-asserted-by":"publisher","unstructured":"Devlin, J., Chang, M.-W., Lee, K. & Toutanova, K. BERT: pre-training of deep bidirectional transformers for language understanding. Preprint at https:\/\/doi.org\/10.48550\/arXiv.1810.04805 (2018).","DOI":"10.48550\/arXiv.1810.04805"},{"key":"1364_CR4","doi-asserted-by":"crossref","unstructured":"He, K., Zhang, X., Ren, S. & Sun, J. Deep residual learning for image recognition. In Proc. 2016 IEEE Conference on Computer Vision and Pattern Recognition 770\u2013778 (IEEE, 2016).","DOI":"10.1109\/CVPR.2016.90"},{"key":"1364_CR5","doi-asserted-by":"publisher","unstructured":"Chen, H. et al. Scaling and quantization of large-scale foundation model enables resource-efficient predictions in network biology. Nat. Comput. Sci. https:\/\/doi.org\/10.1038\/s43588-026-00972-4 (2026).","DOI":"10.1038\/s43588-026-00972-4"},{"key":"1364_CR6","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1038\/s41592-019-0494-8","volume":"16","author":"M Lotfollahi","year":"2019","unstructured":"Lotfollahi, M., Wolf, F. A. & Theis, F. J. scGen predicts single-cell perturbation responses. Nat. Methods 16, 715\u2013721 (2019).","journal-title":"Nat. Methods"},{"key":"1364_CR7","doi-asserted-by":"publisher","unstructured":"Cui, H. et al. scGPT: toward building a foundation model for single-cell multi-omics using generative AI. Nat. Methods https:\/\/doi.org\/10.1038\/s41592-024-02201-0 (2024).","DOI":"10.1038\/s41592-024-02201-0"},{"key":"1364_CR8","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-024-02305-7","author":"M Hao","year":"2024","unstructured":"Hao, M. et al. Large-scale foundation model on single-cell transcriptomics. Nat. Methods https:\/\/doi.org\/10.1038\/s41592-024-02305-7 (2024).","journal-title":"Nat. Methods"},{"key":"1364_CR9","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1038\/s41422-024-01034-y","volume":"34","author":"X Yang","year":"2024","unstructured":"Yang, X. et al. GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model. Cell Res. 34, 830\u2013845 (2024).","journal-title":"Cell Res."},{"key":"1364_CR10","doi-asserted-by":"publisher","unstructured":"Rosen, Y. et al. Universal cell embeddings: a foundation model for cell biology. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.11.28.568918 (2023).","DOI":"10.1101\/2023.11.28.568918"},{"key":"1364_CR11","first-page":"2525","volume":"22","author":"AC Schaar","year":"2024","unstructured":"Schaar, A. C. et al. Nicheformer: a foundation model for single-cell and spatial omics. Bioinformatics 22, 2525\u20132538 (2024).","journal-title":"Bioinformatics"},{"key":"1364_CR12","doi-asserted-by":"publisher","unstructured":"Pearce, J. D. et al. A cross-species generative cell atlas across 1.5 billion years of evolution: the TranscriptFormer single-cell model. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2025.04.25.650731 (2025).","DOI":"10.1101\/2025.04.25.650731"},{"key":"1364_CR13","doi-asserted-by":"publisher","unstructured":"Chen, H. et al. Quantized multi-task learning for context-specific representations of gene network dynamics. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2024.08.16.608180 (2024).","DOI":"10.1101\/2024.08.16.608180"},{"key":"1364_CR14","unstructured":"Quality control in single-cell RNA-seq data. Kaggle https:\/\/kaggle.com\/code\/hrishikeshp\/2-quality-control-in-single-cell-rna-seq-data (2021)."},{"key":"1364_CR15","unstructured":"Quality control\u2014single-cell best practices. Single-cell Best Practices https:\/\/www.sc-best-practices.org\/preprocessing_visualization\/quality_control.html#filtering-low-quality-cells (2023)."},{"key":"1364_CR16","unstructured":"Heil, B. How to convert gene ID formats in Python. Autobencoder https:\/\/autobencoder.com\/2021-10-03-gene-conversion\/ (2021)."},{"key":"1364_CR17","unstructured":"Notebook on nbviewer. https:\/\/nbviewer.org\/gist\/newgene\/6771106."},{"key":"1364_CR18","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1038\/s41586-022-04817-8","volume":"608","author":"M Chaffin","year":"2022","unstructured":"Chaffin, M. et al. Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy. Nature 608, 174\u2013180 (2022).","journal-title":"Nature"}],"container-title":["Nature Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41596-026-01364-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41596-026-01364-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41596-026-01364-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T15:02:17Z","timestamp":1793718137000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41596-026-01364-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,23]]},"references-count":18,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["1364"],"URL":"https:\/\/doi.org\/10.1038\/s41596-026-01364-8","relation":{},"ISSN":["1754-2189","1750-2799"],"issn-type":[{"value":"1754-2189","type":"print"},{"value":"1750-2799","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,23]]},"assertion":[{"value":"27 June 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 March 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 April 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}