{"title":"Editor’s pick: Switch Therapeutics","authors":"Iris Marchal","doi":"10.1038/s41587-024-02423-9","DOIUrl":"10.1038/s41587-024-02423-9","url":null,"abstract":"Each year, Nature Biotechnology highlights companies that have received sizeable early-stage funding in the previous year. Switch Therapeutics is rethinking cell-type specificity, building precision RNAi therapeutics for the brain.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":null,"pages":null},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cellular shuttles put mislocalized proteins in their right place","authors":"Iris Marchal","doi":"10.1038/s41587-024-02444-4","DOIUrl":"10.1038/s41587-024-02444-4","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":null,"pages":null},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Pan-KRAS destruction with a single PROTAC","authors":"Iris Marchal","doi":"10.1038/s41587-024-02445-3","DOIUrl":"10.1038/s41587-024-02445-3","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":null,"pages":null},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Five questions with Weixin Tang","authors":"Michael Francisco","doi":"10.1038/s41587-024-02419-5","DOIUrl":"10.1038/s41587-024-02419-5","url":null,"abstract":"A chemist pioneering the discovery and engineering of CRISPR-derived gene-editing agents for medical adaptation talks about her scientific journey, the challenges of leading a lab and teaching undergraduates.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":null,"pages":null},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41587-024-02419-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A strategy to load, rethread and read protein sequences through a nanopore","authors":"Iris Marchal","doi":"10.1038/s41587-024-02443-5","DOIUrl":"10.1038/s41587-024-02443-5","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":null,"pages":null},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"T cells","authors":"","doi":"10.1038/s41587-024-02415-9","DOIUrl":"10.1038/s41587-024-02415-9","url":null,"abstract":"Recent patents relating to the manufacture, preparation and use of T cells in treating cancer.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":null,"pages":null},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abdul Muntakim Rafi, Daria Nogina, Dmitry Penzar, Dohoon Lee, Danyeong Lee, Nayeon Kim, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il-Youp Kwak, Georgy Meshcheryakov, Andrey Lando, Arsenii Zinkevich, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Eeshit Dhaval Vaishnav, Payman Yadollahpour, Sun Kim, Jake Albrecht, Aviv Regev, Wuming Gong, Ivan V. Kulakovskiy, Pablo Meyer, Carl G. de Boer
{"title":"A community effort to optimize sequence-based deep learning models of gene regulation","authors":"Abdul Muntakim Rafi, Daria Nogina, Dmitry Penzar, Dohoon Lee, Danyeong Lee, Nayeon Kim, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il-Youp Kwak, Georgy Meshcheryakov, Andrey Lando, Arsenii Zinkevich, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Eeshit Dhaval Vaishnav, Payman Yadollahpour, Sun Kim, Jake Albrecht, Aviv Regev, Wuming Gong, Ivan V. Kulakovskiy, Pablo Meyer, Carl G. de Boer","doi":"10.1038/s41587-024-02414-w","DOIUrl":"https://doi.org/10.1038/s41587-024-02414-w","url":null,"abstract":"<p>A systematic evaluation of how model architectures and training strategies impact genomics model performance is needed. To address this gap, we held a DREAM Challenge where competitors trained models on a dataset of millions of random promoter DNA sequences and corresponding expression levels, experimentally determined in yeast. For a robust evaluation of the models, we designed a comprehensive suite of benchmarks encompassing various sequence types. All top-performing models used neural networks but diverged in architectures and training strategies. To dissect how architectural and training choices impact performance, we developed the Prix Fixe framework to divide models into modular building blocks. We tested all possible combinations for the top three models, further improving their performance. The DREAM Challenge models not only achieved state-of-the-art results on our comprehensive yeast dataset but also consistently surpassed existing benchmarks on <i>Drosophila</i> and human genomic datasets, demonstrating the progress that can be driven by gold-standard genomics datasets.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":null,"pages":null},"PeriodicalIF":46.9,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142404936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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