Nature Methods最新文献

Learning the language of biological interactions. 学习生物相互作用的语言。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-07-31 DOI: 10.1038/s41592-025-02725-z

引用次数: 0

GeneAgent: self-verification language agent for gene-set analysis using domain databases. GeneAgent：使用域数据库进行基因集分析的自我验证语言代理。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-07-28 DOI: 10.1038/s41592-025-02748-6

Zhizheng Wang, Qiao Jin, Chih-Hsuan Wei, Shubo Tian, Po-Ting Lai, Qingqing Zhu, Chi-Ping Day, Christina Ross, Robert Leaman, Zhiyong Lu

引用次数: 0

Sliding Window Interaction Grammar (SWING): a generalized interaction language model for peptide and protein interactions. 滑动窗口相互作用语法（SWING）：肽和蛋白质相互作用的通用相互作用语言模型。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-07-28 DOI: 10.1038/s41592-025-02723-1

Jane C Siwek, Alisa A Omelchenko, Prabal Chhibbar, Sanya Arshad, AnnaElaine Rosengart, Iliyan Nazarali, Akash Patel, Kiran Nazarali, Javad Rahimikollu, Jeremy S Tilstra, Mark J Shlomchik, David R Koes, Alok V Joglekar, Jishnu Das

{"title":"Sliding Window Interaction Grammar (SWING): a generalized interaction language model for peptide and protein interactions.","authors":"Jane C Siwek, Alisa A Omelchenko, Prabal Chhibbar, Sanya Arshad, AnnaElaine Rosengart, Iliyan Nazarali, Akash Patel, Kiran Nazarali, Javad Rahimikollu, Jeremy S Tilstra, Mark J Shlomchik, David R Koes, Alok V Joglekar, Jishnu Das","doi":"10.1038/s41592-025-02723-1","DOIUrl":"10.1038/s41592-025-02723-1","url":null,"abstract":"Protein language models embed protein sequences for different tasks. However, these are suboptimal at learning the language of protein interactions. We developed an interaction language model (iLM), Sliding Window Interaction Grammar (SWING) that leverages differences in amino-acid properties to generate an interaction vocabulary. SWING successfully predicted both class I and class II peptide-major histocompatibility complex interactions. Furthermore, the class I SWING model could uniquely cross-predict class II interactions, a complex prediction task not attempted by existing methods. Using human class I and II data, SWING accurately predicted murine class II peptide-major histocompatibility interactions involving risk alleles in systemic lupus erythematosus and type 1 diabetes. SWING accurately predicted how variants can disrupt specific protein-protein interactions, based on sequence information alone. SWING outperformed passive uses of protein language model embeddings, demonstrating the value of the unique iLM architecture. Overall, SWING is a generalizable zero-shot iLM that learns the language of protein-protein interactions.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":32.1,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732394","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}

引用次数: 0

From 2D to 3D and beyond: the evolution and impact of in vitro tumor models in cancer research. 从2D到3D及以后：体外肿瘤模型在癌症研究中的演变和影响。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-25 DOI: 10.1038/s41592-025-02769-1

Gat Rauner, Piyush B Gupta, Charlotte Kuperwasser

{"title":"From 2D to 3D and beyond: the evolution and impact of in vitro tumor models in cancer research.","authors":"Gat Rauner, Piyush B Gupta, Charlotte Kuperwasser","doi":"10.1038/s41592-025-02769-1","DOIUrl":"https://doi.org/10.1038/s41592-025-02769-1","url":null,"abstract":"In vitro tumor models are essential tools for cancer research, offering key insights into not only tumor biology but also therapeutic responses. The transition from traditional two-dimensional to three-dimensional organoid systems marks a paradigm shift in cancer modeling. Although two-dimensional models have been instrumental in elucidating fundamental molecular and genetic mechanisms, they fail to accurately replicate the intricate three-dimensional architecture and dynamic microenvironment characteristic of human tumors. Here we outline how advanced organoid technologies now enable more faithful recapitulation of tumor heterogeneity that better mimic native tissue mechanics and biochemistry. We discuss emerging methods, including air-liquid interface cultures, microfluidic tumor-on-a-chip devices and high-content imaging integrated with machine learning, which collectively address longstanding challenges such as matrix variability and the limited incorporation of immune and vascular elements. These innovations promise to enhance reproducibility and scalability while providing unprecedented insights into tumor biology, cancer progression and therapeutic strategies.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718214","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}

引用次数: 0

Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes. 表面：可视化神经成像网，神经束造影流线和连接体。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-24 DOI: 10.1038/s41592-025-02764-6

Christopher Rorden

引用次数: 0

MRIcroGL: voxel-based visualization for neuroimaging. MRIcroGL：基于体素的神经成像可视化。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-24 DOI: 10.1038/s41592-025-02763-7

Christopher Rorden

引用次数: 0

DSI Studio: an integrated tractography platform and fiber data hub for accelerating brain research. DSI Studio：一个集成的神经束成像平台和光纤数据中心，用于加速大脑研究。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-24 DOI: 10.1038/s41592-025-02762-8

Fang-Cheng Yeh

引用次数: 0

Symmetric alternatives to the ordinary least squares regression. 普通最小二乘回归的对称替代方案。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-23 DOI: 10.1038/s41592-025-02760-w

Luca Greco, George Luta, Martin Krzywinski, Naomi Altman

引用次数: 0

To do a PhD these days. 去读博士。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-21 DOI: 10.1038/s41592-025-02768-2

Vivien Marx

引用次数: 0

Genetically encoded biosensor for monitoring spatiotemporal dynamics of CCR2 ligands in culture and in vivo. 用于监测CCR2配体在培养和体内时空动态的遗传编码生物传感器。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-07-15 DOI: 10.1038/s41592-025-02742-y

Xian Xiao, Chenyu Wang, Xun Guo, Fengxue Xi, Qiuling Qian, Guoteng Liang, Ming Chen, Xiaoting Sun, Balint Szabo, Miao Jing, Kiryl D Piatkevich

{"title":"Genetically encoded biosensor for monitoring spatiotemporal dynamics of CCR2 ligands in culture and in vivo.","authors":"Xian Xiao, Chenyu Wang, Xun Guo, Fengxue Xi, Qiuling Qian, Guoteng Liang, Ming Chen, Xiaoting Sun, Balint Szabo, Miao Jing, Kiryl D Piatkevich","doi":"10.1038/s41592-025-02742-y","DOIUrl":"https://doi.org/10.1038/s41592-025-02742-y","url":null,"abstract":"Chemokines regulate immune cell migration in development, homeostasis and inflammation, but the precise spatiotemporal pattern of chemokine release in vivo remains elusive due to the constraints of existing detection methodologies. Here, we report the engineering and characterization of a genetically encoded green fluorescent chemokine sensor, named CRAFi-CCR2, which utilizes the CCR2 receptor as a sensing moiety. In astrocytes, hCRAFi-CCR2, derived from the human CCR2B receptor, exhibited ~300% increase in fluorescence in response to mCCL2, with nanomolar affinity (2.5 nM). Activation of hCRAFi-CCR2 did not affect downstream signaling pathways, such as calcium mobilization and receptor internalization. Using this sensor, we performed 17-20 h of real-time imaging to observe endogenous mCCL2 release under inflammatory conditions, both in cell culture and in mice. In mouse brain, we observed spatial heterogeneity of CCL2 signal response on a scale of about 20-50 µm, highlighting the complexity of the immune system's spatiotemporal signaling.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642984","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}

引用次数: 0