Nature Methods最新文献_第3页

InterPLM: discovering interpretable features in protein language models via sparse autoencoders InterPLM：通过稀疏自编码器发现蛋白质语言模型中的可解释特征。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-29 DOI: 10.1038/s41592-025-02836-7

Elana Simon, James Zou

{"title":"InterPLM: discovering interpretable features in protein language models via sparse autoencoders","authors":"Elana Simon, James Zou","doi":"10.1038/s41592-025-02836-7","DOIUrl":"10.1038/s41592-025-02836-7","url":null,"abstract":"Despite their success in protein modeling and design, the internal mechanisms of protein language models (PLMs) are poorly understood. Here we present a systematic framework to extract and analyze interpretable features from PLMs using sparse autoencoders. Training sparse autoencoders on ESM-2 embeddings, we identify thousands of interpretable features highlighting biological concepts including binding sites, structural motifs and functional domains. Individual neurons show considerably less conceptual alignment, suggesting PLMs store concepts in superposition. This superposition persists across model scales and larger PLMs capture more interpretable concepts. Beyond known annotations, ESM-2 learns coherent patterns across evolutionarily distinct protein families. To systematically analyze these numerous features, we developed an automated interpretation approach using large language models for feature description and validation. As practical applications, these features can accurately identify missing database annotations and enable targeted steering of sequence generation. Our results show PLM representations can be decomposed into interpretable components, demonstrating the feasibility and utility of mechanistically interpreting these models. InterPLM is a computational framework to extract and analyze interpretable features from protein language models using sparse autoencoders. By training sparse autoencoders on ESM-2 embeddings, this study identifies thousands of interpretable biological features learned by the different layers of the ESM-2 model.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 10","pages":"2107-2117"},"PeriodicalIF":32.1,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191614","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

Uncovering hidden protein modifications with native top-down mass spectrometry 发现隐藏的蛋白质修饰与天然自上而下的质谱。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-29 DOI: 10.1038/s41592-025-02846-5

Jack L. Bennett, Tarick J. El-Baba, Konstantin C. Zouboulis, Carla Kirschbaum, Haigang Song, Frances I. Butroid, Justin L. P. Benesch, Corinne A. Lutomski, Carol V. Robinson

{"title":"Uncovering hidden protein modifications with native top-down mass spectrometry","authors":"Jack L. Bennett, Tarick J. El-Baba, Konstantin C. Zouboulis, Carla Kirschbaum, Haigang Song, Frances I. Butroid, Justin L. P. Benesch, Corinne A. Lutomski, Carol V. Robinson","doi":"10.1038/s41592-025-02846-5","DOIUrl":"10.1038/s41592-025-02846-5","url":null,"abstract":"Protein modifications drive dynamic cellular processes by modulating biomolecular interactions, yet capturing these modifications within their native structural context remains a significant challenge. Native top-down mass spectrometry promises to preserve the critical link between modifications and interactions. However, current methods often fail to detect uncharacterized or low-abundance modifications, limiting insights into proteoform diversity. To address this gap, we introduce precise and accurate Identification Of Native proteoforms (precisION), an interactive end-to-end software package that leverages a robust, data-driven fragment-level open search to detect, localize and quantify ‘hidden’ modifications within intact protein complexes. Applying precisION to four therapeutically relevant targets—PDE6, ACE2, osteopontin (SPP1) and a GABA transporter (GAT1)—we discover undocumented phosphorylation, glycosylation and lipidation, and resolve previously uninterpretable density in an electron cryo-microscopy map of GAT1. As an open-source software package, precisION offers an intuitive means for interpreting complex protein fragmentation data. This tool will empower the community to unlock the potential of native top-down mass spectrometry, advancing integrative structural biology, molecular pathology and drug development. precisION discovers, localizes and quantifies protein modifications within complex proteoform assemblies through data-driven analysis of native top-down mass spectra.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 10","pages":"2127-2137"},"PeriodicalIF":32.1,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41592-025-02846-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191958","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}

引用次数: 0

What does a language model know about proteins? 语言模型对蛋白质了解多少？

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-29 DOI: 10.1038/s41592-025-02837-6

Jeffrey A. Ruffolo

引用次数: 0

Highly multiplexed 3D profiling of cell states and immune niches in human tumors 人类肿瘤细胞状态和免疫龛的高度多路3D分析。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-29 DOI: 10.1038/s41592-025-02824-x

Clarence Yapp, Ajit J. Nirmal, Felix Zhou, Alex Y. H. Wong, Juliann B. Tefft, Yi Daniel Lu, Zhiguo Shang, Zoltan Maliga, Paula Montero Llopis, George F. Murphy, Christine G. Lian, Gaudenz Danuser, Sandro Santagata, Peter K. Sorger

{"title":"Highly multiplexed 3D profiling of cell states and immune niches in human tumors","authors":"Clarence Yapp, Ajit J. Nirmal, Felix Zhou, Alex Y. H. Wong, Juliann B. Tefft, Yi Daniel Lu, Zhiguo Shang, Zoltan Maliga, Paula Montero Llopis, George F. Murphy, Christine G. Lian, Gaudenz Danuser, Sandro Santagata, Peter K. Sorger","doi":"10.1038/s41592-025-02824-x","DOIUrl":"10.1038/s41592-025-02824-x","url":null,"abstract":"Diseases such as cancer involve alterations in cell proportions, states and interactions, as well as complex changes in tissue morphology and architecture. Histopathological diagnosis of disease and most multiplexed spatial profiling relies on inspecting thin (4–5 µm) specimens. Here we describe a high-plex cyclic immunofluorescence method for three-dimensional tissue imaging and use it to show that few, if any, cells are intact in conventional thin tissue sections, reducing the accuracy of cell phenotyping and interaction analysis. However, three-dimensional cyclic immunofluorescence of sections eightfold to tenfold thicker enables accurate morphological assessment of diverse protein markers in intact tumor, immune and stromal cells. Moreover, the high resolution of this confocal approach generates images of cells in a preserved tissue environment at a level of detail previously limited to cell culture. Precise imaging of cell membranes also makes it possible to detect and map cell–cell contacts and juxtracrine signaling complexes in immune cell niches. Confocal microscopy enables high-resolution, high-plex 3D cyclic immunofluorescence of 30- to 50-µm-thick tissue sections. The approach allows for rich phenotypic assessments of intact cells and intercellular interactions with subcellular resolution.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 10","pages":"2180-2193"},"PeriodicalIF":32.1,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41592-025-02824-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191628","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}

引用次数: 0

Mapping chromatin and DNA methylation landscapes at single-cell and single-molecule resolution. 在单细胞和单分子分辨率下绘制染色质和DNA甲基化景观。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-26 DOI: 10.1038/s41592-025-02848-3

引用次数: 0

Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance DNA甲基化和组蛋白修饰的单细胞多组学检测重建表观基因组维持的动力学。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-25 DOI: 10.1038/s41592-025-02847-4

Christoph Geisenberger, Jeroen van den Berg, Vincent van Batenburg, Buys de Barbanson, Anna Lyubimova, Joe Verity-Legg, Xiufei Chen, Yibin Liu, Chun-Xiao Song, Jeroen de Ridder, Alexander van Oudenaarden

{"title":"Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance","authors":"Christoph Geisenberger, Jeroen van den Berg, Vincent van Batenburg, Buys de Barbanson, Anna Lyubimova, Joe Verity-Legg, Xiufei Chen, Yibin Liu, Chun-Xiao Song, Jeroen de Ridder, Alexander van Oudenaarden","doi":"10.1038/s41592-025-02847-4","DOIUrl":"10.1038/s41592-025-02847-4","url":null,"abstract":"DNA methylation and histone modifications encode epigenetic information. Recently, major progress was made to measure either mark at a single-cell resolution; however, a method for simultaneous detection is lacking, preventing study of their interactions. Here, to bridge this gap, we developed scEpi2-seq. Our technique provides a readout of histone modifications and DNA methylation at the single-cell and single-molecule level. Application in a cell line with the FUCCI cell cycle reporter system reveals how DNA methylation maintenance is influenced by the local chromatin context. In addition, profiling of H3K27me3 and DNA methylation in the mouse intestine yields insights into epigenetic interactions during cell type specification. Differentially methylated regions also demonstrated independent cell-type regulation in addition to H3K27me3 regulation, which reinforces that CpG methylation acts as an additional layer of control in facultative heterochromatin. This work presents scEpi2-seq, a method for simultaneous single-cell profiling of DNA methylation and histone modifications, enabling direct investigation of the interplay between these two epigenomic marks.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 10","pages":"2042-2051"},"PeriodicalIF":32.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41592-025-02847-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145150184","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}

引用次数: 0

EpiAgent: foundation model for single-cell epigenomics. EpiAgent：单细胞表观基因组学的基础模型。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-25 DOI: 10.1038/s41592-025-02822-z

Xiaoyang Chen, Keyi Li, Xuejian Cui, Zian Wang, Qun Jiang, Jiacheng Lin, Zhen Li, Zijing Gao, Hairong Lv, Rui Jiang

{"title":"EpiAgent: foundation model for single-cell epigenomics.","authors":"Xiaoyang Chen, Keyi Li, Xuejian Cui, Zian Wang, Qun Jiang, Jiacheng Lin, Zhen Li, Zijing Gao, Hairong Lv, Rui Jiang","doi":"10.1038/s41592-025-02822-z","DOIUrl":"10.1038/s41592-025-02822-z","url":null,"abstract":"<p><p>Although single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) enables the exploration of the epigenomic landscape that governs transcription at the cellular level, the complicated characteristics of the sequencing data and the broad scope of downstream tasks mean that a sophisticated and versatile computational method is urgently needed. Here we introduce EpiAgent, a foundation model pretrained on our manually curated large-scale Human-scATAC-Corpus. EpiAgent encodes chromatin accessibility patterns of cells as concise 'cell sentences' and captures cellular heterogeneity behind regulatory networks via bidirectional attention. Comprehensive benchmarks show that EpiAgent excels in typical downstream tasks, including unsupervised feature extraction, supervised cell type annotation and data imputation. By incorporating external embeddings, EpiAgent enables effective cellular response prediction for both out-of-sample stimulated and unseen genetic perturbations, reference data integration and query data mapping. Through in silico knockout of cis-regulatory elements, EpiAgent demonstrates the potential to model cell state changes. EpiAgent is further extended to directly annotate cell types in a zero-shot manner.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":32.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145150197","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

Merging conformational landscapes in a single consensus space with FlexConsensus algorithm 使用FlexConsensus算法合并单一共识空间中的构象景观。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-25 DOI: 10.1038/s41592-025-02841-w

David Herreros, Carlos Perez Mata, Carlos Oscar Sanchez Sorzano, Jose Maria Carazo

{"title":"Merging conformational landscapes in a single consensus space with FlexConsensus algorithm","authors":"David Herreros, Carlos Perez Mata, Carlos Oscar Sanchez Sorzano, Jose Maria Carazo","doi":"10.1038/s41592-025-02841-w","DOIUrl":"10.1038/s41592-025-02841-w","url":null,"abstract":"Structural heterogeneity analysis in cryogenic electron microscopy is experiencing a breakthrough in estimating more accurate, richer and interpretable conformational landscapes derived from experimental data. The emergence of new methods designed to tackle the heterogeneity challenge reflects this new paradigm, enabling users to gain a better understanding of protein dynamics. However, the question of how intrinsically different heterogeneity algorithms compare remains unsolved, which is crucial for determining the reliability, stability and correctness of the estimated conformational landscapes. Here, to overcome the previous challenge, we introduce FlexConsenus: a multi-autoencoder neural network able to learn the commonalities and differences among several conformational landscapes, enabling them to be placed in a shared consensus space with enhanced reliability. The consensus space enables the measurement of reproducibility in heterogeneity estimations, allowing users to either focus their analysis on particles with a stable estimation of their structural variability or concentrate on specific particle subsets detected by only certain methods. FlexConsensus is a multi-autoencoder-based algorithm for merging different conformational landscapes from cryogenic electron microscopy heterogeneity analysis into a common latent space for the identification of similarities and differences among various methods. This helps in the validation of estimated conformational landscape and provides tools to streamline the heterogeneity workflow.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 10","pages":"2118-2126"},"PeriodicalIF":32.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41592-025-02841-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145150150","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}

引用次数: 0

And the award goes to … 该奖项将颁发给....

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-24 DOI: 10.1038/s41592-025-02842-9

Vivien Marx

引用次数: 0

Cryogenic STEM of thick biological specimens 厚生物标本的低温STEM。

IF 32.1 1区生物学

Nature Methods Pub Date : 2025-09-23 DOI: 10.1038/s41592-025-02818-9

Carsten Sachse

引用次数: 0