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MultiSTAAR delivers multi-trait rare variant analysis of biobank-scale sequencing data
IF 12
Nature computational science Pub Date : 2025-02-07 DOI: 10.1038/s43588-025-00766-0
{"title":"MultiSTAAR delivers multi-trait rare variant analysis of biobank-scale sequencing data","authors":"","doi":"10.1038/s43588-025-00766-0","DOIUrl":"10.1038/s43588-025-00766-0","url":null,"abstract":"Identifying pleiotropic associations for rare variants in multi-ethnic biobank-scale whole-genome sequencing data poses considerable challenges. This study introduced MultiSTAAR as a scalable and robust multi-trait rare variant analysis framework designed for both coding and noncoding regions by integrating multiple variant functional annotations and leveraging multivariate modeling across diverse phenotypes.","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":"5 2","pages":"101-102"},"PeriodicalIF":12.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143371350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Balancing autonomy and expertise in autonomous synthesis laboratories
IF 12
Nature computational science Pub Date : 2025-02-05 DOI: 10.1038/s43588-025-00769-x
Xiaozhao Liu, Bin Ouyang, Yan Zeng
{"title":"Balancing autonomy and expertise in autonomous synthesis laboratories","authors":"Xiaozhao Liu, Bin Ouyang, Yan Zeng","doi":"10.1038/s43588-025-00769-x","DOIUrl":"10.1038/s43588-025-00769-x","url":null,"abstract":"Autonomous synthesis laboratories promise to streamline the plan–make–measure–analyze iteration loop. Here, we comment on the barriers in the field, the promise of a human on-the-loop approach, and strategies for optimizing accessibility, accuracy, and efficiency of autonomous laboratories.","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":"5 2","pages":"92-94"},"PeriodicalIF":12.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143257622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Shedding light on spatial signal transduction in cells using computational simulations
IF 12
Nature computational science Pub Date : 2025-02-04 DOI: 10.1038/s43588-025-00772-2
{"title":"Shedding light on spatial signal transduction in cells using computational simulations","authors":"","doi":"10.1038/s43588-025-00772-2","DOIUrl":"10.1038/s43588-025-00772-2","url":null,"abstract":"We present Spatial Modeling Algorithms for Reactions and Transport (SMART), a software package that simulates spatiotemporally detailed biochemical reaction networks within realistic cellular and subcellular geometries. This paper highlights the use of SMART in several biological test cases including cellular mechanotransduction, calcium signaling in neurons and cardiomyocytes, and adenosine triphosphate synthesis.","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":"5 2","pages":"99-100"},"PeriodicalIF":12.0,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143191505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Author Correction: Spatial modeling algorithms for reactions and transport in biological cells
IF 12
Nature computational science Pub Date : 2025-02-03 DOI: 10.1038/s43588-025-00773-1
Emmet A. Francis, Justin G. Laughlin, Jørgen S. Dokken, Henrik N. T. Finsberg, Christopher T. Lee, Marie E. Rognes, Padmini Rangamani
{"title":"Author Correction: Spatial modeling algorithms for reactions and transport in biological cells","authors":"Emmet A. Francis, Justin G. Laughlin, Jørgen S. Dokken, Henrik N. T. Finsberg, Christopher T. Lee, Marie E. Rognes, Padmini Rangamani","doi":"10.1038/s43588-025-00773-1","DOIUrl":"10.1038/s43588-025-00773-1","url":null,"abstract":"","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":"5 2","pages":"185-185"},"PeriodicalIF":12.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43588-025-00773-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143124138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biologically inspired graphs to explore massive genetic datasets
IF 12
Nature computational science Pub Date : 2025-01-31 DOI: 10.1038/s43588-024-00763-9
Ryan M. Layer
{"title":"Biologically inspired graphs to explore massive genetic datasets","authors":"Ryan M. Layer","doi":"10.1038/s43588-024-00763-9","DOIUrl":"10.1038/s43588-024-00763-9","url":null,"abstract":"A recent study proposes a data structure that addresses crucial challenges related to storage and computation of large genome databases.","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":"5 2","pages":"97-98"},"PeriodicalIF":12.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Multimodal learning for mapping genotype-phenotype dynamics.
IF 12
Nature computational science Pub Date : 2025-01-28 DOI: 10.1038/s43588-024-00765-7
Farhan Khodaee, Rohola Zandie, Elazer R Edelman
{"title":"Multimodal learning for mapping genotype-phenotype dynamics.","authors":"Farhan Khodaee, Rohola Zandie, Elazer R Edelman","doi":"10.1038/s43588-024-00765-7","DOIUrl":"10.1038/s43588-024-00765-7","url":null,"abstract":"<p><p>How complex phenotypes emerge from intricate gene expression patterns is a fundamental question in biology. Integrating high-content genotyping approaches such as single-cell RNA sequencing and advanced learning methods such as language models offers an opportunity for dissecting this complex relationship. Here we present a computational integrated genetics framework designed to analyze and interpret the high-dimensional landscape of genotypes and their associated phenotypes simultaneously. We applied this approach to develop a multimodal foundation model to explore the genotype-phenotype relationship manifold for human transcriptomics at the cellular level. Analyzing this joint manifold showed a refined resolution of cellular heterogeneity, uncovered potential cross-tissue biomarkers and provided contextualized embeddings to investigate the polyfunctionality of genes shown for the von Willebrand factor (VWF) gene in endothelial cells. Overall, this study advances our understanding of the dynamic interplay between gene expression and phenotypic manifestation and demonstrates the potential of integrated genetics in uncovering new dimensions of cellular function and complexity.</p>","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Author Correction: Approaching coupled-cluster accuracy for molecular electronic structures with multi-task learning
IF 12
Nature computational science Pub Date : 2025-01-22 DOI: 10.1038/s43588-025-00767-z
Hao Tang, Brian Xiao, Wenhao He, Pero Subasic, Avetik R. Harutyunyan, Yao Wang, Fang Liu, Haowei Xu, Ju Li
{"title":"Author Correction: Approaching coupled-cluster accuracy for molecular electronic structures with multi-task learning","authors":"Hao Tang,&nbsp;Brian Xiao,&nbsp;Wenhao He,&nbsp;Pero Subasic,&nbsp;Avetik R. Harutyunyan,&nbsp;Yao Wang,&nbsp;Fang Liu,&nbsp;Haowei Xu,&nbsp;Ju Li","doi":"10.1038/s43588-025-00767-z","DOIUrl":"10.1038/s43588-025-00767-z","url":null,"abstract":"","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":"5 2","pages":"184-184"},"PeriodicalIF":12.0,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43588-025-00767-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Boosting AI with neuromorphic computing 用神经形态计算增强人工智能。
IF 12
Nature computational science Pub Date : 2025-01-21 DOI: 10.1038/s43588-025-00770-4
{"title":"Boosting AI with neuromorphic computing","authors":"","doi":"10.1038/s43588-025-00770-4","DOIUrl":"10.1038/s43588-025-00770-4","url":null,"abstract":"We highlight the important role of neuromorphic computing in enhancing the power efficiency and performance of AI.","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":"5 1","pages":"1-2"},"PeriodicalIF":12.0,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43588-025-00770-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Memristors enabling probabilistic AI at the edge 在边缘启用概率AI的忆阻器。
IF 12
Nature computational science Pub Date : 2025-01-17 DOI: 10.1038/s43588-024-00761-x
Damien Querlioz
{"title":"Memristors enabling probabilistic AI at the edge","authors":"Damien Querlioz","doi":"10.1038/s43588-024-00761-x","DOIUrl":"10.1038/s43588-024-00761-x","url":null,"abstract":"By combining several probabilistic AI algorithms, a recent study demonstrates experimentally that the inherent noise and variation in memristor nanodevices can be exploited as features for energy-efficient on-chip learning.","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":"5 1","pages":"7-8"},"PeriodicalIF":12.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Efficient large language model with analog in-memory computing 高效的大型语言模型与模拟内存计算。
IF 12
Nature computational science Pub Date : 2025-01-17 DOI: 10.1038/s43588-024-00760-y
Anand Subramoney
{"title":"Efficient large language model with analog in-memory computing","authors":"Anand Subramoney","doi":"10.1038/s43588-024-00760-y","DOIUrl":"10.1038/s43588-024-00760-y","url":null,"abstract":"A recent study demonstrates through numerical simulations that implementing large language models based on sparse mixture-of-experts architectures on 3D in-memory computing technologies can substantially reduce energy consumption.","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":"5 1","pages":"5-6"},"PeriodicalIF":12.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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