Nature Reviews Genetics最新文献_第6页

SLAM-RT&Tag: spatiotemporal profiling of RNA within nuclear compartments in situ SLAM-RT&Tag：原位核室内RNA的时空分析

IF 52 1区生物学

Nature Reviews Genetics Pub Date : 2025-05-19 DOI: 10.1038/s41576-025-00856-9

Nadiya Khyzha

引用次数: 0

Methodological opportunities in genomic data analysis to advance health equity 基因组数据分析中促进卫生公平的方法学机会

IF 52 1区生物学

Nature Reviews Genetics Pub Date : 2025-05-15 DOI: 10.1038/s41576-025-00839-w

Brieuc Lehmann, Leandra Bräuninger, Yoonsu Cho, Fabian Falck, Smera Jayadeva, Michael Katell, Thuy Nguyen, Antonella Perini, Sam Tallman, Maxine Mackintosh, Matt Silver, Karoline Kuchenbäcker, David Leslie, Nilanjan Chatterjee, Chris Holmes

{"title":"Methodological opportunities in genomic data analysis to advance health equity","authors":"Brieuc Lehmann, Leandra Bräuninger, Yoonsu Cho, Fabian Falck, Smera Jayadeva, Michael Katell, Thuy Nguyen, Antonella Perini, Sam Tallman, Maxine Mackintosh, Matt Silver, Karoline Kuchenbäcker, David Leslie, Nilanjan Chatterjee, Chris Holmes","doi":"10.1038/s41576-025-00839-w","DOIUrl":"10.1038/s41576-025-00839-w","url":null,"abstract":"The causes and consequences of inequities in genomic research and medicine are complex and widespread. However, it is widely acknowledged that underrepresentation of diverse populations in human genetics research risks exacerbating existing health disparities. Efforts to improve diversity are ongoing, but an often-overlooked source of inequity is the choice of analytical methods used to process, analyse and interpret genomic data. This choice can influence all areas of genomic research, from genome-wide association studies and polygenic score development to variant prioritization and functional genomics. New statistical and machine learning techniques to understand, quantify and correct for the impact of biases in genomic data are emerging within the wider genomic research and genomic medicine ecosystems. At this crucial time point, it is important to clarify where improvements in methods and practices can, or cannot, have a role in improving equity in genomics. Here, we review existing approaches to promote equity and fairness in statistical analysis for genomics, and propose future methodological developments that are likely to yield the most impact for equity. New statistical and machine learning techniques to understand, quantify and correct for the impact of biases in genomic data are emerging. The authors review how the choice of analytical methods used to process, analyse and interpret genomic data can influence genomic research, as well as existing methodological approaches to promote equity and fairness in genomics.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 9","pages":"635-649"},"PeriodicalIF":52.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143979479","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

Cell-type deconvolution methods for spatial transcriptomics 空间转录组学的细胞型反褶积方法

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2025-05-14 DOI: 10.1038/s41576-025-00845-y

Lucie C. Gaspard-Boulinc, Luca Gortana, Thomas Walter, Emmanuel Barillot, Florence M. G. Cavalli

引用次数: 0

Predicting gene expression from DNA sequence using deep learning models 利用深度学习模型从DNA序列预测基因表达

IF 52 1区生物学

Nature Reviews Genetics Pub Date : 2025-05-13 DOI: 10.1038/s41576-025-00841-2

Lucía Barbadilla-Martínez, Noud Klaassen, Bas van Steensel, Jeroen de Ridder

{"title":"Predicting gene expression from DNA sequence using deep learning models","authors":"Lucía Barbadilla-Martínez, Noud Klaassen, Bas van Steensel, Jeroen de Ridder","doi":"10.1038/s41576-025-00841-2","DOIUrl":"10.1038/s41576-025-00841-2","url":null,"abstract":"Transcription of genes is regulated by DNA elements such as promoters and enhancers, the activity of which are in turn controlled by many transcription factors. Owing to the highly complex combinatorial logic involved, it has been difficult to construct computational models that predict gene activity from DNA sequence. Recent advances in deep learning techniques applied to data from epigenome mapping and high-throughput reporter assays have made substantial progress towards addressing this complexity. Such models can capture the regulatory grammar with remarkable accuracy and show great promise in predicting the effects of non-coding variants, uncovering detailed molecular mechanisms of gene regulation and designing synthetic regulatory elements for biotechnology. Here, we discuss the principles of these approaches, the types of training data sets that are available and the strengths and limitations of different approaches. Barbadilla-Martínez et al. review recent progress in deep-learning-based sequence-to-expression models, which predict gene expression levels solely from DNA sequence. These models are providing new insights into the complex combinatorial logic underlying cis-regulatory control of gene expression.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 10","pages":"666-680"},"PeriodicalIF":52.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143939954","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

Genomics of schizophrenia, bipolar disorder and major depressive disorder 精神分裂症、双相情感障碍和重度抑郁症的基因组学研究

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2025-05-12 DOI: 10.1038/s41576-025-00843-0

Michael J. Owen, Nicholas J. Bray, James T. R. Walters, Michael C. O’Donovan

引用次数: 0

X-linked competition — implications for human development and disease x连锁竞争——对人类发展和疾病的影响

IF 52 1区生物学

Nature Reviews Genetics Pub Date : 2025-05-12 DOI: 10.1038/s41576-025-00840-3

Philip M. Boone, Teresa Buenaventura, James W. D. King, Matthias Merkenschlager

{"title":"X-linked competition — implications for human development and disease","authors":"Philip M. Boone, Teresa Buenaventura, James W. D. King, Matthias Merkenschlager","doi":"10.1038/s41576-025-00840-3","DOIUrl":"10.1038/s41576-025-00840-3","url":null,"abstract":"During early mammalian female development, X chromosome inactivation leads to random transcriptional silencing of one of the two X chromosomes. This inactivation is maintained through subsequent cell divisions, leading to intra-individual diversity, whereby cells express either the maternal or paternal X chromosome. Differences in X chromosome sequence content can trigger competitive interactions between clones that may alter organismal development and skew the representation of X-linked sequence variants in a cell-type-specific manner — a recently described phenomenon termed X-linked competition in analogy to existing cell competition paradigms. Skewed representation can define the phenotypic impact of X-linked variants, for example, the manifestation of disease in female carriers of X-linked disease alleles. Here, we review what is currently known about X-linked competition, reflect on what remains to be learnt and map out the implications for X-linked human disease. Differences in X chromosome sequence content can trigger competitive interactions between clones that may alter organismal development and skew the representation of X-linked sequence variants in a cell-type-specific manner. The authors review this recently described phenomenon of X-linked competition and map out the implications for X-linked human diseases.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 8","pages":"571-580"},"PeriodicalIF":52.0,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143933472","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

Simultaneous single-cell sequencing of RNA and DNA at scale with DEFND-seq 同时单细胞测序的RNA和DNA的规模与DEFND-seq

IF 52 1区生物学

Nature Reviews Genetics Pub Date : 2025-05-12 DOI: 10.1038/s41576-025-00853-y

Timothy R. Olsen

引用次数: 0

One but not the same — the many genomes of the brain 一个但又不一样——大脑的许多基因组

IF 52 1区生物学

Nature Reviews Genetics Pub Date : 2025-05-09 DOI: 10.1038/s41576-025-00852-z

Tracy A. Bedrosian

引用次数: 0

An uneasy truce between population health and the gene pools within our bodies 人口健康和我们体内的基因库之间不稳定的休战