Pub Date : 2025-09-16DOI: 10.1038/s41576-025-00894-3
For the 25th anniversary of Nature Reviews Genetics, we reflect on exciting progress towards decoding the regulatory genome and its mechanisms, a central goal in genetics that must be solved with interdisciplinary research to yield widespread insights into evolution, development and disease.
{"title":"Making sense of the regulatory genome","authors":"","doi":"10.1038/s41576-025-00894-3","DOIUrl":"10.1038/s41576-025-00894-3","url":null,"abstract":"For the 25th anniversary of Nature Reviews Genetics, we reflect on exciting progress towards decoding the regulatory genome and its mechanisms, a central goal in genetics that must be solved with interdisciplinary research to yield widespread insights into evolution, development and disease.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 10","pages":"651-652"},"PeriodicalIF":52.0,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41576-025-00894-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145067698","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}
Pub Date : 2025-09-15DOI: 10.1038/s41576-025-00888-1
Gitta Szabó, Emiley A. Eloe-Fadrosh, Jennifer Pett-Ridge, Tanja Woyke
Microorganisms are essential to all life on Earth through critical roles in key biological processes and diverse interactions with other organisms that shape ecosystems, drive biogeochemical cycles and influence both human health and environmental health. High-throughput sequencing from environmental samples has revolutionized the understanding of microbial diversity and functions. With vast amounts of genomes now available across Earth’s biomes, these data provide a blueprint of microbial life that can be harnessed for a more holistic understanding of microbiome structure and function across the various ecosystems on Earth. Here we review the application of genome-centric approaches, including recent advances in single-cell sequencing and functional profiling, to survey microbial and viral diversity. We highlight some of the most impactful evolutionary and functional discoveries, explore the spatial diversity and temporal dynamics of microorganisms across diverse environments, and discuss genome-enabled insights into host-associated microorganisms. Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucidate the evolution, biogeography and ecological dynamics of Earth’s microbiomes.
{"title":"A genomic view of Earth’s biomes","authors":"Gitta Szabó, Emiley A. Eloe-Fadrosh, Jennifer Pett-Ridge, Tanja Woyke","doi":"10.1038/s41576-025-00888-1","DOIUrl":"10.1038/s41576-025-00888-1","url":null,"abstract":"Microorganisms are essential to all life on Earth through critical roles in key biological processes and diverse interactions with other organisms that shape ecosystems, drive biogeochemical cycles and influence both human health and environmental health. High-throughput sequencing from environmental samples has revolutionized the understanding of microbial diversity and functions. With vast amounts of genomes now available across Earth’s biomes, these data provide a blueprint of microbial life that can be harnessed for a more holistic understanding of microbiome structure and function across the various ecosystems on Earth. Here we review the application of genome-centric approaches, including recent advances in single-cell sequencing and functional profiling, to survey microbial and viral diversity. We highlight some of the most impactful evolutionary and functional discoveries, explore the spatial diversity and temporal dynamics of microorganisms across diverse environments, and discuss genome-enabled insights into host-associated microorganisms. Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucidate the evolution, biogeography and ecological dynamics of Earth’s microbiomes.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"27 1","pages":"13-31"},"PeriodicalIF":52.0,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145059287","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}
Pub Date : 2025-09-11DOI: 10.1038/s41576-025-00897-0
Paul Meller, Peter Kilroy, Helen Sims, Helena R. R. Wells, Michael Dunn
The importance of ethics and inclusivity in genomics is widely recognized. Less explored is the huge potential for transdisciplinary collaboration at the intersection of genomics, the humanities and social sciences, and wider societal stakeholders to drive research innovation and discovery. Transdisciplinary collaboration fuels innovation and discovery. Meller et al. call for broader collaboration at the intersection of genomics, the humanities and social sciences, and wider societal stakeholders, to test new ways of working across disciplines and co-develop future research agendas.
{"title":"Collaborating at the nexus of genomics, humanities, social science and stakeholders","authors":"Paul Meller, Peter Kilroy, Helen Sims, Helena R. R. Wells, Michael Dunn","doi":"10.1038/s41576-025-00897-0","DOIUrl":"10.1038/s41576-025-00897-0","url":null,"abstract":"The importance of ethics and inclusivity in genomics is widely recognized. Less explored is the huge potential for transdisciplinary collaboration at the intersection of genomics, the humanities and social sciences, and wider societal stakeholders to drive research innovation and discovery. Transdisciplinary collaboration fuels innovation and discovery. Meller et al. call for broader collaboration at the intersection of genomics, the humanities and social sciences, and wider societal stakeholders, to test new ways of working across disciplines and co-develop future research agendas.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 11","pages":"737-738"},"PeriodicalIF":52.0,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145031924","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}
Pub Date : 2025-09-05DOI: 10.1038/s41576-025-00893-4
Jian Zeng, Peter M. Visscher
Polygenic scores (PGS) have shown promise in predicting complex traits and disease risk, but their accuracy remains limited and poorly transferable across ancestries. Integrating functional annotations with whole-genome sequencing data can improve prediction by prioritizing likely causal variants shared across populations and by assigning greater weight to variants in biologically relevant regions. The accuracy of polygenic scores (PGS) remains limited and poorly transferable across ancestries. In this Comment, Zeng and Visscher discuss how integrating functional annotations with whole-genome sequencing data can improve PGS by prioritizing likely causal variants shared across populations and by assigning greater weight to variants in biologically relevant regions.
{"title":"Harnessing functional annotation to improve the accuracy and transferability of polygenic scores","authors":"Jian Zeng, Peter M. Visscher","doi":"10.1038/s41576-025-00893-4","DOIUrl":"10.1038/s41576-025-00893-4","url":null,"abstract":"Polygenic scores (PGS) have shown promise in predicting complex traits and disease risk, but their accuracy remains limited and poorly transferable across ancestries. Integrating functional annotations with whole-genome sequencing data can improve prediction by prioritizing likely causal variants shared across populations and by assigning greater weight to variants in biologically relevant regions. The accuracy of polygenic scores (PGS) remains limited and poorly transferable across ancestries. In this Comment, Zeng and Visscher discuss how integrating functional annotations with whole-genome sequencing data can improve PGS by prioritizing likely causal variants shared across populations and by assigning greater weight to variants in biologically relevant regions.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 12","pages":"805-806"},"PeriodicalIF":52.0,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144995189","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}
Pub Date : 2025-08-21DOI: 10.1038/s41576-025-00891-6
Kellie Wise, Anna Pascual-Reguant
In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or protein expression in fixed cells or nuclei.
{"title":"Imaging-based multimodal profiling of single cells with STAMP","authors":"Kellie Wise, Anna Pascual-Reguant","doi":"10.1038/s41576-025-00891-6","DOIUrl":"10.1038/s41576-025-00891-6","url":null,"abstract":"In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or protein expression in fixed cells or nuclei.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 12","pages":"809-809"},"PeriodicalIF":52.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144898381","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}
Pub Date : 2025-08-20DOI: 10.1038/s41576-025-00890-7
Daudi Jjingo
Daudi Jjingo highlights a recent publication by Chu et al., who performed an integrative single-cell analysis of human colorectal cancer to characterize the tumour microenvironment (TME) and stratify patients according to their heterogeneous TMEs, which exploit different immune evasion mechanisms.
{"title":"Prospects for personalized cancer treatment in the era of single-cell sequencing","authors":"Daudi Jjingo","doi":"10.1038/s41576-025-00890-7","DOIUrl":"10.1038/s41576-025-00890-7","url":null,"abstract":"Daudi Jjingo highlights a recent publication by Chu et al., who performed an integrative single-cell analysis of human colorectal cancer to characterize the tumour microenvironment (TME) and stratify patients according to their heterogeneous TMEs, which exploit different immune evasion mechanisms.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 11","pages":"741-741"},"PeriodicalIF":52.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144898189","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}
Pub Date : 2025-08-15DOI: 10.1038/s41576-025-00884-5
Elaine R. Mardis, Richard K. Wilson
Accelerated discovery in biomedical science is typically punctuated by technological advances, and the past decade has been exemplary regarding breakthroughs in our genomic understanding of human biology in health and disease. This phenomenon was facilitated by the availability of a human genome reference sequence and the development and continuous improvement of next-generation and single-molecule sequencing technologies, accompanied by advances in computational analytics. These fundamental tools have driven the emergence of innovative methods that capture different aspects of human cell biology, with exquisite detail genome wide, in a sequence-based readout. The resulting expansion of knowledge has poised these approaches for clinical adoption, fulfilling the original intention of decoding the human genome and ushering in the era of genomic medicine. Extraordinary advances in genomic science have defined the twenty-first century, transforming our understanding of human biology in both health and disease. This timeline Perspective charts two decades of genomic innovation since the human genome reference sequence became available, highlighting the evolution of sequencing technologies and how they, combined with computational advances, paved the way for genomic medicine.
{"title":"Tracing the evolution of sequencing into the era of genomic medicine","authors":"Elaine R. Mardis, Richard K. Wilson","doi":"10.1038/s41576-025-00884-5","DOIUrl":"10.1038/s41576-025-00884-5","url":null,"abstract":"Accelerated discovery in biomedical science is typically punctuated by technological advances, and the past decade has been exemplary regarding breakthroughs in our genomic understanding of human biology in health and disease. This phenomenon was facilitated by the availability of a human genome reference sequence and the development and continuous improvement of next-generation and single-molecule sequencing technologies, accompanied by advances in computational analytics. These fundamental tools have driven the emergence of innovative methods that capture different aspects of human cell biology, with exquisite detail genome wide, in a sequence-based readout. The resulting expansion of knowledge has poised these approaches for clinical adoption, fulfilling the original intention of decoding the human genome and ushering in the era of genomic medicine. Extraordinary advances in genomic science have defined the twenty-first century, transforming our understanding of human biology in both health and disease. This timeline Perspective charts two decades of genomic innovation since the human genome reference sequence became available, highlighting the evolution of sequencing technologies and how they, combined with computational advances, paved the way for genomic medicine.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 10","pages":"719-734"},"PeriodicalIF":52.0,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144851398","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}
Pub Date : 2025-08-11DOI: 10.1038/s41576-025-00889-0
Ali R. Awan, Mehrdad Oveisi, Mohammad M. Karimi
Prompt-based bioinformatics redefines how scientists interact with biological data, enabling natural language queries across multi-omics layers. By removing coding barriers and streamlining integration, this paradigm facilitates accessible, hypothesis-driven discovery. We call for community standards, educational adoption and collaborative development to realize its full potential in research and clinical settings. Prompt-based methods, which involve the careful design of inputs to guide large language model (LLM) outputs, are beginning to reshape bioinformatic analytical workflows. The authors compare prompt-driven approaches to conventional bioinformatics pipelines, outline their potential for multi-omics analysis and explore how these models may shape the future of computational biology.
{"title":"Prompt-based bioinformatics: a new interface for multi-omics analysis","authors":"Ali R. Awan, Mehrdad Oveisi, Mohammad M. Karimi","doi":"10.1038/s41576-025-00889-0","DOIUrl":"10.1038/s41576-025-00889-0","url":null,"abstract":"Prompt-based bioinformatics redefines how scientists interact with biological data, enabling natural language queries across multi-omics layers. By removing coding barriers and streamlining integration, this paradigm facilitates accessible, hypothesis-driven discovery. We call for community standards, educational adoption and collaborative development to realize its full potential in research and clinical settings. Prompt-based methods, which involve the careful design of inputs to guide large language model (LLM) outputs, are beginning to reshape bioinformatic analytical workflows. The authors compare prompt-driven approaches to conventional bioinformatics pipelines, outline their potential for multi-omics analysis and explore how these models may shape the future of computational biology.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 12","pages":"807-808"},"PeriodicalIF":52.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812930","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}
Pub Date : 2025-07-31DOI: 10.1038/s41576-025-00886-3
Chikara Furusawa
In this Journal Club, Chikara Furusawa reflects on a 1991 publication by Tom Ray that presented Tierra, an evolvable computer program that pioneered the use of artificial life to study biological phenomena.
在本杂志俱乐部，Chikara Furusawa回顾了Tom Ray 1991年发表的一篇文章，该文章介绍了Tierra，这是一个可进化的计算机程序，开创了使用人工生命来研究生物现象的先河。
{"title":"Rethinking life through digital evolution","authors":"Chikara Furusawa","doi":"10.1038/s41576-025-00886-3","DOIUrl":"10.1038/s41576-025-00886-3","url":null,"abstract":"In this Journal Club, Chikara Furusawa reflects on a 1991 publication by Tom Ray that presented Tierra, an evolvable computer program that pioneered the use of artificial life to study biological phenomena.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 11","pages":"740-740"},"PeriodicalIF":52.0,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756631","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}
Pub Date : 2025-07-31DOI: 10.1038/s41576-025-00883-6
Hamad Ali, Barrak Alahmad, Faisal H. Al-Refaei, Ahmad Abou Tayoun, Hilal A. Lashuel, Salman Al Sabah, Fahd Al-Mulla
Extreme environmental conditions create stressors that can interact with genetic predispositions to influence health outcomes. With some of the highest global rates of chronic complex diseases and a high prevalence of consanguinity, Kuwait offers an unprecedented opportunity to study gene–environment interactions at scale. Extreme environmental conditions create stressors that can interact with genetic risk factors to influence health outcomes. In this Comment, the authors discuss their vision for a national programme in Kuwait that combines the genome and exposome to uncover gene–environment interactions and inform tailored disease-prevention strategies.
{"title":"Integrating the genome and exposome for precision health in Kuwait","authors":"Hamad Ali, Barrak Alahmad, Faisal H. Al-Refaei, Ahmad Abou Tayoun, Hilal A. Lashuel, Salman Al Sabah, Fahd Al-Mulla","doi":"10.1038/s41576-025-00883-6","DOIUrl":"10.1038/s41576-025-00883-6","url":null,"abstract":"Extreme environmental conditions create stressors that can interact with genetic predispositions to influence health outcomes. With some of the highest global rates of chronic complex diseases and a high prevalence of consanguinity, Kuwait offers an unprecedented opportunity to study gene–environment interactions at scale. Extreme environmental conditions create stressors that can interact with genetic risk factors to influence health outcomes. In this Comment, the authors discuss their vision for a national programme in Kuwait that combines the genome and exposome to uncover gene–environment interactions and inform tailored disease-prevention strategies.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 11","pages":"735-736"},"PeriodicalIF":52.0,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756180","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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