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Article
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Whole-cortex in situ sequencing reveals input-dependent area identity
BARseq interrogates the expression of 104 cell-type marker genes in 10.3 million cells over nine mouse forebrain hemispheres to reveal the role of peripheral inputs on cortical area development.
- Xiaoyin Chen
- , Stephan Fischer
- & Anthony M. Zador
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Technology Feature |
One year, three researchers, millions of cells: how a small team created the largest mouse-embryo atlas so far
A map of mouse development from conception to birth tracks 12.4 million cells at single-cell resolution as they mature into organs and other tissues.
- Sara Reardon
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Nature Video |
Building a heart atlas: researchers map organ in stunning detail
Cutting edge imaging techniques reveal how cells organise as the heart develops.
- Dan Fox
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Technology Feature |
Super-speedy sequencing puts genomic diagnosis in the fast lane
Streamlined workflows for DNA and RNA sequencing are helping clinicians to deliver prompt, targeted care to people in days — or even hours.
- Michael Eisenstein
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Article
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Genomic data in the All of Us Research Program
A study describes the release of clinical-grade whole-genome sequence data for 245,388 diverse participants by the All of Us Research Program and characterizes the properties of the dataset.
- Alexander G. Bick
- , Ginger A. Metcalf
- & Joshua C. Denny
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Article |
The Born in Guangzhou Cohort Study enables generational genetic discoveries
Analysis of data from the Born in Guangzhou Cohort Study comprising mainly of trios and mother–infant pairs reveals novel East Asian-specific genetic associations with maternal bile acid, gestational weight gain and infant cord blood traits.
- Shujia Huang
- , Siyang Liu
- & Xiu Qiu
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Article
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Alternative splicing of latrophilin-3 controls synapse formation
Latrophilin-3 organizes synapses through a convergent dual-pathway mechanism in which Gαs signalling is activated and phase-separated postsynaptic protein scaffolds are recruited.
- Shuai Wang
- , Chelsea DeLeon
- & Thomas C. Südhof
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News |
Australian Indigenous genomes are highly diverse and unlike those anywhere else
In collecting genomic data for Indigenous Australians, scientists hope to expand knowledge of human genetic diversity and improve health for this group.
- Bianca Nogrady
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Article
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The landscape of genomic structural variation in Indigenous Australians
Population-scale whole-genome sequencing across four remote Indigenous Australian communities reveals a large fraction of structural variants that are unique to these populations, emphasizing the genetic distinctiveness of and diversity among Indigenous Australians.
- Andre L. M. Reis
- , Melissa Rapadas
- & Ira W. Deveson
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Article |
A genomic mutational constraint map using variation in 76,156 human genomes
A genomic constraint map for the human genome constructed using data from 76,156 human genomes from the Genome Aggregation Database shows that non-coding constrained regions are enriched for regulatory elements and variants associated with complex diseases and traits.
- Siwei Chen
- , Laurent C. Francioli
- & Konrad J. Karczewski
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Article |
Latent human herpesvirus 6 is reactivated in CAR T cells
Genomics analyses reveal that in vitro culture of CAR T cells can lead to reactivation of a latent herpesvirus, which might be involved in complications in patients receiving associated cell therapies.
- Caleb A. Lareau
- , Yajie Yin
- & Ansuman T. Satpathy
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Article
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Genotyping, sequencing and analysis of 140,000 adults from Mexico City
Genotype and exome sequencing of 150,000 participants and whole-genome sequencing of 9,950 selected individuals recruited into the Mexico City Prospective Study constitute a valuable, publicly available resource of non-European sequencing data.
- Andrey Ziyatdinov
- , Jason Torres
- & Roberto Tapia-Conyer
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Article
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Ultra-fast deep-learned CNS tumour classification during surgery
Sturgeon is a pretrained neural network that uses incremental results from nanopore sequencing to rapidly classify central nervous system tumours and can be used to aid critical decision-making during surgery.
- C. Vermeulen
- , M. Pagès-Gallego
- & J. de Ridder
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Article
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Spatial atlas of the mouse central nervous system at molecular resolution
In situ spatial transcriptomic analysis of more than 1 million cells are used to create a 200-nm-resolution spatial molecular atlas of the adult mouse central nervous system and identify previously unknown tissue architectures.
- Hailing Shi
- , Yichun He
- & Xiao Wang
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Article
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Transgenic ferret models define pulmonary ionocyte diversity and function
Conditional genetic ferret models enable ionocyte lineage tracing, ionocyte ablation and ionocyte-specific deletion of CFTR to elucidate the roles of pulmonary ionocyte biology and function during human health and disease.
- Feng Yuan
- , Grace N. Gasser
- & John F. Engelhardt
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Book Review |
Geneticist J. Craig Venter: ‘I consider retirement tantamount to death’
The human genome ‘maverick’ talks sequencing the ocean, setting up a health-screening company after checking his own genes — and why he has no plans to stop.
- Heidi Ledford
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Article
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Gut microbial carbohydrate metabolism contributes to insulin resistance
Faecal carbohydrates, particularly host-accessible monosaccharides, are increased in individuals with insulin resistance and are associated with microbial carbohydrate metabolisms and host inflammatory cytokines.
- Tadashi Takeuchi
- , Tetsuya Kubota
- & Hiroshi Ohno
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Article |
Assembly of 43 human Y chromosomes reveals extensive complexity and variation
De novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution reveal considerable diversity in the size and structure of the human Y chromosome.
- Pille Hallast
- , Peter Ebert
- & Charles Lee
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Article
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Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers
Linked-read whole-genome sequencing reveals patterns of structural DNA variants that are specific to homologous recombination deficiency and can be used to distinguish between BRCA1- and BRCA2-deficient phenotypes.
- Jeremy Setton
- , Kevin Hadi
- & Marcin Imieliński
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News |
This moss survived 165 million years — and now it's under threat from climate change
Ancient plant survived the formation of the Himalayas, but might now be facing extinction.
- Jude Coleman
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Article
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Spatially resolved multiomics of human cardiac niches
Single-cell and spatial transcriptomic analysis of eight human heart tissues reveals the cellular profiles and tissue architecture of niches including the cardiac conduction system, and a new tool, drug2cell, identifies drug target expression.
- Kazumasa Kanemaru
- , James Cranley
- & Sarah A. Teichmann
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News |
Ancient-DNA researcher fired for ‘serious misconduct’ lands new role
Former co-workers have expressed shock that Charles Sturt University in southeastern Australia has appointed Alan Cooper to its faculty.
- Dyani Lewis
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Article
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A pangenome reference of 36 Chinese populations
A study reports data from the first phase of the Chinese Pangenome Consortium including 116 de novo assemblies from 58 core samples representing 36 minority Chinese ethnic groups.
- Yang Gao
- , Xiaofei Yang
- & Shuhua Xu
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Nature Podcast |
‘Pangenome’ aims to capture the breadth of human diversity
Mapping a more diverse human genome, and the latest from the Nature Briefing.
- Nick Petrić Howe
- & Shamini Bundell
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Technology Feature |
Every base everywhere all at once: pangenomics comes of age
Multi-genome assemblies called pangenomes can capture genetic diversity in a species, but researchers are still working out how best to build and explore them.
- Michael Eisenstein
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Article |
Adeno-associated virus type 2 in US children with acute severe hepatitis
A retrospective analysis using PCR testing, viral enrichment-based sequencing and agnostic metagenomic sequencing finds an association between adeno-associated virus type 2 and paediatric hepatitis of unknown cause.
- Venice Servellita
- , Alicia Sotomayor Gonzalez
- & Charles Y. Chiu
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Obituary |
Paul Berg (1926–2023)
Biochemist who invented recombinant DNA technology.
- Errol Friedberg
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Article
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Spatial epigenome–transcriptome co-profiling of mammalian tissues
The authors present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications and gene expression on the same tissue section at near-single-cell resolution.
- Di Zhang
- , Yanxiang Deng
- & Rong Fan
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News |
Was famed poet Pablo Neruda poisoned? Scientists warn case not closed
Forensic investigation uncovers evidence that a lethal bacterium could have been in his body when he died.
- Michele Catanzaro
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News |
Dads older than mums since dawn of humanity, study suggests
Scientists used modern human DNA to estimate when new generations were born over 250,000 years — and the age of parents at conception.
- Freda Kreier
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Article |
Identification of astrocyte regulators by nucleic acid cytometry
The pathogenic function of XBP1-expressing astrocytes in experimental autoimmune encephalomyelitis and multiple sclerosis have been studied using FIND-seq, a new method combining microfluidics cytometry, PCR-based detection of nucleic acids and cell sorting for in-depth single-cell transcriptomics analyses of rare cells.
- Iain C. Clark
- , Michael A. Wheeler
- & Adam R. Abate
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Nature Video |
Record-breaking ancient DNA found in frozen soil
Two-million-year-old DNA from extinct mammals has been sequenced, revealing a lost world in Greenland .
- Shamini Bundell
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Matters Arising
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Reply to: When did mammoths go extinct?
- Yucheng Wang
- , Ana Prohaska
- & Eske Willerslev
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Article
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Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD
RNA sequencing reveals widespread transcriptomic changes across the cerebral cortex in autism spectrum disorder, including primary sensory regions, in addition to association regions, as well as an attenuation of regional identity.
- Michael J. Gandal
- , Jillian R. Haney
- & Daniel H. Geschwind
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Article
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Inferring and perturbing cell fate regulomes in human brain organoids
A multi-omic atlas of brain organoid development facilitates the inference of an underlying gene regulatory network using the newly developed Pando framework and shows—in conjunction with perturbation experiments—that GLI3 controls forebrain fate establishment through interaction with HES4/5 regulomes.
- Jonas Simon Fleck
- , Sophie Martina Johanna Jansen
- & Barbara Treutlein
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Article
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Spatial profiling of chromatin accessibility in mouse and human tissues
Spatial-ATAC-seq—spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing—delineated tissue-region-specific epigenetic landscapes in mouse embryos and identified gene regulators involved in the development of the central nervous system and the lymphoid tissue.
- Yanxiang Deng
- , Marek Bartosovic
- & Rong Fan
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Article |
Transcriptome variation in human tissues revealed by long-read sequencing
To understand the contribution of variants to transcript expression regulation, long-read transcriptome data are generated from the GTEx resource, and a new software package to perform allele-specific analysis is developed.
- Dafni A. Glinos
- , Garrett Garborcauskas
- & Beryl B. Cummings
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Article
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The sequences of 150,119 genomes in the UK Biobank
To measure selection on variants, whole-genome sequencing of approximately 150,000 individuals from the UK Biobank is used to rank sequence variants by their level of depletion.
- Bjarni V. Halldorsson
- , Hannes P. Eggertsson
- & Kari Stefansson
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Article |
Somatic mosaicism reveals clonal distributions of neocortical development
A comprehensive analysis of brain somatic mosaicism across the neocortex demonstrates the origins and distribution patterns of cells within the human brain.
- Martin W. Breuss
- , Xiaoxu Yang
- & Joseph G. Gleeson
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Article
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Local and systemic responses to SARS-CoV-2 infection in children and adults
Mechanisms explaining the milder clinical syndrome that is observed in children with SARS-CoV-2 infection.
- Masahiro Yoshida
- , Kaylee B. Worlock
- & Kerstin B. Meyer
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Article |
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues
A technique using barcoded beads for DNA sequencing within tissue sections enables spatial resolution of tumour clonal heterogeneity and can be multiplexed with other analytical techniques for analysis of complex cellular phenotypes.
- Tongtong Zhao
- , Zachary D. Chiang
- & Fei Chen
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News & Views |
A massive effort links protein-coding gene variants to health
The protein-coding portions of more than 450,000 individuals’ genomes have been sequenced, and analysed together with the individuals’ health data, revealing rare and common gene variants linked to various health-related traits.
- Yukinori Okada
- & Qingbo S. Wang
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Article
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Late Quaternary dynamics of Arctic biota from ancient environmental genomics
A large-scale metagenomic analysis of plant and mammal environmental DNA reveals complex ecological changes across the circumpolar region over the past 50,000 years, as biota responded to changing climates, culminating in the postglacial extinction of large mammals and emergence of modern ecosystems.
- Yucheng Wang
- , Mikkel Winther Pedersen
- & Eske Willerslev
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Article
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Exome sequencing and analysis of 454,787 UK Biobank participants
Whole-exome sequencing analysis of 454,787 individuals in the UK Biobank is used to examine the association of protein-coding variants with nearly 4,000 health-related traits, identifying 564 distinct genes with significant trait associations.
- Joshua D. Backman
- , Alexander H. Li
- & Manuel A. R. Ferreira
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Article |
Single-cell Ribo-seq reveals cell cycle-dependent translational pausing
Highly sensitive ribosome profiling of single cells at single-codon resolution enables identification of distinct cell cycle-dependent translational dynamic states in individual cells.
- Michael VanInsberghe
- , Jeroen van den Berg
- & Alexander van Oudenaarden
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News |
A complete human genome sequence is close: how scientists filled in the gaps
Researchers added 200 million DNA base pairs and 115 protein-coding genes — but they’ve yet to entirely sequence the Y chromosome.
- Sara Reardon
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News |
What scientists know about new, fast-spreading coronavirus variants
Key questions remain about how quickly B.1.617 variants can spread, their potential to evade immunity and how they might affect the course of the pandemic.
- David Adam
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Research Summary |
Mining the gaps of chromosome 8
The first gapless, telomere-to-telomere sequence of a human autosome, chromosome 8, is complete. Sequencing and assembly of the corresponding centromere in the chimpanzee, orangutan and macaque reveals details of its rapid evolution over the past 25 million years.
- Glennis A. Logsdon
- & Evan E. Eichler
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News |
India’s neighbours race to sequence genomes as COVID surges
From Sri Lanka to Nepal, scientists with limited resources are working feverishly to discover which variants are driving outbreaks.
- Smriti Mallapaty
Single-cell analysis reveals context-dependent, cell-level selection of mtDNA