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Nature Genetics
Scopus
ISSN 1061-4036 · Nature Portfolio · 161 articles in the index
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Journal Article
High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer
A comprehensive understanding of cellular behavior and response to the tumor microenvironment (TME) in colorectal cancer (CRC) remains elusive. Here, we introduce the high-definition Visium spatial transcriptomic technology (Visium HD) and investigate formalin-fixed paraffin-embedded human CRC…
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BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis
Spatial omics data are clustered to define both cell types and tissue domains. We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these two spatial clustering problems by embedding cells in a product space of their own and the local…
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A compendium of genetic regulatory effects across pig tissues
Abstract The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and…
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Genome-wide prediction of disease variant effects with a deep protein language model
Predicting the effects of coding variants is a major challenge. While recent deep-learning models have improved variant effect prediction accuracy, they cannot analyze all coding variants due to dependency on close homologs or software limitations. Here we developed a workflow using ESM1b, a…
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A complete telomere-to-telomere assembly of the maize genome
A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a complete genome assembly of maize with each chromosome entirely traversed in a…
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The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions
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Systematic differences in discovery of genetic effects on gene expression and complex traits
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Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments
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Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes…
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Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases
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Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains
Attention-deficit hyperactivity disorder (ADHD) is a prevalent neurodevelopmental disorder with a major genetic component. Here, we present a genome-wide association study meta-analysis of ADHD comprising 38,691 individuals with ADHD and 186,843 controls. We identified 27 genome-wide significant…
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Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases
Identification of therapeutic targets from genome-wide association studies (GWAS) requires insights into downstream functional consequences. We harmonized 8,613 RNA-sequencing samples from 14 brain datasets to create the MetaBrain resource and performed cis- and trans-expression quantitative trait…
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Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank
Phasing involves distinguishing the two parentally inherited copies of each chromosome into haplotypes. Here, we introduce SHAPEIT5, a new phasing method that quickly and accurately processes large sequencing datasets and applied it to UK Biobank (UKB) whole-genome and whole-exome sequencing data…
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Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries
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A graph-based genome and pan-genome variation of the model plant Setaria
Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide…
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Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes
Abstract To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance ( P < 2.5 × 10 −6 )…
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Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles
Migraine affects over a billion individuals worldwide but its genetic underpinning remains largely unknown. Here, we performed a genome-wide association study of 102,084 migraine cases and 771,257 controls and identified 123 loci, of which 86 are previously unknown. These loci provide an…
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Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer
The consensus molecular subtype (CMS) classification of colorectal cancer is based on bulk transcriptomics. The underlying epithelial cell diversity remains unclear. We analyzed 373,058 single-cell transcriptomes from 63 patients, focusing on 49,155 epithelial cells. We identified a pervasive…
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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
Typical genotyping workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Furthermore, short-read lengths limit the ability to characterize repetitive genomic regions…