Nature Genetics

Article	Citations
New insights into the genetic etiology of Alzheimer’s disease and related dementias	1044
Large-scale association analyses identify host factors influencing human gut microbiome composition	976
A cross-population atlas of genetic associations for 220 human phenotypes	925
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression	810
Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology	801
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis	765
A single-cell and spatially resolved atlas of human breast cancers	716
Computationally efficient whole-genome regression for quantitative and binary traits	630
A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease	559
Large-scale integration of the plasma proteome with genetics and disease	555
Genetics of 35 blood and urine biomarkers in the UK Biobank	448
The trans-ancestral genomic architecture of glycemic traits	427
Base-resolution models of transcription-factor binding reveal soft motif syntax	382
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation	360
Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation	350
Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing	348
Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease	341
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro	312
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes	310
Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction	307
Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic	292
Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology	285
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals	284
A generalized linear mixed model association tool for biobank-scale data	280
An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci	279

Improving polygenic prediction in ancestrally diverse populations	275
Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants	258
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation	255
Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation	245
Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank	242
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism	233
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture	225
Efficient phasing and imputation of low-coverage sequencing data using large reference panels	224
A compendium of uniformly processed human gene expression and splicing quantitative trait loci	222
Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases	222
Functionally informed fine-mapping and polygenic localization of complex trait heritability	220
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort	216
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project	212
Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors	207
Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains	204
Polygenic basis and biomedical consequences of telomere length variation	203
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication	203
Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis	200
Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis	199
Common genetic variants and modifiable risk factors underpin hypertrophic cardiomyopathy susceptibility and expressivity	191
Trans-ancestry analysis reveals genetic and nongenetic associations with COVID-19 susceptibility and severity	191
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment	185
A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes	182
Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects	182
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles	181
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation	176
Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2	176
Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits	175
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome	172
Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect	171
Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma	171
Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction	170
Global landscape of SARS-CoV-2 genomic surveillance and data sharing	170
Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data	169
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes	165
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer	163
The association between tumor mutational burden and prognosis is dependent on treatment context	163
Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes	162
An integrated framework for local genetic correlation analysis	161
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment	160
Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential	156
Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies	154
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1	153
The genomic landscape of pediatric acute lymphoblastic leukemia	151
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis	147
Genetic analyses identify widespread sex-differential participation bias	147
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer	141
Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores	141
Genome-wide association analyses of post-traumatic stress disorder and its symptom subdomains in the Million Veteran Program	140
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion	140

Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power	140
Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements	140
Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis	139
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses	137
Comprehensive characterization of protein–protein interactions perturbed by disease mutations	136
Genetic architecture of 11 major psychiatric disorders at biobehavioral, functional genomic and molecular genetic levels of analysis	134
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response	134
A map of transcriptional heterogeneity and regulatory variation in human microglia	134
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers	133
Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts	130
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders	130
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer	129
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis	128
Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states	126
Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies	125
Mammalian SWI/SNF continuously restores local accessibility to chromatin	125
A cross-platform approach identifies genetic regulators of human metabolism and health	124
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities	124
A quantitative genomics map of rice provides genetic insights and guides breeding	124
Breast tumor microenvironment structures are associated with genomic features and clinical outcome	123
Acute BAF perturbation causes immediate changes in chromatin accessibility	122
A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection	120
Genome-wide prediction of disease variant effects with a deep protein language model	119
Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin	117
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar	117
Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning	117
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens	116
Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars	116
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains	115
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development	114
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes	114
cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing	114
Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease	114
Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk	113
A sequence-based global map of regulatory activity for deciphering human genetics	113
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes	113
Cohesin and CTCF control the dynamics of chromosome folding	112
Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals	112
Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome	112
Sequence determinants of human gene regulatory elements	111
Alternative splicing during mammalian organ development	110
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus	110
Genomic and evolutionary classification of lung cancer in never smokers	109
An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability	109
Deep learning enables genetic analysis of the human thoracic aorta	105
Systematic reconstruction of cellular trajectories across mouse embryogenesis	104
The genomic basis of geographic differentiation and fiber improvement in cultivated cotton	102
A first-generation pediatric cancer dependency map	101
Insights into the genetic architecture of the human face	101
Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer	100
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer	100
A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation	100
WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation	99
Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms	99
Increased somatic mutation burdens in normal human cells due to defective DNA polymerases	98
Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments	98
Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos	97
Multiomics study of nonalcoholic fatty liver disease	97
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics	97
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease	97
Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale	95
GestaltMatcher facilitates rare disease matching using facial phenotype descriptors	95
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species	95
Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning	94
Genome-wide association analyses highlight etiological differences underlying newly defined subtypes of diabetes	94
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention	93
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	93
The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts	92
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics	92
Differences between germline genomes of monozygotic twins	92
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity	91
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement	91
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank	91
Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson’s disease	90
Exome sequencing in bipolar disorder identifies AKAP11 as a risk gene shared with schizophrenia	88
Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s disease	87
H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos	87
Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways	87
The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions	85
Systematic differences in discovery of genetic effects on gene expression and complex traits	85

Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility	84
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence	83
A complete telomere-to-telomere assembly of the maize genome	82
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response	82
Genomic insights into the origin, domestication and diversification of Brassica juncea	81
A multi-tissue atlas of regulatory variants in cattle	81
Sex differences in genetic architecture in the UK Biobank	81
Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19	81
Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals	81
Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers	79
Gene–environment correlations across geographic regions affect genome-wide association studies	79
Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce	78
Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases	78
The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste	78
Chromothripsis followed by circular recombination drives oncogene amplification in human cancer	77
Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function	77
DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits	77
A plasma membrane transporter coordinates phosphate reallocation and grain filling in cereals	76
Large uncertainty in individual polygenic risk score estimation impacts PRS-based risk stratification	76
Recent ultra-rare inherited variants implicate new autism candidate risk genes	76
Genome-wide association analyses identify new Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility	75
PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants	75
Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data	75
Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants	75
The NCI Genomic Data Commons	74
Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation	74
Molecular map of chronic lymphocytic leukemia and its impact on outcome	74
Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries	74
Genetics of the human microglia regulome refines Alzheimer’s disease risk loci	74
Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases	74
Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics	73
Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation	73
Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding	73
An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank	73
Genetic control of RNA splicing and its distinct role in complex trait variation	73
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location	73
Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection	72
Genome-edited crops for improved food security of smallholder farmers	72
Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries	72
Genetic drivers of m6A methylation in human brain, lung, heart and muscle	71
Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments	71
A PARTHENOGENESIS allele from apomictic dandelion can induce egg cell division without fertilization in lettuce	70
RNA m6A regulates transcription via DNA demethylation and chromatin accessibility	70
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche	70
Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness	70
The evolutionary dynamics of extrachromosomal DNA in human cancers	70
Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition	69
A resource of targeted mutant mouse lines for 5,061 genes	69
Prediction of histone post-translational modification patterns based on nascent transcription data	69
Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands	69
Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS	68
p53 convergently activates Dux/DUX4 in embryonic stem cells and in facioscapulohumeral muscular dystrophy cell models	68
Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation	68
Enhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion	67
Gain-of-function variants in SYK cause immune dysregulation and systemic inflammation in humans and mice	67
Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk	67
Discovery of 42 genome-wide significant loci associated with dyslexia	66
Renal plasticity revealed through reversal of polycystic kidney disease in mice	66
Shared heritability of human face and brain shape	66
Reference genome assemblies reveal the origin and evolution of allohexaploid oat	65
Genome-wide RNA polymerase stalling shapes the transcriptome during aging	65
Genetic correlates of phenotypic heterogeneity in autism	65
A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals	64
Genome-wide meta-analysis identifies 93 risk loci and enables risk prediction equivalent to monogenic forms of venous thromboembolism	63
Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking	63
BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis	62
Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum	61
Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells	61
Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish	61
Challenges and future directions for studying effects of host genetics on the gut microbiome	60
Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs	60
H3K27me3 conditions chemotolerance in triple-negative breast cancer	59
Transcription of MERVL retrotransposons is required for preimplantation embryo development	59
DNMT3A-dependent DNA methylation is required for spermatogonial stem cells to commit to spermatogenesis	59
Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements	59
Origin and function of activated fibroblast states during zebrafish heart regeneration	58
Genome-scale screens identify factors regulating tumor cell responses to natural killer cells	58
MLL4-associated condensates counterbalance Polycomb-mediated nuclear mechanical stress in Kabuki syndrome	58
Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk	58
Advancing crop genomics from lab to field	57
DNA replication fork speed underlies cell fate changes and promotes reprogramming	56
Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits	56
Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome	55
Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries	55
Rapid genotype imputation from sequence with reference panels	55
BRD4 orchestrates genome folding to promote neural crest differentiation	55
K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas	55
An unusual tandem kinase fusion protein confers leaf rust resistance in wheat	54
Human–chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution	54
Common variants contribute to intrinsic human brain functional networks	54
Enhancer–promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness	54
Silencing of LINE-1 retrotransposons is a selective dependency of myeloid leukemia	54
SAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests	54
Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet	53
Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii	53