Nature Genetics

Article	Citations
New insights into the genetic etiology of Alzheimer’s disease and related dementias	884
Large-scale association analyses identify host factors influencing human gut microbiome composition	831
A cross-population atlas of genetic associations for 220 human phenotypes	733
Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology	727
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression	700
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis	690
A single-cell and spatially resolved atlas of human breast cancers	625
Computationally efficient whole-genome regression for quantitative and binary traits	545
A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease	494
Large-scale integration of the plasma proteome with genetics and disease	447
Genetics of 35 blood and urine biomarkers in the UK Biobank	401
Cancer therapy shapes the fitness landscape of clonal hematopoiesis	387
The trans-ancestral genomic architecture of glycemic traits	381
Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases	355
Base-resolution models of transcription-factor binding reveal soft motif syntax	347
Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing	323
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation	321
Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease	309
Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation	299
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers	289
Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction	287
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes	287
Complex genetic signatures in immune cells underlie autoimmunity and inform therapy	279
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro	273
Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic	271

Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology	256
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals	252
An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci	242
Improving polygenic prediction in ancestrally diverse populations	240
Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity	237
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation	234
Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation	231
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases	228
Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank	227
A generalized linear mixed model association tool for biobank-scale data	225
Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease	215
The DNA methylation landscape of advanced prostate cancer	208
Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants	207
Efficient phasing and imputation of low-coverage sequencing data using large reference panels	205
A compendium of uniformly processed human gene expression and splicing quantitative trait loci	205
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture	204
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease	204
Functionally informed fine-mapping and polygenic localization of complex trait heritability	202
Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor	200
Triticum population sequencing provides insights into wheat adaptation	192
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism	192
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort	187
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication	186
Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors	185
Trans-ancestry analysis reveals genetic and nongenetic associations with COVID-19 susceptibility and severity	185
Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis	182
Common genetic variants and modifiable risk factors underpin hypertrophic cardiomyopathy susceptibility and expressivity	182
Prostate cancer reactivates developmental epigenomic programs during metastatic progression	179
Polygenic basis and biomedical consequences of telomere length variation	179
A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes	172
Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis	170
Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2	169
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project	168
N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2	167
Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects	165
Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect	164
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment	162
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles	162
Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits	161
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation	161
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale	160
Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains	159
Global landscape of SARS-CoV-2 genomic surveillance and data sharing	157
Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma	155
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome	154
Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction	153
Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data	151
Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes	150
Haplotype-resolved genome analyses of a heterozygous diploid potato	149
The association between tumor mutational burden and prognosis is dependent on treatment context	146

A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis	145
An integrated framework for local genetic correlation analysis	141
Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential	141
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes	139
Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases	138
Genetic analyses identify widespread sex-differential participation bias	138
Regulation of single-cell genome organization into TADs and chromatin nanodomains	138
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer	136
Genome-wide association analyses of post-traumatic stress disorder and its symptom subdomains in the Million Veteran Program	135
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer	135
Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements	134
Guidelines for human gene nomenclature	133
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment	133
Landscape of G-quadruplex DNA structural regions in breast cancer	132
Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power	132
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1	131
The genomic landscape of pediatric acute lymphoblastic leukemia	129
Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies	126
Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts	125
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response	125
Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores	125
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion	124
Comprehensive characterization of protein–protein interactions perturbed by disease mutations	124
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis	123
A map of transcriptional heterogeneity and regulatory variation in human microglia	120
A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection	120
Mammalian SWI/SNF continuously restores local accessibility to chromatin	119
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers	119
Genetic architecture of 11 major psychiatric disorders at biobehavioral, functional genomic and molecular genetic levels of analysis	119
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders	117
A cross-platform approach identifies genetic regulators of human metabolism and health	117
A quantitative genomics map of rice provides genetic insights and guides breeding	116
Acute BAF perturbation causes immediate changes in chromatin accessibility	116
Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response	115
Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states	114
Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning	113
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis	113
Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies	112
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses	111
cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing	110
Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis	109
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development	109
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer	107
Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk	107
Breast tumor microenvironment structures are associated with genomic features and clinical outcome	107
RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells	106
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities	105
Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome	105
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens	105
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes	105
Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin	104
Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals	103
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus	103
Alternative splicing during mammalian organ development	103
Mutations disrupting neuritogenesis genes confer risk for cerebral palsy	103
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes	102
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains	102
Sequence determinants of human gene regulatory elements	101
Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars	100
An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability	99
Insights into the genetic architecture of the human face	99
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar	99
NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing	99
Genomic and evolutionary classification of lung cancer in never smokers	98
APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis	97
Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease	97
Cohesin and CTCF control the dynamics of chromosome folding	97
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer	95
Deep learning enables genetic analysis of the human thoracic aorta	94
Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments	94
A sequence-based global map of regulatory activity for deciphering human genetics	93
WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation	93
Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms	92
Increased somatic mutation burdens in normal human cells due to defective DNA polymerases	92
A first-generation pediatric cancer dependency map	91
The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts	91
Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos	90
The mutational signature profile of known and suspected human carcinogens in mice	90
Genome-wide association analyses highlight etiological differences underlying newly defined subtypes of diabetes	89
The genomic basis of geographic differentiation and fiber improvement in cultivated cotton	89

Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics	88
GestaltMatcher facilitates rare disease matching using facial phenotype descriptors	88
Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson’s disease	87
Systematic reconstruction of cellular trajectories across mouse embryogenesis	87
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement	86
Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer	85
Genome-wide prediction of disease variant effects with a deep protein language model	85
A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation	85
Differences between germline genomes of monozygotic twins	85
Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	84
Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure	83
Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning	83
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics	83
European maize genomes highlight intraspecies variation in repeat and gene content	82
H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos	82
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank	82
Characterizing the ecological and evolutionary dynamics of cancer	80
Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option	80
Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19	80
Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale	79
Exome sequencing in bipolar disorder identifies AKAP11 as a risk gene shared with schizophrenia	79
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence	79
Subclonal reconstruction of tumors by using machine learning and population genetics	78
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response	78
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	78
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention	78
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease	77
The critical roles of somatic mutations and environmental tumor-promoting agents in cancer risk	77
Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer	77
Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways	77
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity	77
Multiomics study of nonalcoholic fatty liver disease	75
Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance	75
Recent ultra-rare inherited variants implicate new autism candidate risk genes	75
The UCSC SARS-CoV-2 Genome Browser	74
DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers	74
Genomic insights into the origin, domestication and diversification of Brassica juncea	74
Gene–environment correlations across geographic regions affect genome-wide association studies	74
Sex differences in genetic architecture in the UK Biobank	73
A multi-tissue atlas of regulatory variants in cattle	73
The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste	73
Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility	73
Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce	72
Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals	71
An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank	71
The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions	71
Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants	71
Chromothripsis followed by circular recombination drives oncogene amplification in human cancer	70
Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers	70
Large uncertainty in individual polygenic risk score estimation impacts PRS-based risk stratification	69
Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s disease	69
Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases	68
Cross-species chromatin interactions drive transcriptional rewiring in Epstein–Barr virus–positive gastric adenocarcinoma	68
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species	68
The NCI Genomic Data Commons	67
Evolutionary dynamics of neoantigens in growing tumors	67
Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness	67
Genome-wide association analyses identify new Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility	67
Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries	66
Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function	66
Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk	65
A PARTHENOGENESIS allele from apomictic dandelion can induce egg cell division without fertilization in lettuce	65
Shared heritability of human face and brain shape	65
Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection	65
Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation	65
DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits	64
The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism	64
A plasma membrane transporter coordinates phosphate reallocation and grain filling in cereals	64
Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition	64
Molecular map of chronic lymphocytic leukemia and its impact on outcome	64
p53 convergently activates Dux/DUX4 in embryonic stem cells and in facioscapulohumeral muscular dystrophy cell models	64
A resource of targeted mutant mouse lines for 5,061 genes	64
Genetic control of RNA splicing and its distinct role in complex trait variation	63
The evolutionary dynamics of extrachromosomal DNA in human cancers	63
Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands	63
Genetic drivers of m6A methylation in human brain, lung, heart and muscle	63
Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS	63
Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding	63
Renal plasticity revealed through reversal of polycystic kidney disease in mice	63
Prediction of histone post-translational modification patterns based on nascent transcription data	62
Genome-edited crops for improved food security of smallholder farmers	62
Transcription imparts architecture, function and logic to enhancer units	62
PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants	62
Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation	62
Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics	61
Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells	61
RNA m6A regulates transcription via DNA demethylation and chromatin accessibility	61
Genetics of the human microglia regulome refines Alzheimer’s disease risk loci	61
Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation	60
Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	60
Gain-of-function variants in SYK cause immune dysregulation and systemic inflammation in humans and mice	60
Discovery of 42 genome-wide significant loci associated with dyslexia	60
Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries	59
A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals	59
BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis	59