Nature Genetics

Article	Citations
New insights into the genetic etiology of Alzheimer’s disease and related dementias	703
Large-scale association analyses identify host factors influencing human gut microbiome composition	682
Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology	626
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis	601
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression	582
A cross-population atlas of genetic associations for 220 human phenotypes	558
A single-cell and spatially resolved atlas of human breast cancers	537
Computationally efficient whole-genome regression for quantitative and binary traits	450
Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis	432
A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease	432
Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer	375
Genetics of 35 blood and urine biomarkers in the UK Biobank	369
Cancer therapy shapes the fitness landscape of clonal hematopoiesis	353
Large-scale integration of the plasma proteome with genetics and disease	345
The trans-ancestral genomic architecture of glycemic traits	338
Base-resolution models of transcription-factor binding reveal soft motif syntax	315
Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases	300
Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics	298
Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing	298
Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases	289
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation	281
Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease	265
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers	264
Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic	258
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes	257

Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses	255
Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction	254
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro	243
Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation	242
Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement	236
Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution	227
Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology	222
Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity	220
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals	219
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases	214
Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank	210
Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation	209
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation	208
An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci	203
Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease	202
Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor	199
Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease	198
Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases	193
Improving polygenic prediction in ancestrally diverse populations	193
The DNA methylation landscape of advanced prostate cancer	192
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease	188
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture	188
A compendium of uniformly processed human gene expression and splicing quantitative trait loci	182
Functionally informed fine-mapping and polygenic localization of complex trait heritability	181
Efficient phasing and imputation of low-coverage sequencing data using large reference panels	179
Quantifying genetic effects on disease mediated by assayed gene expression levels	179
Trans-ancestry analysis reveals genetic and nongenetic associations with COVID-19 susceptibility and severity	176
Triticum population sequencing provides insights into wheat adaptation	176
A generalized linear mixed model association tool for biobank-scale data	174
Prostate cancer reactivates developmental epigenomic programs during metastatic progression	170
Cas9 activates the p53 pathway and selects for p53-inactivating mutations	166
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort	165
Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors	164
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication	164
A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes	164
Common genetic variants and modifiable risk factors underpin hypertrophic cardiomyopathy susceptibility and expressivity	164
Complex genetic signatures in immune cells underlie autoimmunity and inform therapy	162
Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2	161
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism	157
Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis	154
Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect	153
N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2	153
Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis	150
Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits	149
Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants	147
Genome-wide selection and genetic improvement during modern maize breeding	147
Polygenic basis and biomedical consequences of telomere length variation	146
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation	144
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale	144
Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction	140

Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data	136
Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects	136
The association between tumor mutational burden and prognosis is dependent on treatment context	136
Global landscape of SARS-CoV-2 genomic surveillance and data sharing	135
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project	134
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment	134
Haplotype-resolved genome analyses of a heterozygous diploid potato	134
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome	134
Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility	134
Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy	133
Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential	133
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles	133
Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma	132
Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes	131
A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis	130
Guidelines for human gene nomenclature	130
Regulation of single-cell genome organization into TADs and chromatin nanodomains	128
Exploring and visualizing large-scale genetic associations by using PheWeb	127
Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements	126
Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power	125
Landscape of G-quadruplex DNA structural regions in breast cancer	123
Genetic analyses identify widespread sex-differential participation bias	122
Genome-wide association analyses of post-traumatic stress disorder and its symptom subdomains in the Million Veteran Program	120
Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts	118
A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection	117
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer	115
An integrated framework for local genetic correlation analysis	115
Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts	113
A cross-platform approach identifies genetic regulators of human metabolism and health	112
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response	111
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion	110
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability	110
High-definition likelihood inference of genetic correlations across human complex traits	110
A map of transcriptional heterogeneity and regulatory variation in human microglia	109
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis	108
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes	108
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer	107
Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning	107
The genomic landscape of pediatric acute lymphoblastic leukemia	107
Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium	107
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1	106
Comprehensive characterization of protein–protein interactions perturbed by disease mutations	106
Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains	105
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis	105
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment	105
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development	105
A quantitative genomics map of rice provides genetic insights and guides breeding	104
Mammalian SWI/SNF continuously restores local accessibility to chromatin	104
cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing	103
Acute BAF perturbation causes immediate changes in chromatin accessibility	103
Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response	102
Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores	102
Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk	100
Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome	99
Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies	98
Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies	98
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders	98
Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states	98
RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells	98
APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis	97
Genomic analyses implicate noncoding de novo variants in congenital heart disease	97
Mutations disrupting neuritogenesis genes confer risk for cerebral palsy	97
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers	96
Identifying genetic variants underlying phenotypic variation in plants without complete genomes	96
CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response	96
Genetic architecture of 11 major psychiatric disorders at biobehavioral, functional genomic and molecular genetic levels of analysis	95
The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility	95
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer	94
NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing	93
Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes	93
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer	93
Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin	93
Insights into the genetic architecture of the human face	93
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes	91
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens	91
Breast tumor microenvironment structures are associated with genomic features and clinical outcome	91
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus	91
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains	90
WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation	90
Alternative splicing during mammalian organ development	90

Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses	90
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities	88
Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals	88
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar	87
Sequence determinants of human gene regulatory elements	87
Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars	87
Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments	86
Deep learning enables genetic analysis of the human thoracic aorta	86
Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease	86
An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability	85
Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos	84
Increased somatic mutation burdens in normal human cells due to defective DNA polymerases	84
Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms	83
Genomic and evolutionary classification of lung cancer in never smokers	83
The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts	83
Selective Mediator dependence of cell-type-specifying transcription	83
Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson’s disease	82
Privacy challenges and research opportunities for genomic data sharing	82
Genome-wide association analyses highlight etiological differences underlying newly defined subtypes of diabetes	82
The mutational signature profile of known and suspected human carcinogens in mice	81
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes	81
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics	81
European maize genomes highlight intraspecies variation in repeat and gene content	79
Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option	79
Differences between germline genomes of monozygotic twins	79
TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers	79
A first-generation pediatric cancer dependency map	78
Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes	78
Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure	77
The genomic basis of geographic differentiation and fiber improvement in cultivated cotton	77
Cohesin and CTCF control the dynamics of chromosome folding	77
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer	77
H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos	76
Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	76
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement	76
Systematic reconstruction of cellular trajectories across mouse embryogenesis	75
Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19	75
A sequence-based global map of regulatory activity for deciphering human genetics	74
The UCSC SARS-CoV-2 Genome Browser	73
Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation	73
GestaltMatcher facilitates rare disease matching using facial phenotype descriptors	73
Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer	73
Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases	73
Characterizing the ecological and evolutionary dynamics of cancer	73
Subclonal reconstruction of tumors by using machine learning and population genetics	72
Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis	71
A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation	71
The critical roles of somatic mutations and environmental tumor-promoting agents in cancer risk	70
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics	70
The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste	70
DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers	69
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank	69
Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance	69
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence	68
Genomic insights into the origin, domestication and diversification of Brassica juncea	68
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response	67
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease	67
Recent ultra-rare inherited variants implicate new autism candidate risk genes	67
Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer	67
Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells	66
Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases	66
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	65
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention	64
Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants	64
Sex differences in genetic architecture in the UK Biobank	64
Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning	64
Exome sequencing in bipolar disorder identifies AKAP11 as a risk gene shared with schizophrenia	63
Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction	63
Cross-species chromatin interactions drive transcriptional rewiring in Epstein–Barr virus–positive gastric adenocarcinoma	63
An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank	62
Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers	62
Evolutionary dynamics of neoantigens in growing tumors	62
Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce	61
Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS	61
Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways	61
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity	61
Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition	60
Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection	60
Chromothripsis followed by circular recombination drives oncogene amplification in human cancer	60
Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility	60
Transcription imparts architecture, function and logic to enhancer units	60
The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism	59
Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function	59
Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals	59
Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale	59
A multi-tissue atlas of regulatory variants in cattle	59
A resource of targeted mutant mouse lines for 5,061 genes	59
p53 convergently activates Dux/DUX4 in embryonic stem cells and in facioscapulohumeral muscular dystrophy cell models	58
Gene–environment correlations across geographic regions affect genome-wide association studies	58
Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells	58
Shared heritability of human face and brain shape	58
Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands	58
Liability threshold modeling of case–control status and family history of disease increases association power	57
A PARTHENOGENESIS allele from apomictic dandelion can induce egg cell division without fertilization in lettuce	57
Renal plasticity revealed through reversal of polycystic kidney disease in mice	57