Nature Genetics

Article	Citations
New insights into the genetic etiology of Alzheimer’s disease and related dementias	759
Large-scale association analyses identify host factors influencing human gut microbiome composition	734
Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology	663
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis	631
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression	620
A cross-population atlas of genetic associations for 220 human phenotypes	603
A single-cell and spatially resolved atlas of human breast cancers	569
Computationally efficient whole-genome regression for quantitative and binary traits	477
A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease	457
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	443
Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer	388
Genetics of 35 blood and urine biomarkers in the UK Biobank	383
Large-scale integration of the plasma proteome with genetics and disease	382
Cancer therapy shapes the fitness landscape of clonal hematopoiesis	369
The trans-ancestral genomic architecture of glycemic traits	350
Base-resolution models of transcription-factor binding reveal soft motif syntax	329
Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases	315
Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics	312
Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases	307
Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing	304
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation	294
Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease	277
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers	277
Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction	269
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes	267

Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation	263
Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic	261
Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses	260
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro	255
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals	233
Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology	230
Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity	225
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases	219
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation	219
Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation	216
Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank	215
An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci	211
Improving polygenic prediction in ancestrally diverse populations	206
Complex genetic signatures in immune cells underlie autoimmunity and inform therapy	204
Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease	204
Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor	200
Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases	199
The DNA methylation landscape of advanced prostate cancer	196
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease	195
Functionally informed fine-mapping and polygenic localization of complex trait heritability	192
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture	192
A generalized linear mixed model association tool for biobank-scale data	191
A compendium of uniformly processed human gene expression and splicing quantitative trait loci	187
Efficient phasing and imputation of low-coverage sequencing data using large reference panels	184
Quantifying genetic effects on disease mediated by assayed gene expression levels	183
Triticum population sequencing provides insights into wheat adaptation	181
Trans-ancestry analysis reveals genetic and nongenetic associations with COVID-19 susceptibility and severity	180
Prostate cancer reactivates developmental epigenomic programs during metastatic progression	173
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism	172
Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors	170
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication	170
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort	170
Cas9 activates the p53 pathway and selects for p53-inactivating mutations	168
Common genetic variants and modifiable risk factors underpin hypertrophic cardiomyopathy susceptibility and expressivity	168
A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes	167
Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2	164
Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis	163
Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants	162
Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis	160
Polygenic basis and biomedical consequences of telomere length variation	160
N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2	156
Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect	154
Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits	153
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale	152
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation	149
Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects	148
Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction	147
Global landscape of SARS-CoV-2 genomic surveillance and data sharing	143
Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data	142
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project	142

Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment	142
Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma	141
The association between tumor mutational burden and prognosis is dependent on treatment context	141
Haplotype-resolved genome analyses of a heterozygous diploid potato	140
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles	139
A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis	139
Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential	138
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome	138
Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes	136
Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy	135
Exploring and visualizing large-scale genetic associations by using PheWeb	133
Regulation of single-cell genome organization into TADs and chromatin nanodomains	131
Guidelines for human gene nomenclature	131
Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power	128
Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements	128
An integrated framework for local genetic correlation analysis	127
Genome-wide association analyses of post-traumatic stress disorder and its symptom subdomains in the Million Veteran Program	127
Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains	126
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer	125
Genetic analyses identify widespread sex-differential participation bias	124
Landscape of G-quadruplex DNA structural regions in breast cancer	124
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes	120
Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts	119
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1	117
A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection	117
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer	116
Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores	116
Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts	115
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion	115
A map of transcriptional heterogeneity and regulatory variation in human microglia	115
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability	115
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis	114
The genomic landscape of pediatric acute lymphoblastic leukemia	114
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment	114
Comprehensive characterization of protein–protein interactions perturbed by disease mutations	113
A cross-platform approach identifies genetic regulators of human metabolism and health	113
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response	113
High-definition likelihood inference of genetic correlations across human complex traits	112
Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning	111
Mammalian SWI/SNF continuously restores local accessibility to chromatin	109
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis	108
Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response	107
A quantitative genomics map of rice provides genetic insights and guides breeding	107
Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium	107
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development	105
Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies	105
Genetic architecture of 11 major psychiatric disorders at biobehavioral, functional genomic and molecular genetic levels of analysis	105
Acute BAF perturbation causes immediate changes in chromatin accessibility	105
cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing	104
Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk	103
Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies	103
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers	103
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders	103
Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states	102
Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome	100
Mutations disrupting neuritogenesis genes confer risk for cerebral palsy	100
RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells	99
Genomic analyses implicate noncoding de novo variants in congenital heart disease	99
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus	99
Alternative splicing during mammalian organ development	97
Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin	97
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities	96
Breast tumor microenvironment structures are associated with genomic features and clinical outcome	96
The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility	96
APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis	96
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens	96
CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response	96
Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes	95
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar	95
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses	94
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes	94
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer	94
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains	94
NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing	94
Insights into the genetic architecture of the human face	93
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes	92
Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease	92
Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals	92
Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms	91
Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars	91

WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation	91
Deep learning enables genetic analysis of the human thoracic aorta	89
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer	89
Sequence determinants of human gene regulatory elements	89
An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability	88
Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos	88
Increased somatic mutation burdens in normal human cells due to defective DNA polymerases	87
Privacy challenges and research opportunities for genomic data sharing	87
Genomic and evolutionary classification of lung cancer in never smokers	87
The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts	86
A sequence-based global map of regulatory activity for deciphering human genetics	86
Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments	86
Selective Mediator dependence of cell-type-specifying transcription	85
Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases	84
Differences between germline genomes of monozygotic twins	83
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics	83
A first-generation pediatric cancer dependency map	83
Genome-wide association analyses highlight etiological differences underlying newly defined subtypes of diabetes	83
Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson’s disease	83
The genomic basis of geographic differentiation and fiber improvement in cultivated cotton	82
The mutational signature profile of known and suspected human carcinogens in mice	82
European maize genomes highlight intraspecies variation in repeat and gene content	81
Cohesin and CTCF control the dynamics of chromosome folding	81
TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers	80
Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips	80
Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes	79
Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option	79
Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure	78
H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos	78
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement	78
Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19	77
Systematic reconstruction of cellular trajectories across mouse embryogenesis	77
Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis	76
A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation	76
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank	75
GestaltMatcher facilitates rare disease matching using facial phenotype descriptors	75
Subclonal reconstruction of tumors by using machine learning and population genetics	74
Characterizing the ecological and evolutionary dynamics of cancer	74
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics	74
Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer	74
Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases	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
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence	73
The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste	72
Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning	72
Genomic insights into the origin, domestication and diversification of Brassica juncea	72
The critical roles of somatic mutations and environmental tumor-promoting agents in cancer risk	72
Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance	71
DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers	71
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease	70
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response	70
Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer	70
Recent ultra-rare inherited variants implicate new autism candidate risk genes	70
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	70
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity	70
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention	69
Exome sequencing in bipolar disorder identifies AKAP11 as a risk gene shared with schizophrenia	69
Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways	68
Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale	67
Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers	66
Sex differences in genetic architecture in the UK Biobank	66
Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells	66
Cross-species chromatin interactions drive transcriptional rewiring in Epstein–Barr virus–positive gastric adenocarcinoma	65
Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants	65
Multiomics study of nonalcoholic fatty liver disease	65
Gene–environment correlations across geographic regions affect genome-wide association studies	65
Chromothripsis followed by circular recombination drives oncogene amplification in human cancer	64
Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals	64
Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS	63
Evolutionary dynamics of neoantigens in growing tumors	63
An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank	63
Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility	63
Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection	63
A multi-tissue atlas of regulatory variants in cattle	63
Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce	63
p53 convergently activates Dux/DUX4 in embryonic stem cells and in facioscapulohumeral muscular dystrophy cell models	62
Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness	62
Large uncertainty in individual polygenic risk score estimation impacts PRS-based risk stratification	61
Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function	61
Genome-wide prediction of disease variant effects with a deep protein language model	61
The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism	61
The NCI Genomic Data Commons	61
Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition	61
Two competing mechanisms of DNMT3A recruitment regulate the dynamics of de novo DNA methylation at PRC1-targeted CpG islands	60
Transcription imparts architecture, function and logic to enhancer units	60
Noncoding RNA processing by DIS3 regulates chromosomal architecture and somatic hypermutation in B cells	60
PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants	60
Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s disease	59
Shared heritability of human face and brain shape	59
Genetic drivers of m6A methylation in human brain, lung, heart and muscle	59
Renal plasticity revealed through reversal of polycystic kidney disease in mice	59
The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions	59
A resource of targeted mutant mouse lines for 5,061 genes	59
A PARTHENOGENESIS allele from apomictic dandelion can induce egg cell division without fertilization in lettuce	58