Nature Genetics

Article	Citations
A versatile functional assay for genetic variants in human disease	1391
Deciphering the evolutionary dynamics of extrachromosomal DNA in human cancer	1319
Improved pathogenicity prediction using primate genomics	1070
Calling SNVs in single cells	1003
Neuronal chromatin meta-domains	920
Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression	877
Somatic mutations of GNA11 and GNAQ in CTNNB1-mutant aldosterone-producing adenomas presenting in puberty, pregnancy or menopause	800
sortChIC enables detailed chromatin analysis of rare cell types	682
A scalable technology for measuring cell-type-specific activity of cis-regulatory sequences	505
Quantifying fitness effects and mutation rates of mCAs in blood	449
Linking non-coding variants to function in microglia in Alzheimer’s disease	432
Inferring phylogenies from pandemic-scale genome datasets	425
Prevalent putative chromatin bivalency and partial resetting of H3K27me3 in plant sperm	401
Mitochondrial DNA mosaicism in normal human somatic cells	391
RNU4-2 variants cause neurodevelopmental disorders	390
Dynamics of DNA hydroxymethylation and methylation during mouse embryonic and germline development	373
Inseparable RNA binding and chromatin modification activities of a nucleosome-interacting surface in EZH2	372
Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits	371
In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization	368
Functional characterization of Alzheimer’s disease genetic variants in microglia	353
Genome-wide RNA polymerase stalling shapes the transcriptome during aging	348
Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis	333
Genomic analysis of 1,325 Camellia accessions sheds light on agronomic and metabolic traits for tea plant improvement	325
Identifying critical cell types and gene regulatory pathways for hair and skin disease	308
Rare-variant genetic architecture	289

Role of gene–gene loops in fine-tuning cross-regulation	279
Implementing polygenic risk scores in the clinic	278
Temperature-induced RNA recoding in octopus	275
Mapping dog behavior	272
G6PD deficiency and diabetes complications	245
Chromosome organization from the Ice Age	241
GeneMAP enables discovery of metabolic gene function	240
The evolving cancer genome	237
Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns	232
Increased enhancer–promoter interactions during developmental enhancer activation in mammals	222
Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans	221
GATTACA is still pertinent 25 years later	218
Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes	217
Complex synthetic lethality in cancer	216
Perturbational phenotyping of human blood cells reveals genetically determined latent traits associated with subsets of common diseases	214
Transposition enables low-input single-molecule concurrent genomics and epigenomics	213
A mass balance principle for finding loose ends in cancer genomes	204
Chromatin modifications integrate cis genomic context to instruct transcriptional outputs	204
Rewriting the mammalian genome, one locus at a time	203
Integration of genetic data with dynamic gene regulatory elements identifies autoimmune effector cell states	202
Epigenetic memory in 3D	201
African-ancestry-associated genomic differences in cancer	201
Personalizing pangenome graphs with k-mers	193
Identifying genetic subtypes of disease from hospital diagnosis records	191
A call for spatial omics submissions	188
TP53-dependent genomic instability	185
The NAT1–bHLH110–CER1/CER1L module regulates heat stress tolerance in rice	173
Cellular plasticity of the bone marrow niche promotes hematopoietic stem cell regeneration	173
Reactivation of embryonic genetic programs in tissue regeneration and disease	167
Publisher Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors	166
Tomato super-pangenome highlights the potential use of wild relatives in tomato breeding	164
Blood DNA virome associates with autoimmune diseases and COVID-19	163
Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness	162
Comprehensive genomic characterization of early-stage bladder cancer	161
Brain metastasis prediction	158
DNA loop extrusion is asymmetric but can switch direction	157
How transposable elements are spliced out	156
Disentangling extrachromosomal circular DNA heterogeneity in single cells with scEC&T-seq	155
Publisher Correction: Functional innovation through new genes as a general evolutionary process	149
Single-cell mapping of HTT somatic repeat expansions	147
Polyguanine microsatellites are robust replication clocks in cancer	146
Cancer-independent somatic mutation of the wild-type NF1 allele in normal tissues in neurofibromatosis type 1	146
Hyperactive histone genes fuel cancer	145
Genomics of rare diseases in the Greater Middle East	144
DRAGEN optimizes genomic variant detection	143
Rare coding variants in CHRNB2 reduce the likelihood of smoking	141
A modified fluctuation-test framework characterizes the population dynamics and mutation rate of colorectal cancer persister cells	141
Library size normalization affects spatial domain identification	141
Metagenomics of the human gut mycobiome	141
BRD2 compartmentalizes the accessible genome	140

Author Correction: From Mendel to quantitative genetics in the genome era: the scientific legacy of W. G. Hill	139
Automated sequence-based annotation and interpretation of the human genome	138
Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation	138
Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease	133
NECTIN1 is a melanoma metastasis suppressor gene	132
Skip to the end: metastasis before tumorigenesis	129
Author Correction: Genetic effects on the timing of parturition and links to fetal birth weight	128
Author Correction: Bipotent transitional liver progenitor cells contribute to liver regeneration	128
Identifying type 2 diabetes risk genes by β-cell CRISPR screening	128
Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries	128
Identifying individuals at extreme risk of venous thromboembolism using polygenic risk scores	127
Studying the genetics of participation using footprints left on the ascertained genotypes	126
Problems with dystopian representations in genetic futurism	126
Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases	126
A combinatorial genetic strategy for exploring complex genotype–phenotype associations in cancer	124
Machine learning drives genetic discovery for binge eating disorder	124
Proteogenomic insights into early-onset endometrioid endometrial carcinoma: predictors for fertility-sparing therapy response	122
Genetic mapping across autoimmune diseases reveals shared associations and mechanisms	122
Understanding liver repair through space and time	121
Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast	121
Single-mitosis dissection of acute and chronic DNA mutagenesis and repair	121
Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer	120
Mobile element insertions affect human pigmentation and skin cancer risk	120
Saturation genome editing maps the functional spectrum of pathogenic VHL alleles	120
Single-cell technologies meet Hi-C	118
Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells	117
Promoting equity in polygenic risk assessment through global collaboration	117
Widespread position-dependent transcriptional regulatory sequences in plants	117
Rare coding variant analysis for human diseases across biobanks and ancestries	117
Toward advances in retinoblastoma genetics in Kenya	116
Harnessing cancer genomes for precision oncology	116
Context-specific targeting of the androgen receptor in prostate cancer	116
Base editing screens define the genetic landscape of cancer drug resistance mechanisms	115
Toward GDPR compliance with the Helmholtz Munich genotype imputation server	115
Obesity-dependent selection of driver mutations in cancer	115
Split-pool barcoding serves up an epigenomic smorgasbord	115
Genome-wide association analysis provides insights into the molecular etiology of dilated cardiomyopathy	114
Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER	114
SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma	113
Finding hidden treasures in summary statistics from genome-wide association studies	110
Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum	109
Extreme conservation encodes the structural dynamics and function of 5′ UTRs	109
Publisher Correction: Epigenomic contributions to tumor cell heterogeneity and plasticity	106
Using advanced spatial and single-cell transcriptomics to characterize the human endometrium	105
Metastable epialleles are stable in their instability	104
Author Correction: Genetics of 35 blood and urine biomarkers in the UK Biobank	104
Translating amyotrophic lateral sclerosis genes into drug development leads	104
Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease	103
Biallelic mutations in cancer genomes reveal local mutational determinants	103
Author Correction: Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk	103
A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation	102
A new method for multiancestry polygenic prediction improves performance across diverse populations	102
Optimizing combination immunotherapy in lung cancer	101
Connecting clinical and genetic heterogeneity in ADHD	101
From Mendel to quantitative genetics in the genome era: the scientific legacy of W. G. Hill	100
DNA polymerase ε produces elevated C-to-T mutations at methylated CpG dinucleotides	100
Genetics and dietary restriction impact lifespan	100
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma	99
Brca1 haploinsufficiency promotes early tumor onset and epigenetic alterations in a mouse model of hereditary breast cancer	99
PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants	98
Origin and evolution of the triploid cultivated banana genome	98
Deciphering single-cell transcriptional programs across species	96
Author Correction: Mutations in PYCR1 cause cutis laxa with progeroid features	96
Primate-specific ZNF808 is essential for pancreatic development in humans	95
Multiomic profiling identifies predictors of survival in African American patients with acute myeloid leukemia	94
Pangenome graphs and their applications in biodiversity genomics	93
Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis	93
Retrotransposon activation during Drosophila metamorphosis conditions adult antiviral responses	92
Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits	91
Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation	91
Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity	91
The homeobox transcription factor DUXBL controls exit from totipotency	90
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis	90
H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos	90
A cautionary tale for Alzheimer’s disease GWAS by proxy	90
The NALCN channel regulates metastasis and nonmalignant cell dissemination	90
A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk	89
An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank	89
Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank	89
Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers	89

Ten challenges for clinical translation in psychiatric genetics	88
Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder	88
Genetic architecture reconciles linkage and association studies of complex traits	88
Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens	88
Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases	88
Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data	87
Stepwise de novo establishment of inactive X chromosome architecture in early development	86
Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells	84
LINE-1 transcription activates long-range gene expression	84
Genetic correlates of phenotypic heterogeneity in autism	84
Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk	83
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles	83
Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways	83
Genetic architecture of cardiac dynamic flow volumes	83
Thymidine nucleotide metabolism controls human telomere length	83
Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing	83
Harnessing clonal gametes in hybrid crops to engineer polyploid genomes	82
Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars	82
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro	82
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location	81
Cohesin maintains replication timing to suppress DNA damage on cancer genes	81
Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings	81
Systematic rare variant analyses identify RAB32 as a susceptibility gene for familial Parkinson’s disease	80
MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution	80
An integrated single-cell reference atlas of the human endometrium	79
Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis	79
YAP induces an oncogenic transcriptional program through TET1-mediated epigenetic remodeling in liver growth and tumorigenesis	77
High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR–Cas9 editing	77
A plasma membrane transporter coordinates phosphate reallocation and grain filling in cereals	77
Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification	77
Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis	76
Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea	76
Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity	76
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers	75
Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet	75
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence	75
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals	74
A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation	74
Shared heritability of human face and brain shape	73
The genomic and spatial mobility of extrachromosomal DNA and its implications for cancer therapy	72
Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression	72
Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet	72
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer	72
An atlas of genetic determinants of forearm fracture	72
Systematic reconstruction of cellular trajectories across mouse embryogenesis	71
Improving polygenic prediction in ancestrally diverse populations	71
Variation in TaSPL6-D confers salinity tolerance in bread wheat by activating TaHKT1;5-D while preserving yield-related traits	70
Molecular basis for maternal inheritance of human mitochondrial DNA	70
In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis	70
Selection for somatic escape variants in SERPINA1 in the liver of patients with alpha-1 antitrypsin deficiency	69
Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases	69
Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain	69
CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity	68
Renal plasticity revealed through reversal of polycystic kidney disease in mice	68
Multi-ancestry genome-wide association meta-analysis of Parkinson’s disease	67
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort	67
Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity	67
Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology	67
Multivariate genomic analysis of 5 million people elucidates the genetic architecture of shared components of the metabolic syndrome	66
Genetic effects on the timing of parturition and links to fetal birth weight	66
Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome	66
Distinct and shared genetic architectures of gestational diabetes mellitus and type 2 diabetes	66
The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes	66
Human intestinal immuno-organoids	65
Implicating XIST in sex-biased autoimmunity	65
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease	65
A genetic research story of giving back and returning to the country of a thousand hills	65
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome	65
Structural variations fine-tune gene expression to steer Brassica oleracea diversification	64
Code deposition is unskippable	63
Our genes, our microbes	63
Machine learning to examine the genetic underpinnings of cardiac fibrosis at scale	63
Mapping the regulators of key immune genes and disease networks	63
Transient activated fibroblasts contribute to zebrafish heart regeneration	63
Genetic associations of human metabolic traits	63
Gene therapy for Parkinson’s disease models	62
Embracing communication	61
Author Correction: Pangenome graphs and their applications in biodiversity genomics	61
Mouse embryonic development requires transposable element expression	61
Unraveling the role of succinyl-CoA in tumor immunity	61
Transitioning cancer cells and the surrounding tumor environment in pancreatic cancer	61
The Federated European Genome–Phenome Archive as a global network for sharing human genomics data	61
Safeguard repressor locks hepatocyte identity and blocks liver cancer	59
Novel mRNA isoforms in human microglia refine genetic associations with neurodegeneration	59
Alterations in PD-L1 succinylation shape anti-tumor immune responses in melanoma	58
NR5A2 activates the zygotic genome	58
The transcriptomic architecture of common cancers reflects synthetic lethal interactions	58
Author Correction: The NAT1–bHLH110–CER1/CER1L module regulates heat stress tolerance in rice	58
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing	58
Comparative analysis of the Mexico City Prospective Study and the UK Biobank identifies ancestry-specific effects on clonal hematopoiesis	58
An enhanced framework for local genetic correlation analysis	58
A single-nucleus pan-cancer epigenetic and transcriptomic landscape	57
A biology-aware mutation rate model for human germline	57
Functional genomics of height heritability	57
Nitrogen uptake and productive tiller formation in rice	56