Nature Genetics

Article	Citations
Deciphering the evolutionary dynamics of extrachromosomal DNA in human cancer	1489
Mapping dog behavior	1435
Epigenetic memory in 3D	1164
Temperature-induced RNA recoding in octopus	981
Toward advances in retinoblastoma genetics in Kenya	881
DNA polymerase ε produces elevated C-to-T mutations at methylated CpG dinucleotides	722
Role of gene–gene loops in fine-tuning cross-regulation	495
Problems with dystopian representations in genetic futurism	484
Machine learning drives genetic discovery for binge eating disorder	464
Identifying individuals at extreme risk of venous thromboembolism using polygenic risk scores	422
GeneMAP enables discovery of metabolic gene function	412
Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness	410
Understanding liver repair through space and time	397
Rare coding variant analysis for human diseases across biobanks and ancestries	395
Complete genomes of six ape species	393
An atlas of genetic determinants of forearm fracture	382
Reactivation of embryonic genetic programs in tissue regeneration and disease	373
Genome-wide RNA polymerase stalling shapes the transcriptome during aging	365
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease	329
Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells	315
Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea	305
Dominant variants in major spliceosome U4 and U5 small nuclear RNA genes cause neurodevelopmental disorders through splicing disruption	304
The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes	287
Mitochondrial DNA mosaicism in normal human somatic cells	286
Dynamics of DNA hydroxymethylation and methylation during mouse embryonic and germline development	267

Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases	258
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome	256
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals	250
Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways	244
In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization	243
A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation	242
Renal plasticity revealed through reversal of polycystic kidney disease in mice	240
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence	240
A biology-aware mutation rate model for human germline	237
Shared genetics of substance use disorders	236
Identification of two intrinsic epithelial subtypes of colorectal cancer	227
Genes influence complex traits through environments that vary between geographic regions	226
Histone gene editing probes functions of H3K27 modifications in mammals	225
Synthetic surrogates improve power for genome-wide association studies of partially missing phenotypes in population biobanks	224
Somatic mutations in the stomach	215
Epigenomic contributions to tumor cell heterogeneity and plasticity	213
Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon	208
Finding causal genes underlying risk for coronary artery disease	201
Author Correction: EMPReSS: standardized phenotype screens for functional annotation of the mouse genome	199
Genetic and non-genetic HLA disruption is widespread in lung and breast tumors	188
Finding cancer mutagens using signature analysis	184
Author Correction: The NAT1–bHLH110–CER1/CER1L module regulates heat stress tolerance in rice	180
Safeguard repressor locks hepatocyte identity and blocks liver cancer	177
Author Correction: Pangenome graphs and their applications in biodiversity genomics	177
The Federated European Genome–Phenome Archive as a global network for sharing human genomics data	176
Interpreting cis-regulatory interactions from large-scale deep neural networks	173
An alternative model for maternal mtDNA inheritance	169
K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas	168
Bayesian estimation of gene constraint from an evolutionary model with gene features	167
When RNA methylation meets DNA methylation	166
Establishing African genomics and bioinformatics programs through annual regional workshops	163
Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns	161
Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors	161
Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction	159
HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription	158
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders	156
RNA polymerase II dynamics shape enhancer–promoter interactions	154
APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer	153
Increasing diversity in genomics requires investment in equitable partnerships and capacity building	152
Single duplex DNA sequencing with CODEC detects mutations with high sensitivity	150
Meta-analysis of genome-wide associations and polygenic risk prediction for atrial fibrillation in more than 180,000 cases	149
H3K27me3 conditions chemotolerance in triple-negative breast cancer	146
Recent ultra-rare inherited variants implicate new autism candidate risk genes	146
APOBEC mutagenesis is a common process in normal human small intestine	145
Systematic prioritization of functional variants and effector genes underlying colorectal cancer risk	141
Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function	140
HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors	140
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment	139
A generalized linear mixed model association tool for biobank-scale data	137
Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice	137

Redefining teleost phylogeny	136
Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits	136
Mutation rates across species	136
Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance	132
Somatic recombination of repetitive elements	132
An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs	130
Equity, ethics and the promise of partnership in genomic medicine	130
Sarcoma predisposition	128
Systematic perturbation screens identify regulators of inflammatory macrophage states and a role for TNF mRNA m6A modification	128
Sox2 expression can be regulated across boundaries generated by CTCF–cohesin loops	128
Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes	128
Genetic and biological insights into spontaneous coronary artery dissection	127
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements	127
Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype	126
The genetic origins of multiple sclerosis	126
Defining and pursuing diversity in human genetic studies	126
Epigenetic scars of Brca1 loss point toward breast cancer cell of origin	124
Defining genome access of transcription factors	123
Polygenic basis for seedless grapes	123
Indirect paths from genetics to education	121
New genes helped acorn barnacles adapt to a sessile lifestyle	119
Planting the milestones of human genetics in Senegal	117
Improving estimates of loss-of-function constraint for short genes	115
Mathematical modeling of neuroblastoma associates evolutionary patterns with outcomes	114
Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition	113
Deep learning-based phenotype imputation on population-scale biobank data increases genetic discoveries	113
Schizophrenia risk conferred by rare protein-truncating variants is conserved across diverse human populations	112
Disease prediction with multi-omics and biomarkers empowers case–control genetic discoveries in the UK Biobank	112
Integrating population genetics, stem cell biology and cellular genomics to study complex human diseases	111
Consensus prediction of cell type labels in single-cell data with popV	111
Federated analysis of autosomal recessive coding variants in 29,745 developmental disorder patients from diverse populations	109
Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish	109
A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription	108
A complete telomere-to-telomere assembly of the maize genome	108
Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution	106
Precise modulation of transcription factor levels identifies features underlying dosage sensitivity	106
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells	105
Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits	105
GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture	104
Sequencing genetic and epigenetic bases	103
Genomics of the oldest domesticated wheat	103
Disrupted β-cell-specific gene silencing causes congenital hyperinsulinism	103
The language of genetics	103
High-throughput screening identifies modulators of gene bursting	102
Profiling oncogenic extra-chromosomal DNA in cancer	102
Publisher Correction: A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	101
Transposable element evolution in mammals	101
In silico saturation mutagenesis of cancer genes	101
Deciphering the regulatory logic of a chromatin domain boundary	101
Potential approaches to create ultimate genotypes in crops and livestock	99
Extraordinary collateral mutagenesis induced by CX-5461	99
Age-associated transcriptional stress due to accelerated elongation and increased stalling of RNAPII	99
Human genetic diversity alters off-target outcomes of therapeutic gene editing	98
Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view	98
Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk	96
Mapping interindividual dynamics of innate immune response at single-cell resolution	95
Base editing as a therapeutic strategy for somatic repeat expansion diseases	94
Epigenetic variation impacts individual differences in the transcriptional response to influenza infection	94
The elite haplotype OsGATA8-H coordinates nitrogen uptake and productive tiller formation in rice	94
Genetics of sexually dimorphic adipose distribution in humans	94
Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells	93
Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A–menin to bivalent promoters	93
A single-cell transcriptome atlas of human euploid and aneuploid blastocysts	91
Bipotent transitional liver progenitor cells contribute to liver regeneration	91
LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion	91
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors	91
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche	91
A compendium of genetic regulatory effects across pig tissues	90
The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize	90
Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants	90
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention	90
Dissecting endometriosis by single-cell transcriptomic and genomic analysis	89
Sickle-cell anemia gene therapy	89
Potato genome diversity	88
A one-stop shop for 3D spatial transcriptomics	88
A ΔNp63–MED12 axis drives basal-like identity in pancreatic cancer	88
Deep learning model improves COPD risk prediction and gene discovery	88
Intermediate cells with activated JAK/STAT signaling in prostate regeneration and diseases	87
X chromosome dosage shapes renal cell carcinoma risk	87
Publisher Correction: Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors	86

Applying compressed Perturb-seq to genetic screens	85
Decoding complex patterns of oncogene amplification	85
LINE1 mediates long-range DNA interactions	85
Functional analysis of cancer-associated germline risk variants	84
Our ancestry dictates clonal architecture and skin cancer susceptibility	84
Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation	84
Tumor heterogeneity impairs immunogenicity in mismatch repair deficient tumors	83
Wheat tandem kinase RWT4 directly binds a fungal effector to activate defense	82
Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts	81
A single-cell-type transcriptomics map of human tissues	81
Pathogen perception and deception in plant immunity by kinase fusion proteins	81
Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking	79
The disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development	78
Most large structural variants in cancer genomes can be detected without long reads	77
Converging evidence from exome sequencing and common variants implicates target genes for osteoporosis	77
Mapping extrachromosomal DNA amplifications during cancer progression	77
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank	77
Genetic insights into depression	76
GWAS of random glucose in 476,326 individuals provide insights into diabetes pathophysiology, complications and treatment stratification	75
Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk	75
Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea	75
Understanding the genetic complexity of puberty timing across the allele frequency spectrum	74
Author Correction: Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos	74
Exploring the genetic overlap between twelve psychiatric disorders	74
The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance	74
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes	73
Genetic contribution to heterogeneity in type 2 diabetes	73
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities	72
Phospholipid modifier PLAAT3 links defective PPARγ-dependent signaling to lipodystrophy	71
DNA methylation provides molecular links underlying complex traits	71
A molecular map of T cell activation gives insights into immune disease	71
Diverse mutations in autism-related genes and their expression in the developing brain	71
Author Correction: Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk	70
Engineering extrachromosomal DNA	70
Decoding the zebrafish genome	70
Publisher Correction: Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells	70
Author Correction: LINE-1 transcription activates long-range gene expression	69
How cauliflower got its curd	69
Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles	68
Activating the dark genome to illuminate cancer vaccine targets	68
SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs	68
Author Correction: Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains	68
Borzoi decodes the complex DNA signals governing gene regulation	68
Variably methylated retrotransposons are refractory to a range of environmental perturbations	68
Charles David Allis (1951–2023)	68
Multiomic analysis of homologous recombination-deficient end-stage high-grade serous ovarian cancer	67
Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology	67
Gene discovery and biological insights into anxiety disorders from a large-scale multi-ancestry genome-wide association study	67
CHOIR improves significance-based detection of cell types and states from single-cell data	66
The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes	66
Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes	65
RNA Pol II enters the ring of cohesin-mediated loop extrusion	64
Structural polymorphism and diversity of human segmental duplications	64
Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer’s disease	63
Genome synteny reveals hidden enhancer conservation	63
Multi-ancestry genome-wide association study of major depression aids locus discovery, fine mapping, gene prioritization and causal inference	63
Aberrant splicing prediction across human tissues	63
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer	63
Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing	63
Pervasive biases in proxy genome-wide association studies based on parental history of Alzheimer’s disease	63
Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma	62
New insights into the genetic etiology of Alzheimer’s disease and related dementias	62
Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution	62
The Ruminant Telomere-to-Telomere (RT2T) Consortium	62
CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses	61
RNA m6A regulates transcription via DNA demethylation and chromatin accessibility	61
Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis	61
Annotating and prioritizing human non-coding variants with RegulomeDB v.2	61
Genome-wide prediction of disease variant effects with a deep protein language model	60
Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders	59
Large-scale integration of the plasma proteome with genetics and disease	59
Genetic analysis of right heart structure and function in 40,000 people	59
Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer	59
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses	59
Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm	59
The genomic landscape of pediatric acute lymphoblastic leukemia	58
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	58
Single-cell mapping of HTT somatic repeat expansions	57
Publisher Correction: Functional innovation through new genes as a general evolutionary process	57
A mass balance principle for finding loose ends in cancer genomes	57
The evolving cancer genome	57
Integration of genetic data with dynamic gene regulatory elements identifies autoimmune effector cell states	56
Metastable epialleles are stable in their instability	56
Stepwise de novo establishment of inactive X chromosome architecture in early development	56
Publisher Correction: Epigenomic contributions to tumor cell heterogeneity and plasticity	56
Single-cell technologies meet Hi-C	56
Publisher Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors	56
Prevalent putative chromatin bivalency and partial resetting of H3K27me3 in plant sperm	55
Blood DNA virome associates with autoimmune diseases and COVID-19	55
DNA loop extrusion is asymmetric but can switch direction	55
Brain metastasis prediction	55
Disentangling extrachromosomal circular DNA heterogeneity in single cells with scEC&T-seq	54
Connecting clinical and genetic heterogeneity in ADHD	53
Author Correction: Bipotent transitional liver progenitor cells contribute to liver regeneration	52
G6PD deficiency and diabetes complications	52