Nature Genetics

Article	Citations
Deciphering the evolutionary dynamics of extrachromosomal DNA in human cancer	1428
Mapping dog behavior	1375
Epigenetic memory in 3D	1114
Temperature-induced RNA recoding in octopus	1030
Toward advances in retinoblastoma genetics in Kenya	951
Reactivation of embryonic genetic programs in tissue regeneration and disease	906
Mitochondrial DNA mosaicism in normal human somatic cells	839
DNA polymerase ε produces elevated C-to-T mutations at methylated CpG dinucleotides	702
Role of gene–gene loops in fine-tuning cross-regulation	514
Problems with dystopian representations in genetic futurism	472
Machine learning drives genetic discovery for binge eating disorder	469
Identifying individuals at extreme risk of venous thromboembolism using polygenic risk scores	449
GeneMAP enables discovery of metabolic gene function	405
Understanding liver repair through space and time	405
Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness	396
An atlas of genetic determinants of forearm fracture	386
In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization	380
Genome-wide RNA polymerase stalling shapes the transcriptome during aging	377
A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation	362
Renal plasticity revealed through reversal of polycystic kidney disease in mice	357
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease	351
Dynamics of DNA hydroxymethylation and methylation during mouse embryonic and germline development	328
Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways	322
Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases	302
Rare coding variant analysis for human diseases across biobanks and ancestries	293

Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea	289
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome	283
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence	279
Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells	256
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals	249
The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes	248
A biology-aware mutation rate model for human germline	241
An alternative model for maternal mtDNA inheritance	239
Identification of two intrinsic epithelial subtypes of colorectal cancer	231
Shared genetics of substance use disorders	231
Genes influence complex traits through environments that vary between geographic regions	230
Histone gene editing probes functions of H3K27 modifications in mammals	228
APOBEC mutagenesis is a common process in normal human small intestine	225
K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas	220
Establishing African genomics and bioinformatics programs through annual regional workshops	220
Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice	220
Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors	217
Synthetic surrogates improve power for genome-wide association studies of partially missing phenotypes in population biobanks	214
Somatic mutations in the stomach	212
Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns	209
Recent ultra-rare inherited variants implicate new autism candidate risk genes	204
Epigenomic contributions to tumor cell heterogeneity and plasticity	198
Systematic prioritization of functional variants and effector genes underlying colorectal cancer risk	196
Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon	192
When RNA methylation meets DNA methylation	183
Finding causal genes underlying risk for coronary artery disease	179
Author Correction: EMPReSS: standardized phenotype screens for functional annotation of the mouse genome	171
Interpreting cis-regulatory interactions from large-scale deep neural networks	171
Genetic and non-genetic HLA disruption is widespread in lung and breast tumors	170
Author Correction: The NAT1–bHLH110–CER1/CER1L module regulates heat stress tolerance in rice	170
Finding cancer mutagens using signature analysis	170
Author Correction: Pangenome graphs and their applications in biodiversity genomics	165
Bayesian estimation of gene constraint from an evolutionary model with gene features	162
Safeguard repressor locks hepatocyte identity and blocks liver cancer	162
Meta-analysis of genome-wide associations and polygenic risk prediction for atrial fibrillation in more than 180,000 cases	158
The Federated European Genome–Phenome Archive as a global network for sharing human genomics data	156
Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction	155
Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function	155
HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors	151
Single duplex DNA sequencing with CODEC detects mutations with high sensitivity	151
H3K27me3 conditions chemotolerance in triple-negative breast cancer	151
HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription	150
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders	149
Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits	149
Increasing diversity in genomics requires investment in equitable partnerships and capacity building	148
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment	145
APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer	143
RNA polymerase II dynamics shape enhancer–promoter interactions	142
A generalized linear mixed model association tool for biobank-scale data	141
Redefining teleost phylogeny	139

Mutation rates across species	137
Somatic recombination of repetitive elements	136
An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs	136
Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance	136
Equity, ethics and the promise of partnership in genomic medicine	133
Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes	131
Deep learning-based phenotype imputation on population-scale biobank data increases genetic discoveries	131
Federated analysis of autosomal recessive coding variants in 29,745 developmental disorder patients from diverse populations	131
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells	129
Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish	128
A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription	127
GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture	126
Integrating population genetics, stem cell biology and cellular genomics to study complex human diseases	126
Precise modulation of transcription factor levels identifies features underlying dosage sensitivity	126
Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits	125
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer	124
Schizophrenia risk conferred by rare protein-truncating variants is conserved across diverse human populations	124
Disease prediction with multi-omics and biomarkers empowers case–control genetic discoveries in the UK Biobank	124
Sarcoma predisposition	123
Genetic and biological insights into spontaneous coronary artery dissection	121
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements	121
Sox2 expression can be regulated across boundaries generated by CTCF–cohesin loops	121
The genetic origins of multiple sclerosis	120
Systematic perturbation screens identify regulators of inflammatory macrophage states and a role for TNF mRNA m6A modification	120
Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype	120
Epigenetic scars of Brca1 loss point toward breast cancer cell of origin	119
Defining and pursuing diversity in human genetic studies	119
Polygenic basis for seedless grapes	118
Defining genome access of transcription factors	117
Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition	116
New genes helped acorn barnacles adapt to a sessile lifestyle	114
Indirect paths from genetics to education	114
Planting the milestones of human genetics in Senegal	111
Improving estimates of loss-of-function constraint for short genes	110
Consensus prediction of cell type labels in single-cell data with popV	109
Mathematical modeling of neuroblastoma associates evolutionary patterns with outcomes	109
A complete telomere-to-telomere assembly of the maize genome	109
Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution	108
The language of genetics	107
Genomics of the oldest domesticated wheat	106
Disrupted β-cell-specific gene silencing causes congenital hyperinsulinism	105
Sequencing genetic and epigenetic bases	105
High-throughput screening identifies modulators of gene bursting	104
Transposable element evolution in mammals	104
Profiling oncogenic extra-chromosomal DNA in cancer	104
In silico saturation mutagenesis of cancer genes	104
Publisher Correction: A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	103
Deciphering the regulatory logic of a chromatin domain boundary	102
Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A–menin to bivalent promoters	101
Extraordinary collateral mutagenesis induced by CX-5461	101
Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view	100
The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize	100
The elite haplotype OsGATA8-H coordinates nitrogen uptake and productive tiller formation in rice	99
Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells	98
Epigenetic variation impacts individual differences in the transcriptional response to influenza infection	97
Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk	97
Mapping interindividual dynamics of innate immune response at single-cell resolution	97
Potential approaches to create ultimate genotypes in crops and livestock	96
A single-cell transcriptome atlas of human euploid and aneuploid blastocysts	95
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors	94
Human genetic diversity alters off-target outcomes of therapeutic gene editing	94
Age-associated transcriptional stress due to accelerated elongation and increased stalling of RNAPII	94
Genetics of sexually dimorphic adipose distribution in humans	93
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention	93
A compendium of genetic regulatory effects across pig tissues	92
Bipotent transitional liver progenitor cells contribute to liver regeneration	92
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche	92
LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion	92
Dissecting endometriosis by single-cell transcriptomic and genomic analysis	91
Converging evidence from exome sequencing and common variants implicates target genes for osteoporosis	91
Sickle-cell anemia gene therapy	91
Potato genome diversity	91
Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants	91
Genetic insights into depression	90
Deep learning model improves COPD risk prediction and gene discovery	90
A ΔNp63–MED12 axis drives basal-like identity in pancreatic cancer	89
A one-stop shop for 3D spatial transcriptomics	88
Intermediate cells with activated JAK/STAT signaling in prostate regeneration and diseases	87
Genetic contribution to heterogeneity in type 2 diabetes	87
X chromosome dosage shapes renal cell carcinoma risk	87

LINE1 mediates long-range DNA interactions	86
Publisher Correction: Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors	86
A single-cell-type transcriptomics map of human tissues	86
Applying compressed Perturb-seq to genetic screens	85
Most large structural variants in cancer genomes can be detected without long reads	85
Decoding complex patterns of oncogene amplification	85
Functional analysis of cancer-associated germline risk variants	85
Pathogen perception and deception in plant immunity by kinase fusion proteins	84
Wheat tandem kinase RWT4 directly binds a fungal effector to activate defense	84
The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance	84
Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation	83
Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts	83
Our ancestry dictates clonal architecture and skin cancer susceptibility	83
The disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development	83
Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk	82
GWAS of random glucose in 476,326 individuals provide insights into diabetes pathophysiology, complications and treatment stratification	82
Tumor heterogeneity impairs immunogenicity in mismatch repair deficient tumors	82
Mapping extrachromosomal DNA amplifications during cancer progression	81
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank	81
Understanding the genetic complexity of puberty timing across the allele frequency spectrum	80
Exploring the genetic overlap between twelve psychiatric disorders	79
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes	79
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities	78
Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking	78
Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea	78
A molecular map of T cell activation gives insights into immune disease	76
Diverse mutations in autism-related genes and their expression in the developing brain	76
DNA methylation provides molecular links underlying complex traits	76
Phospholipid modifier PLAAT3 links defective PPARγ-dependent signaling to lipodystrophy	74
Publisher Correction: Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells	73
Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing	73
Decoding the zebrafish genome	73
Engineering extrachromosomal DNA	73
Author Correction: Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains	72
Charles David Allis (1951–2023)	72
Author Correction: Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk	72
How cauliflower got its curd	71
Variably methylated retrotransposons are refractory to a range of environmental perturbations	71
Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer’s disease	71
Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology	70
The Ruminant Telomere-to-Telomere (RT2T) Consortium	70
Activating the dark genome to illuminate cancer vaccine targets	70
The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes	70
Author Correction: LINE-1 transcription activates long-range gene expression	69
Structural polymorphism and diversity of human segmental duplications	69
Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm	68
SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs	68
Pervasive biases in proxy genome-wide association studies based on parental history of Alzheimer’s disease	68
Borzoi decodes the complex DNA signals governing gene regulation	68
Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders	67
Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes	67
Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution	66
Aberrant splicing prediction across human tissues	66
Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles	65
The genomic landscape of pediatric acute lymphoblastic leukemia	65
Gene discovery and biological insights into anxiety disorders from a large-scale multi-ancestry genome-wide association study	65
Multi-ancestry genome-wide association study of major depression aids locus discovery, fine mapping, gene prioritization and causal inference	65
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	65
RNA m6A regulates transcription via DNA demethylation and chromatin accessibility	65
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer	64
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses	64
Annotating and prioritizing human non-coding variants with RegulomeDB v.2	64
Large-scale integration of the plasma proteome with genetics and disease	64
CHOIR improves significance-based detection of cell types and states from single-cell data	63
RNA Pol II enters the ring of cohesin-mediated loop extrusion	63
CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses	63
Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma	62
Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis	62
Genetic analysis of right heart structure and function in 40,000 people	62
Multiomic analysis of homologous recombination-deficient end-stage high-grade serous ovarian cancer	62
Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer	61
New insights into the genetic etiology of Alzheimer’s disease and related dementias	61
Genome-wide prediction of disease variant effects with a deep protein language model	61
Publisher Correction: Functional innovation through new genes as a general evolutionary process	60
A call for spatial omics submissions	60
The evolving cancer genome	60
Single-cell mapping of HTT somatic repeat expansions	59
A mass balance principle for finding loose ends in cancer genomes	59
Integration of genetic data with dynamic gene regulatory elements identifies autoimmune effector cell states	59
A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk	58
Publisher Correction: Epigenomic contributions to tumor cell heterogeneity and plasticity	58
Single-cell technologies meet Hi-C	58
Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis	58
Stepwise de novo establishment of inactive X chromosome architecture in early development	58
Metastable epialleles are stable in their instability	58
Publisher Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors	57
Prevalent putative chromatin bivalency and partial resetting of H3K27me3 in plant sperm	57
Brain metastasis prediction	57
DNA loop extrusion is asymmetric but can switch direction	57
Blood DNA virome associates with autoimmune diseases and COVID-19	57
Disentangling extrachromosomal circular DNA heterogeneity in single cells with scEC&T-seq	56
Connecting clinical and genetic heterogeneity in ADHD	55
Author Correction: Bipotent transitional liver progenitor cells contribute to liver regeneration	55
Genetic mapping across autoimmune diseases reveals shared associations and mechanisms	55
Single-mitosis dissection of acute and chronic DNA mutagenesis and repair	55