Nature Genetics

Article	Citations
Deciphering the evolutionary dynamics of extrachromosomal DNA in human cancer	1665
Mapping dog behavior	1611
Epigenetic memory in 3D	1334
Temperature-induced RNA recoding in octopus	1091
Toward advances in retinoblastoma genetics in Kenya	1041
DNA polymerase ε produces elevated C-to-T mutations at methylated CpG dinucleotides	775
Role of gene–gene loops in fine-tuning cross-regulation	597
Problems with dystopian representations in genetic futurism	521
Machine learning drives genetic discovery for binge eating disorder	481
Identifying individuals at extreme risk of venous thromboembolism using polygenic risk scores	477
GeneMAP enables discovery of metabolic gene function	450
Understanding liver repair through space and time	445
Complete genomes of six ape species	444
An atlas of genetic determinants of forearm fracture	442
Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells	427
Renal plasticity revealed through reversal of polycystic kidney disease in mice	409
Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases	406
In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization	364
Mitochondrial DNA mosaicism in normal human somatic cells	353
Dominant variants in major spliceosome U4 and U5 small nuclear RNA genes cause neurodevelopmental disorders through splicing disruption	343
Genome-wide RNA polymerase stalling shapes the transcriptome during aging	342
Rare coding variant analysis for human diseases across biobanks and ancestries	319
Reactivation of embryonic genetic programs in tissue regeneration and disease	300
The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes	281
Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize	277

Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea	277
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome	275
Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness	268
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals	265
A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation	265
Dynamics of DNA hydroxymethylation and methylation during mouse embryonic and germline development	263
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence	262
Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways	258
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease	257
A biology-aware mutation rate model for human germline	256
Shared genetics of substance use disorders	250
Genes influence complex traits through environments that vary between geographic regions	235
Somatic mutations in the stomach	227
When RNA methylation meets DNA methylation	225
Identification of two intrinsic epithelial subtypes of colorectal cancer	213
Author Correction: The NAT1–bHLH110–CER1/CER1L module regulates heat stress tolerance in rice	204
Bayesian estimation of gene constraint from an evolutionary model with gene features	201
APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer	198
Interpreting cis-regulatory interactions from large-scale deep neural networks	197
Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon	196
Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice	192
K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas	191
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders	190
Synthetic surrogates improve power for genome-wide association studies of partially missing phenotypes in population biobanks	189
Finding causal genes underlying risk for coronary artery disease	181
Epigenomic contributions to tumor cell heterogeneity and plasticity	181
Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction	181
Author Correction: EMPReSS: standardized phenotype screens for functional annotation of the mouse genome	180
Genetic and non-genetic HLA disruption is widespread in lung and breast tumors	177
Finding cancer mutagens using signature analysis	174
Safeguard repressor locks hepatocyte identity and blocks liver cancer	173
Author Correction: Pangenome graphs and their applications in biodiversity genomics	173
The Federated European Genome–Phenome Archive as a global network for sharing human genomics data	170
Histone gene editing probes functions of H3K27 modifications in mammals	166
Human subcutaneous and visceral adipocyte atlases uncover classical and nonclassical adipocytes and depot-specific patterns	166
A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen	166
An alternative model for maternal mtDNA inheritance	165
Systematic prioritization of functional variants and effector genes underlying colorectal cancer risk	161
HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription	159
Establishing African genomics and bioinformatics programs through annual regional workshops	158
Increasing diversity in genomics requires investment in equitable partnerships and capacity building	156
RNA polymerase II dynamics shape enhancer–promoter interactions	155
HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors	155
Meta-analysis of genome-wide associations and polygenic risk prediction for atrial fibrillation in more than 180,000 cases	154
Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits	153
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment	152
Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors	150
Single duplex DNA sequencing with CODEC detects mutations with high sensitivity	148
H3K27me3 conditions chemotolerance in triple-negative breast cancer	147
APOBEC mutagenesis is a common process in normal human small intestine	147

Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function	146
A generalized linear mixed model association tool for biobank-scale data	145
Natural variation in SBRR1 shows high potential for sheath blight resistance breeding in rice	145
Redefining teleost phylogeny	141
Mutation rates across species	140
Somatic recombination of repetitive elements	137
An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs	137
Equity, ethics and the promise of partnership in genomic medicine	136
Defining and pursuing diversity in human genetic studies	135
Sarcoma predisposition	135
Genetic and biological insights into spontaneous coronary artery dissection	134
Sox2 expression can be regulated across boundaries generated by CTCF–cohesin loops	134
Polygenic basis for seedless grapes	133
Epigenetic scars of Brca1 loss point toward breast cancer cell of origin	133
The genetic origins of multiple sclerosis	133
Defining genome access of transcription factors	132
Indirect paths from genetics to education	130
Planting the milestones of human genetics in Senegal	129
Improving estimates of loss-of-function constraint for short genes	129
Mathematical modeling of neuroblastoma associates evolutionary patterns with outcomes	128
Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance	127
Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition	127
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements	126
Integrating population genetics, stem cell biology and cellular genomics to study complex human diseases	126
Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish	124
Coordinated function of paired NLRs confers Yr84-mediated stripe rust resistance in wheat	123
Schizophrenia risk conferred by rare protein-truncating variants is conserved across diverse human populations	121
Federated analysis of autosomal recessive coding variants in 29,745 developmental disorder patients from diverse populations	119
Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas	117
A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription	117
Precise modulation of transcription factor levels identifies features underlying dosage sensitivity	117
Disease prediction with multi-omics and biomarkers empowers case–control genetic discoveries in the UK Biobank	116
New genes helped acorn barnacles adapt to a sessile lifestyle	116
Deep learning-based phenotype imputation on population-scale biobank data increases genetic discoveries	115
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells	115
Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits	114
Systematic perturbation screens identify regulators of inflammatory macrophage states and a role for TNF mRNA m6A modification	114
SBRR1-R variant regulates sheath blight resistance in rice	114
Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution	114
Why genomic diversity should not be framed by census alone	113
Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes	112
A complete telomere-to-telomere assembly of the maize genome	111
Consensus prediction of cell type labels in single-cell data with popV	111
Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype	111
GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture	110
The language of genetics	109
Genomics of the oldest domesticated wheat	107
Sequencing genetic and epigenetic bases	107
High-throughput screening identifies modulators of gene bursting	106
In silico saturation mutagenesis of cancer genes	106
Profiling oncogenic extra-chromosomal DNA in cancer	106
Transposable element evolution in mammals	106
Publisher Correction: A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	105
Deciphering the regulatory logic of a chromatin domain boundary	104
Genetics of sexually dimorphic adipose distribution in humans	103
Disrupted β-cell-specific gene silencing causes congenital hyperinsulinism	102
Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells	102
Base editing as a therapeutic strategy for somatic repeat expansion diseases	102
Extraordinary collateral mutagenesis induced by CX-5461	101
Age-associated transcriptional stress due to accelerated elongation and increased stalling of RNAPII	100
Mapping interindividual dynamics of innate immune response at single-cell resolution	99
The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize	99
Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A–menin to bivalent promoters	99
KidneyGenAfrica, a pan-African partnership to deliver research and training excellence in genomics of kidney disease	97
Single-cell and spatial transcriptomics reveal mechanisms of radioresistance and immune escape in recurrent nasopharyngeal carcinoma	97
A single-cell transcriptome atlas of human euploid and aneuploid blastocysts	97
Human genetic diversity alters off-target outcomes of therapeutic gene editing	96
Epigenetic variation impacts individual differences in the transcriptional response to influenza infection	96
Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view	96
Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk	94
Bipotent transitional liver progenitor cells contribute to liver regeneration	93
Potential approaches to create ultimate genotypes in crops and livestock	93
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche	92
Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants	92
The elite haplotype OsGATA8-H coordinates nitrogen uptake and productive tiller formation in rice	92
A compendium of genetic regulatory effects across pig tissues	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	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	90

A ΔNp63–MED12 axis drives basal-like identity in pancreatic cancer	88
Potato genome diversity	88
A one-stop shop for 3D spatial transcriptomics	88
X chromosome dosage shapes renal cell carcinoma risk	87
Intermediate cells with activated JAK/STAT signaling in prostate regeneration and diseases	86
LINE1 mediates long-range DNA interactions	85
Publisher Correction: Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors	85
Applying compressed Perturb-seq to genetic screens	84
Converging evidence from exome sequencing and common variants implicates target genes for osteoporosis	84
Genome assembly of two allotetraploid cotton germplasms reveals mechanisms of somatic embryogenesis and enables precise genome editing	83
LDAK-KVIK performs fast and powerful mixed-model association analysis of quantitative and binary phenotypes	83
Understanding the genetic complexity of puberty timing across the allele frequency spectrum	83
Functional analysis of cancer-associated germline risk variants	83
Tumor heterogeneity impairs immunogenicity in mismatch repair deficient tumors	83
NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling	82
Pathogen perception and deception in plant immunity by kinase fusion proteins	82
Haplotype-resolved, gap-free genome assemblies provide insights into the divergence between Asian and European pears	82
Our ancestry dictates clonal architecture and skin cancer susceptibility	81
Genetic insights into depression	80
Decoding complex patterns of oncogene amplification	80
Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation	80
A single-cell-type transcriptomics map of human tissues	79
GWAS of random glucose in 476,326 individuals provide insights into diabetes pathophysiology, complications and treatment stratification	79
Cell-state-specific enhancer design in hematopoiesis	79
KDM4C shields breast cancer from the histone scissor cathepsin L	79
Genetic contribution to heterogeneity in type 2 diabetes	79
Author Correction: Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos	79
Deep learning model improves COPD risk prediction and gene discovery	78
Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution	78
Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking	77
The disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development	77
Mapping extrachromosomal DNA amplifications during cancer progression	77
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities	76
Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts	76
Wheat tandem kinase RWT4 directly binds a fungal effector to activate defense	75
Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea	74
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank	74
Exploring the genetic overlap between twelve psychiatric disorders	74
The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance	74
Most large structural variants in cancer genomes can be detected without long reads	74
A molecular map of T cell activation gives insights into immune disease	73
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes	73
DNA methylation provides molecular links underlying complex traits	73
Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk	73
Diverse mutations in autism-related genes and their expression in the developing brain	73
Publisher Correction: Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells	72
Engineering extrachromosomal DNA	72
Author Correction: Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk	72
Phospholipid modifier PLAAT3 links defective PPARγ-dependent signaling to lipodystrophy	72
How cauliflower got its curd	71
Author Correction: LINE-1 transcription activates long-range gene expression	70
Towards trustworthiness of precision medicine research for people with disabilities	69
Genome synteny reveals hidden enhancer conservation	69
CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses	68
Activating the dark genome to illuminate cancer vaccine targets	68
Author Correction: Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains	68
Multiomic analysis of homologous recombination-deficient end-stage high-grade serous ovarian cancer	68
Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer	68
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
RNA Pol II enters the ring of cohesin-mediated loop extrusion	67
Charles David Allis (1951–2023)	65
Borzoi decodes the complex DNA signals governing gene regulation	65
The Ruminant Telomere-to-Telomere (RT2T) Consortium	64
Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution	64
Using large-scale population-based data to improve disease risk assessment of clinical variants	64
CHOIR improves significance-based detection of cell types and states from single-cell data	64
The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes	63
The future of polygenic risk scores in direct-to-consumer genomics	62
Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles	61
Genetic analysis of right heart structure and function in 40,000 people	61
SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs	61
Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing	60
RNA m6A regulates transcription via DNA demethylation and chromatin accessibility	60
Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes	60
Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer’s disease	60
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer	60
Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm	60
Decoding the zebrafish genome	60
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex	60
Aberrant splicing prediction across human tissues	59
Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders	59
Pervasive biases in proxy genome-wide association studies based on parental history of Alzheimer’s disease	59
Annotating and prioritizing human non-coding variants with RegulomeDB v.2	59
Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma	59
Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis	59
New insights into the genetic etiology of Alzheimer’s disease and related dementias	59
Gene discovery and biological insights into anxiety disorders from a large-scale multi-ancestry genome-wide association study	59
Structural polymorphism and diversity of human segmental duplications	58
Genome-wide prediction of disease variant effects with a deep protein language model	58
Multi-ancestry genome-wide association study of major depression aids locus discovery, fine mapping, gene prioritization and causal inference	58
Large-scale integration of the plasma proteome with genetics and disease	58
The evolving cancer genome	58
The genomic landscape of pediatric acute lymphoblastic leukemia	58
Publisher Correction: Functional innovation through new genes as a general evolutionary process	57
Single-cell mapping of HTT somatic repeat expansions	57