Nature Genetics

(The TQCC of Nature Genetics is 52. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-02-01 to 2024-02-01.)
New insights into the genetic etiology of Alzheimer’s disease and related dementias618
Large-scale association analyses identify host factors influencing human gut microbiome composition576
Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology565
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis561
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression513
A single-cell and spatially resolved atlas of human breast cancers487
A cross-population atlas of genetic associations for 220 human phenotypes468
Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis417
Computationally efficient whole-genome regression for quantitative and binary traits405
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing394
A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease392
Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer347
Genetics of 35 blood and urine biomarkers in the UK Biobank343
Cancer therapy shapes the fitness landscape of clonal hematopoiesis338
The trans-ancestral genomic architecture of glycemic traits305
Large-scale integration of the plasma proteome with genetics and disease301
Base-resolution models of transcription-factor binding reveal soft motif syntax296
Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases285
Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics278
Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing275
Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases261
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation257
The landscape of viral associations in human cancers250
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition250
Genomic landscape of lung adenocarcinoma in East Asians248
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers243
Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses242
Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction241
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes240
Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease239
Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic237
Comprehensive molecular characterization of mitochondrial genomes in human cancers233
Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement224
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro223
Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution220
Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication214
Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation209
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases207
Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity206
Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank202
Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology201
Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation199
Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease196
Minimal phenotyping yields genome-wide association signals of low specificity for major depression194
Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor191
Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases188
An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci187
Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease186
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals181
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation180
The DNA methylation landscape of advanced prostate cancer178
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease175
Improving polygenic prediction in ancestrally diverse populations175
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture174
Efficient phasing and imputation of low-coverage sequencing data using large reference panels171
Quantifying genetic effects on disease mediated by assayed gene expression levels171
Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia171
A compendium of uniformly processed human gene expression and splicing quantitative trait loci170
Functionally informed fine-mapping and polygenic localization of complex trait heritability170
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer170
Trans-ancestry analysis reveals genetic and nongenetic associations with COVID-19 susceptibility and severity168
Genomic characterization of human brain metastases identifies drivers of metastatic lung adenocarcinoma163
Triticum population sequencing provides insights into wheat adaptation163
Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2160
Prostate cancer reactivates developmental epigenomic programs during metastatic progression160
Common genetic variants and modifiable risk factors underpin hypertrophic cardiomyopathy susceptibility and expressivity158
Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution156
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication154
Cas9 activates the p53 pathway and selects for p53-inactivating mutations153
DNA methylation disruption reshapes the hematopoietic differentiation landscape153
A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes153
The GWAS Diversity Monitor tracks diversity by disease in real time152
Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors150
Identification of cancer driver genes based on nucleotide context150
Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect149
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort148
N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2147
Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis147
A generalized linear mixed model association tool for biobank-scale data145
Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits140
Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis140
Genome-wide selection and genetic improvement during modern maize breeding137
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation137
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale135
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism134
Polygenic basis and biomedical consequences of telomere length variation132
Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction132
The association between tumor mutational burden and prognosis is dependent on treatment context132
Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility129
Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy129
Guidelines for human gene nomenclature127
Global landscape of SARS-CoV-2 genomic surveillance and data sharing126
Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential126
Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data126
Haplotype-resolved genome analyses of a heterozygous diploid potato125
Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants125
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles125
Exploring and visualizing large-scale genetic associations by using PheWeb123
Regulation of single-cell genome organization into TADs and chromatin nanodomains123
A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis123
Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes122
Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma120
Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects120
Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements119
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome119
Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power119
Genome-wide association analyses of post-traumatic stress disorder and its symptom subdomains in the Million Veteran Program118
Evaluating and improving heritability models using summary statistics117
Genetic analyses identify widespread sex-differential participation bias115
Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts114
Systematic identification of silencers in human cells114
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project114
Landscape of G-quadruplex DNA structural regions in breast cancer113
A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection112
Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia112
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment112
A cross-platform approach identifies genetic regulators of human metabolism and health111
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer109
An integrated framework for local genetic correlation analysis107
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion107
Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts106
A map of transcriptional heterogeneity and regulatory variation in human microglia105
High-definition likelihood inference of genetic correlations across human complex traits105
Complex genetic signatures in immune cells underlie autoimmunity and inform therapy104
Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning104
Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium103
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability102
A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo101
Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development100
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment100
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis99
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development99
cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing98
A quantitative genomics map of rice provides genetic insights and guides breeding98
Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk96
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response95
Mammalian SWI/SNF continuously restores local accessibility to chromatin95
Comprehensive characterization of protein–protein interactions perturbed by disease mutations95
Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response95
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis94
RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells94
Mutations disrupting neuritogenesis genes confer risk for cerebral palsy94
APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis94
Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores93
CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response93
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer93
Acute BAF perturbation causes immediate changes in chromatin accessibility93
Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states92
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers92
Identifying genetic variants underlying phenotypic variation in plants without complete genomes91
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders91
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes90
Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies90
The genomic landscape of pediatric acute lymphoblastic leukemia89
NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing89
Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome89
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer89
The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility89
Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin88
Genetic architecture of 11 major psychiatric disorders at biobehavioral, functional genomic and molecular genetic levels of analysis87
Genomic analyses implicate noncoding de novo variants in congenital heart disease87
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer86
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains86
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus86
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY185
Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes85
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens83
Alternative splicing during mammalian organ development83
Insights into the genetic architecture of the human face83
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes82
Breast tumor microenvironment structures are associated with genomic features and clinical outcome82
Selective Mediator dependence of cell-type-specifying transcription81
Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies81
Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease81
Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms80
Sequence determinants of human gene regulatory elements80
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses80
Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci80
Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals79
Differences between germline genomes of monozygotic twins79
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes78
Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars78
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities78
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics77
The mutational signature profile of known and suspected human carcinogens in mice77
Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes77
Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments77
An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability76
TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers76
Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson’s disease76
Genome-wide association analyses highlight etiological differences underlying newly defined subtypes of diabetes76
Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option76
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar75
Increased somatic mutation burdens in normal human cells due to defective DNA polymerases75
Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos75
Deep learning enables genetic analysis of the human thoracic aorta75
The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts75
Genomic and evolutionary classification of lung cancer in never smokers75
Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure73
Privacy challenges and research opportunities for genomic data sharing73
A first-generation pediatric cancer dependency map72
Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer72
Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips72
European maize genomes highlight intraspecies variation in repeat and gene content71
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement71
Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation71
Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-1970
The UCSC SARS-CoV-2 Genome Browser70
Characterizing the ecological and evolutionary dynamics of cancer70
The genomic basis of geographic differentiation and fiber improvement in cultivated cotton69
Subclonal reconstruction of tumors by using machine learning and population genetics69
H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos69
Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases69
DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers68
Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains68
Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance68
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer67
The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste66
A sequence-based global map of regulatory activity for deciphering human genetics66
Cohesin and CTCF control the dynamics of chromosome folding66
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank66
The critical roles of somatic mutations and environmental tumor-promoting agents in cancer risk66
Systematic reconstruction of cellular trajectories across mouse embryogenesis65
GestaltMatcher facilitates rare disease matching using facial phenotype descriptors64
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence64
Enhancing African orphan crops with genomics63
Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells63
Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction62
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response61
Genomic insights into the origin, domestication and diversification of Brassica juncea61
Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer61
Evolutionary dynamics of neoantigens in growing tumors60
An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank60
A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation60
Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers60
Cross-species chromatin interactions drive transcriptional rewiring in Epstein–Barr virus–positive gastric adenocarcinoma59
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics59
Recent ultra-rare inherited variants implicate new autism candidate risk genes58
Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition57
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex57
The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism57
Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS57
Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants57
Liability threshold modeling of case–control status and family history of disease increases association power56
Sex differences in genetic architecture in the UK Biobank56
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease56
Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale56
Transcription imparts architecture, function and logic to enhancer units56
Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning56
Exome sequencing in bipolar disorder identifies AKAP11 as a risk gene shared with schizophrenia55