Nature Genetics

Papers
(The median citation count of Nature Genetics is 9. 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 2020-03-01 to 2024-03-01.)
ArticleCitations
New insights into the genetic etiology of Alzheimer’s disease and related dementias664
Large-scale association analyses identify host factors influencing human gut microbiome composition633
Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology593
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis581
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression550
A single-cell and spatially resolved atlas of human breast cancers509
A cross-population atlas of genetic associations for 220 human phenotypes507
Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis427
Computationally efficient whole-genome regression for quantitative and binary traits426
A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease409
Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer363
Genetics of 35 blood and urine biomarkers in the UK Biobank350
Cancer therapy shapes the fitness landscape of clonal hematopoiesis346
The trans-ancestral genomic architecture of glycemic traits325
Large-scale integration of the plasma proteome with genetics and disease325
Base-resolution models of transcription-factor binding reveal soft motif syntax306
Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing292
Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases291
Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics290
Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases276
The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation267
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers256
Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease250
Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses249
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes248
Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic247
Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction245
Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation233
Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro232
Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement231
Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication224
Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution224
Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology212
Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity212
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases210
Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank204
Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation201
An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci198
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals197
Minimal phenotyping yields genome-wide association signals of low specificity for major depression197
Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease196
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation195
Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor195
Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease191
Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases190
The DNA methylation landscape of advanced prostate cancer186
Improving polygenic prediction in ancestrally diverse populations184
Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture183
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease180
Quantifying genetic effects on disease mediated by assayed gene expression levels177
Functionally informed fine-mapping and polygenic localization of complex trait heritability177
A compendium of uniformly processed human gene expression and splicing quantitative trait loci176
Trans-ancestry analysis reveals genetic and nongenetic associations with COVID-19 susceptibility and severity175
Efficient phasing and imputation of low-coverage sequencing data using large reference panels174
Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia173
Triticum population sequencing provides insights into wheat adaptation171
Prostate cancer reactivates developmental epigenomic programs during metastatic progression168
Genomic characterization of human brain metastases identifies drivers of metastatic lung adenocarcinoma167
Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution163
Cas9 activates the p53 pathway and selects for p53-inactivating mutations160
Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2160
Common genetic variants and modifiable risk factors underpin hypertrophic cardiomyopathy susceptibility and expressivity160
Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort159
The GWAS Diversity Monitor tracks diversity by disease in real time158
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication158
Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors158
A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes157
A generalized linear mixed model association tool for biobank-scale data156
DNA methylation disruption reshapes the hematopoietic differentiation landscape154
Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect152
N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2150
Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer’s disease pathogenesis149
Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis146
Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits144
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism144
Genome-wide selection and genetic improvement during modern maize breeding141
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation141
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale138
Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants137
Polygenic basis and biomedical consequences of telomere length variation137
Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction136
The association between tumor mutational burden and prognosis is dependent on treatment context133
Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility132
Global landscape of SARS-CoV-2 genomic surveillance and data sharing132
Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data132
Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy131
Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles131
Haplotype-resolved genome analyses of a heterozygous diploid potato130
Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects129
Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential129
Complex genetic signatures in immune cells underlie autoimmunity and inform therapy129
Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome127
Guidelines for human gene nomenclature127
Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes127
A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis124
Regulation of single-cell genome organization into TADs and chromatin nanodomains124
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project124
Exploring and visualizing large-scale genetic associations by using PheWeb123
Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma123
Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements121
Evaluating and improving heritability models using summary statistics121
Landscape of G-quadruplex DNA structural regions in breast cancer120
Genome-wide association analyses of post-traumatic stress disorder and its symptom subdomains in the Million Veteran Program120
Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power120
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment119
Genetic analyses identify widespread sex-differential participation bias118
Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts116
Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia115
A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection112
A cross-platform approach identifies genetic regulators of human metabolism and health111
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion110
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer110
An integrated framework for local genetic correlation analysis110
Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts108
High-definition likelihood inference of genetic correlations across human complex traits108
A map of transcriptional heterogeneity and regulatory variation in human microglia107
Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium106
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability106
Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning105
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis104
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response104
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development103
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer102
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment102
Mammalian SWI/SNF continuously restores local accessibility to chromatin102
cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing101
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis101
The genomic landscape of pediatric acute lymphoblastic leukemia100
Acute BAF perturbation causes immediate changes in chromatin accessibility100
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes100
A quantitative genomics map of rice provides genetic insights and guides breeding100
Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores98
Comprehensive characterization of protein–protein interactions perturbed by disease mutations98
RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells97
Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response97
Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk97
APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis96
Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states96
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders96
Identifying genetic variants underlying phenotypic variation in plants without complete genomes95
Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies95
CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response95
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers94
Mutations disrupting neuritogenesis genes confer risk for cerebral palsy94
Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome93
Genetic architecture of 11 major psychiatric disorders at biobehavioral, functional genomic and molecular genetic levels of analysis92
Genomic analyses implicate noncoding de novo variants in congenital heart disease92
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY191
Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies91
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer91
NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing91
WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation90
The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility90
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer90
Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin89
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus89
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens88
Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains88
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains87
Alternative splicing during mammalian organ development87
Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes87
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes87
Breast tumor microenvironment structures are associated with genomic features and clinical outcome86
Insights into the genetic architecture of the human face85
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses84
Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals83
Selective Mediator dependence of cell-type-specifying transcription83
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities83
Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease83
Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments82
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar82
Sequence determinants of human gene regulatory elements82
Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms82
Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars82
An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability81
Deep learning enables genetic analysis of the human thoracic aorta80
Increased somatic mutation burdens in normal human cells due to defective DNA polymerases79
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes79
TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers79
The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts79
Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos79
Privacy challenges and research opportunities for genomic data sharing79
Differences between germline genomes of monozygotic twins79
The mutational signature profile of known and suspected human carcinogens in mice79
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics78
Genome-wide association analyses highlight etiological differences underlying newly defined subtypes of diabetes78
Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson’s disease78
Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes77
Genomic and evolutionary classification of lung cancer in never smokers77
Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure76
Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option76
European maize genomes highlight intraspecies variation in repeat and gene content76
The genomic basis of geographic differentiation and fiber improvement in cultivated cotton74
A first-generation pediatric cancer dependency map73
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement73
H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos73
Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-1973
Characterizing the ecological and evolutionary dynamics of cancer73
Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer73
Single-cell transcriptomics identifies a distinct luminal progenitor cell type in distal prostate invagination tips73
The UCSC SARS-CoV-2 Genome Browser72
Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation72
A sequence-based global map of regulatory activity for deciphering human genetics72
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer72
Lymph node metastases develop through a wider evolutionary bottleneck than distant metastases71
Systematic reconstruction of cellular trajectories across mouse embryogenesis70
Subclonal reconstruction of tumors by using machine learning and population genetics70
The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste69
Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance69
The critical roles of somatic mutations and environmental tumor-promoting agents in cancer risk69
Cohesin and CTCF control the dynamics of chromosome folding69
DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers68
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease67
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank67
GestaltMatcher facilitates rare disease matching using facial phenotype descriptors67
Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells65
Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence65
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics65
A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation65
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response65
Genomic insights into the origin, domestication and diversification of Brassica juncea64
Enhancing African orphan crops with genomics63
Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction62
Evolutionary dynamics of neoantigens in growing tumors62
Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer61
Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers61
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention61
An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank61
Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis61
Recent ultra-rare inherited variants implicate new autism candidate risk genes61
A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex60
Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning60
Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS60
Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants60
Sex differences in genetic architecture in the UK Biobank60
Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition59
Cross-species chromatin interactions drive transcriptional rewiring in Epstein–Barr virus–positive gastric adenocarcinoma59
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity59
Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility59
Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways59
Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale58
Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals58
The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism58
Exome sequencing in bipolar disorder identifies AKAP11 as a risk gene shared with schizophrenia58
Transcription imparts architecture, function and logic to enhancer units58
A multi-tissue atlas of regulatory variants in cattle57
Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce57
Liability threshold modeling of case–control status and family history of disease increases association power57
Chromothripsis followed by circular recombination drives oncogene amplification in human cancer57
Renal plasticity revealed through reversal of polycystic kidney disease in mice56
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