PLoS Genetics

Article	Citations
A more accurate method for colocalisation analysis allowing for multiple causal variants	193
Fine-mapping from summary data with the “Sum of Single Effects” model	139
MicroRNAs are minor constituents of extracellular vesicles that are rarely delivered to target cells	132
Combining the strengths of inverse-variance weighting and Egger regression in Mendelian randomization using a mixture of regressions model	128
Evaluation of polygenic prediction methodology within a reference-standardized framework	120
Genotype imputation using the Positional Burrows Wheeler Transform	104
Stability of SARS-CoV-2 phylogenies	89
Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance	88
OsMADS23 phosphorylated by SAPK9 confers drought and salt tolerance by regulating ABA biosynthesis in rice	86
Deleterious mutation accumulation and the long-term fate of chromosomal inversions	81
Nationwide germline whole genome sequencing of 198 consecutive pediatric cancer patients reveals a high incidence of cancer prone syndromes	77
Runx2 is essential for the transdifferentiation of chondrocytes into osteoblasts	73
Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes	71
A powerful method for pleiotropic analysis under composite null hypothesis identifies novel shared loci between Type 2 Diabetes and Prostate Cancer	70
Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)	69
Runx1 is a central regulator of osteogenesis for bone homeostasis by orchestrating BMP and WNT signaling pathways	66
Creating artificial human genomes using generative neural networks	64
Defects in the cytoplasmic assembly of axonemal dynein arms cause morphological abnormalities and dysmotility in sperm cells leading to male infertility	63
The genomic ecosystem of transposable elements in maize	63
Estimating FST and kinship for arbitrary population structures	62
The impact of age on genetic risk for common diseases	62
WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat	60
Selection of GmSWEET39 for oil and protein improvement in soybean	59
Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae	59
α-synuclein impairs autophagosome maturation through abnormal actin stabilization	57

Changes in both trans- and cis-regulatory elements mediate insecticide resistance in a lepidopteron pest, Spodoptera exigua	57
Selective sorting of ancestral introgression in maize and teosinte along an elevational cline	57
Significant sparse polygenic risk scores across 813 traits in UK Biobank	57
Power analysis of transcriptome-wide association study: Implications for practical protocol choice	56
Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm	55
Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus	55
TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage	54
Recombination events are concentrated in the spike protein region of Betacoronaviruses	52
Estimation of causal effects of a time-varying exposure at multiple time points through multivariable mendelian randomization	52
CSF1R-dependent macrophages control postnatal somatic growth and organ maturation	51
Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria	50
MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies	50
Nicotinic acetylcholine receptor modulator insecticides act on diverse receptor subtypes with distinct subunit compositions	50
Identifying drug targets for neurological and psychiatric disease via genetics and the brain transcriptome	50
Steroid hormone ecdysone deficiency stimulates preparation for photoperiodic reproductive diapause	49
Gene regulatory effects of a large chromosomal inversion in highland maize	49
Innate immune signaling in Drosophila shifts anabolic lipid metabolism from triglyceride storage to phospholipid synthesis to support immune function	49
Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing	49
RNA editing at a limited number of sites is sufficient to prevent MDA5 activation in the mouse brain	49
ARID1A regulates R-loop associated DNA replication stress	47
Fine-tuning autophagy maximises lifespan and is associated with changes in mitochondrial gene expression in Drosophila	47
Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images	46
Sex-stratified genome-wide association study of multisite chronic pain in UK Biobank	46
Aurora kinase A is essential for meiosis in mouse oocytes	45
Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improves the power of transcriptome-wide association studies	45
Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA	44
PRSet: Pathway-based polygenic risk score analyses and software	44
Identifying causal variants by fine mapping across multiple studies	44
Diverse LXG toxin and antitoxin systems specifically mediate intraspecies competition in Bacillus subtilis biofilms	43
Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci	43
CRISPR gRNA phenotypic screening in zebrafish reveals pro-regenerative genes in spinal cord injury	43
The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila	43
Causal inference for heritable phenotypic risk factors using heterogeneous genetic instruments	43
Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link	42
The helper NLR immune protein NRC3 mediates the hypersensitive cell death caused by the cell-surface receptor Cf-4	42
NF-κB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1	42
Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation	41
A neuroendocrine pathway modulating osmotic stress in Drosophila	40
Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus	40
Indole-3-acetic acid is a physiological inhibitor of TORC1 in yeast	40
Repeated evolution of circadian clock dysregulation in cavefish populations	40
Novel Variance-Component TWAS method for studying complex human diseases with applications to Alzheimer’s dementia	40
A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics	39
Diversity and determinants of recombination landscapes in flowering plants	39
Inhibition of the de novo pyrimidine biosynthesis pathway limits ribosomal RNA transcription causing nucleolar stress in glioblastoma cells	39
On cross-ancestry cancer polygenic risk scores	39
Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering	38
Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data	38
Absence of YhdP, TamB, and YdbH leads to defects in glycerophospholipid transport and cell morphology in Gram-negative bacteria	38
ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing	36

Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative	36
Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution	35
Mosquito genomes are frequently invaded by transposable elements through horizontal transfer	35
MreC and MreD balance the interaction between the elongasome proteins PBP2 and RodA	35
Regulation of GSTu1-mediated insecticide resistance in Plutella xylostella by miRNA and lncRNA	35
The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic	35
A viral guide RNA delivery system for CRISPR-based transcriptional activation and heritable targeted DNA demethylation in Arabidopsis thaliana	34
PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer’s disease	34
Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals	34
Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology	34
Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster	34
The defense island repertoire of the Escherichia coli pan-genome	34
Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment	33
A genome-wide association study identifies 5 loci associated with frozen shoulder and implicates diabetes as a causal risk factor	33
Genetic analysis of the septal peptidoglycan synthase FtsWI complex supports a conserved activation mechanism for SEDS-bPBP complexes	33
Genetic sensitivity analysis: Adjusting for genetic confounding in epidemiological associations	33
Identification of a gustatory receptor tuned to sinigrin in the cabbage butterfly Pieris rapae	33
A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle	33
Multivariable G-E interplay in the prediction of educational achievement	33
A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis	32
CRISPR/Cas9 modified An. gambiae carrying kdr mutation L1014F functionally validate its contribution in insecticide resistance and combined effect with metabolic enzymes	32
Loss of hepatocyte cell division leads to liver inflammation and fibrosis	32
Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen	32
MAPK-mediated transcription factor GATAd contributes to Cry1Ac resistance in diamondback moth by reducing PxmALP expression	31
Human genetic admixture	31
Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis	31
The genomics of rapid climatic adaptation and parallel evolution in North American house mice	31
UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin	31
Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription–replication conflict regions	31
The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection	31
ANGPTL8 protein-truncating variant associated with lower serum triglycerides and risk of coronary disease	30
A locus at 19q13.31 significantly reduces the ApoE ε4 risk for Alzheimer’s Disease in African Ancestry	30
Tetrahymena meiosis: Simple yet ingenious	30
To “Z” or not to “Z”: Z-RNA, self-recognition, and the MDA5 helicase	30
Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies	30
DNA methylation-mediated modulation of rapid desiccation tolerance acquisition and dehydration stress memory in the resurrection plant Boea hygrometrica	30
Relaxing parametric assumptions for non-linear Mendelian randomization using a doubly-ranked stratification method	30
The capacity of origins to load MCM establishes replication timing patterns	29
High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest	29
Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea	29
A novel type of colistin resistance genes selected from random sequence space	29
A conserved role for AMP-activated protein kinase in NGLY1 deficiency	28
A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome	28
MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity	28
Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis	28
Translational repression of NMD targets by GIGYF2 and EIF4E2	28
Opposing functions of Fng1 and the Rpd3 HDAC complex in H4 acetylation in Fusarium graminearum	28
Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination	28
Resistance to a CRISPR-based gene drive at an evolutionarily conserved site is revealed by mimicking genotype fixation	28
3D genome evolution and reorganization in the Drosophila melanogaster species group	28
Shared genetic loci between depression and cardiometabolic traits	27
The native cistrome and sequence motif families of the maize ear	27
Lotus japonicus karrikin receptors display divergent ligand-binding specificities and organ-dependent redundancy	27
Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles	27
Split versions of Cleave and Rescue selfish genetic elements for measured self limiting gene drive	27
RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays	27
Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales	27
The Vibrio cholerae Seventh Pandemic Islands act in tandem to defend against a circulating phage	27
DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress	27
Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development	26
The clarifying role of time series data in the population genetics of HIV	26
Nuclear lipid droplets and nuclear damage in Caenorhabditis elegans	26
Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification	26
Trehalose and α-glucan mediate distinct abiotic stress responses in Pseudomonas aeruginosa	26
EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time	26
The Candida glabrata Upc2A transcription factor is a global regulator of antifungal drug resistance pathways	26
Pch2 orchestrates the meiotic recombination checkpoint from the cytoplasm	26
Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics	26
Genome-wide association study of fish oil supplementation on lipid traits in 81,246 individuals reveals new gene-diet interaction loci	26
Proteome-wide Mendelian randomization identifies causal links between blood proteins and severe COVID-19	26
Machine learning to predict the source of campylobacteriosis using whole genome data	26
The impact of global and local Polynesian genetic ancestry on complex traits in Native Hawaiians	26
Abnormal global alternative RNA splicing in COVID-19 patients	26
The DNA damage response is required for oocyte cyst breakdown and follicle formation in mice	25
The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes	25
HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation	25
The conserved transmembrane protein TMEM-39 coordinates with COPII to promote collagen secretion and regulate ER stress response	25
The Species-Specific Acquisition and Diversification of a K1-like Family of Killer Toxins in Budding Yeasts of the Saccharomycotina	25
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis	25
Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae	25

Spinal cord extracts of amyotrophic lateral sclerosis spread TDP-43 pathology in cerebral organoids	25
Forward genetics in Wolbachia: Regulation of Wolbachia proliferation by the amplification and deletion of an addictive genomic island	25
RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility	25
A transient apical extracellular matrix relays cytoskeletal patterns to shape permanent acellular ridges on the surface of adult C. elegans	25
Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast	24
Consequences of adaptation of TAL effectors on host susceptibility to Xanthomonas	24
RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics	24
Using genetic variation to disentangle the complex relationship between food intake and health outcomes	24
Toxic Y chromosome: Increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome	24
Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle	24
An atypical NLR protein modulates the NRC immune receptor network in Nicotiana benthamiana	24
Loss of YhcB results in dysregulation of coordinated peptidoglycan, LPS and phospholipid synthesis during Escherichia coli cell growth	24
The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo	24
Double drives and private alleles for localised population genetic control	24
Abnormal accumulation of lipid droplets in neurons induces the conversion of alpha-Synuclein to proteolytic resistant forms in a Drosophila model of Parkinson’s disease	24
Genome-scale CRISPR screening for modifiers of cellular LDL uptake	24
Tau, XMAP215/Msps and Eb1 co-operate interdependently to regulate microtubule polymerisation and bundle formation in axons	24
Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome	24
A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster	24
Genome-wide association meta-analysis identifies pleiotropic risk loci for aerodigestive squamous cell cancers	24
KCTD19 and its associated protein ZFP541 are independently essential for meiosis in male mice	23
miRNA-mediated loss of m6A increases nascent translation in glioblastoma	23
Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans	23
Light affects behavioral despair involving the clock gene Period 1	23
The FASTK family proteins fine-tune mitochondrial RNA processing	23
Deficiency of ASGR1 in pigs recapitulates reduced risk factor for cardiovascular disease in humans	23
Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage	23
Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut	23
The genome variation and developmental transcriptome maps reveal genetic differentiation of skeletal muscle in pigs	23
Circadian control of heparan sulfate levels times phagocytosis of amyloid beta aggregates	23
FIONA1-mediated methylation of the 3’UTR of FLC affects FLC transcript levels and flowering in Arabidopsis	23
Indian genetic heritage in Southeast Asian populations	23
Xrp1 and Irbp18 trigger a feed-forward loop of proteotoxic stress to induce the loser status	23
Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae	23
Vestigial mediates the effect of insulin signaling pathway on wing-morph switching in planthoppers	23
Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers	23
Polygenic adaptation of rosette growth in Arabidopsis thaliana	22
Ether lipid deficiency disrupts lipid homeostasis leading to ferroptosis sensitivity	22
Transposable element landscapes in aging Drosophila	22
Endothelial lipase mediates efficient lipolysis of triglyceride-rich lipoproteins	22
Sense-overlapping lncRNA as a decoy of translational repressor protein for dimorphic gene expression	22
Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies	22
Synaptonemal Complex dimerization regulates chromosome alignment and crossover patterning in meiosis	22
Natural variation in the sequestosome-related gene, sqst-5, underlies zinc homeostasis in Caenorhabditis elegans	22
The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics	22
Cell competition is driven by Xrp1-mediated phosphorylation of eukaryotic initiation factor 2α	22
Genome-wide analyses of light-regulated genes in Aspergillus nidulans reveal a complex interplay between different photoreceptors and novel photoreceptor functions	22
Salt responsive alternative splicing of a RING finger E3 ligase modulates the salt stress tolerance by fine-tuning the balance of COP9 signalosome subunit 5A	22
The nitrate-inducible NAC transcription factor NAC056 controls nitrate assimilation and promotes lateral root growth in Arabidopsis thaliana	22
Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense	22
Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach	22
A spectrum of verticality across genes	22
How did the guppy Y chromosome evolve?	22
Natural variation in temperature-modulated immunity uncovers transcription factor bHLH059 as a thermoresponsive regulator in Arabidopsis thaliana	22
RanBP2/Nup358 enhances miRNA activity by sumoylating Argonautes	22
Low immunogenicity of common cancer hot spot mutations resulting in false immunogenic selection signals	22
Inferring causal direction between two traits in the presence of horizontal pleiotropy with GWAS summary data	22
Pleiotropy method reveals genetic overlap between orofacial clefts at multiple novel loci from GWAS of multi-ethnic trios	22
Inducible expression of (pp)pGpp synthetases in Staphylococcus aureus is associated with activation of stress response genes	22
Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density	22
Genes in human obesity loci are causal obesity genes in C. elegans	21
Krüppel-like factor 15 integrated autophagy and gluconeogenesis to maintain glucose homeostasis under 20-hydroxyecdysone regulation	21
A MYB4-MAN3-Mannose-MNB1 signaling cascade regulates cadmium tolerance in Arabidopsis	21
Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network	21
Sugar inhibits brassinosteroid signaling by enhancing BIN2 phosphorylation of BZR1	21
A degron-based strategy reveals new insights into Aurora B function in C. elegans	21
The velvet protein Vel1 controls initial plant root colonization and conidia formation for xylem distribution in Verticillium wilt	21
Gtsf1 is essential for proper female sex determination and transposon silencing in the silkworm, Bombyx mori	21
An autoregulatory negative feedback loop controls thermomorphogenesis in Arabidopsis	21
Glucocerebrosidase reduces the spread of protein aggregation in a Drosophila melanogaster model of neurodegeneration by regulating proteins trafficked by extracellular vesicles	21
Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation	21
Dynamic neurogenomic responses to social interactions and dominance outcomes in female paper wasps	21
Identification of common predisposing loci to hematopoietic cancers in four dog breeds	21
Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii	21
The H3.3K27M oncohistone affects replication stress outcome and provokes genomic instability in pediatric glioma	21
Multiple sensors provide spatiotemporal oxygen regulation of gene expression in a Rhizobium-legume symbiosis	21
The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency	21
NIGT1 family proteins exhibit dual mode DNA recognition to regulate nutrient response-associated genes in Arabidopsis	20
Viral protein instability enhances host-range evolvability	20
Strategies to investigate and mitigate collider bias in genetic and Mendelian randomisation studies of disease progression	20
Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health	20
Evolutionary dynamics of the human pseudoautosomal regions	20
Regulation of gliotoxin biosynthesis and protection in Aspergillus species	20
Multitrait GWAS to connect disease variants and biological mechanisms	20
Aberrant regulation of a poison exon caused by a non-coding variant in a mouse model of Scn1a-associated epileptic encephalopathy	20
The CovR regulatory network drives the evolution of Group B Streptococcus virulence	20
Genomic and transcriptomic landscape of conjunctival melanoma	20
Increased mitochondrial protein import and cardiolipin remodelling upon early mtUPR	20
A CENH3 mutation promotes meiotic exit and restores fertility in SMG7-deficient Arabidopsis	20
MYB44-ENAP1/2 restricts HDT4 to regulate drought tolerance in Arabidopsis	20
Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology	20
Essential gene acquisition destabilizes plasmid inheritance	20
Perspectives on rigor and reproducibility in single cell genomics	20
AMPK-dependent and -independent coordination of mitochondrial function and muscle fiber type by FNIP1	20
Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents	20