PLoS Genetics

Article	Citations
RNA-directed DNA Methylation	171
A more accurate method for colocalisation analysis allowing for multiple causal variants	139
Phylogenetic background and habitat drive the genetic diversification of Escherichia coli	128
MicroRNAs are minor constituents of extracellular vesicles that are rarely delivered to target cells	126
Beyond SNP heritability: Polygenicity and discoverability of phenotypes estimated with a univariate Gaussian mixture model	123
Osteocalcin is necessary for the alignment of apatite crystallites, but not glucose metabolism, testosterone synthesis, or muscle mass	120
Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits	102
Evaluation of polygenic prediction methodology within a reference-standardized framework	99
Fine-mapping from summary data with the “Sum of Single Effects” model	96
Horizontal transmission and recombination maintain forever young bacterial symbiont genomes	87
Combining the strengths of inverse-variance weighting and Egger regression in Mendelian randomization using a mixture of regressions model	86
Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements	85
Genotype imputation using the Positional Burrows Wheeler Transform	84
Stability of SARS-CoV-2 phylogenies	83
An osteocalcin-deficient mouse strain without endocrine abnormalities	81
Deleterious mutation accumulation and the long-term fate of chromosomal inversions	75
Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph	75
OsMADS23 phosphorylated by SAPK9 confers drought and salt tolerance by regulating ABA biosynthesis in rice	73
Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance	73
A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank	73
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism	73
Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution	65
Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes	65
Nationwide germline whole genome sequencing of 198 consecutive pediatric cancer patients reveals a high incidence of cancer prone syndromes	64
Runx2 is essential for the transdifferentiation of chondrocytes into osteoblasts	63

Introns mediate post-transcriptional enhancement of nuclear gene expression in the green microalga Chlamydomonas reinhardtii	63
Osteocalcin promotes bone mineralization but is not a hormone	62
VolcanoFinder: Genomic scans for adaptive introgression	60
Creating artificial human genomes using generative neural networks	59
­­­­­­Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods	58
Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae	56
Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)	56
Estimating FST and kinship for arbitrary population structures	56
The impact of age on genetic risk for common diseases	56
Runx1 is a central regulator of osteogenesis for bone homeostasis by orchestrating BMP and WNT signaling pathways	56
The evolution and functional divergence of the histone H2B family in plants	55
The genomic ecosystem of transposable elements in maize	55
WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat	54
Selection of GmSWEET39 for oil and protein improvement in soybean	54
Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study	54
Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension in Drosophila	53
Changes in both trans- and cis-regulatory elements mediate insecticide resistance in a lepidopteron pest, Spodoptera exigua	52
A cross-disorder PRS-pheWAS of 5 major psychiatric disorders in UK Biobank	52
α-synuclein impairs autophagosome maturation through abnormal actin stabilization	52
Defects in the cytoplasmic assembly of axonemal dynein arms cause morphological abnormalities and dysmotility in sperm cells leading to male infertility	52
TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage	52
Dual function of perivascular fibroblasts in vascular stabilization in zebrafish	51
Selective sorting of ancestral introgression in maize and teosinte along an elevational cline	51
Elevated exopolysaccharide levels in Pseudomonas aeruginosa flagellar mutants have implications for biofilm growth and chronic infections	51
Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus	50
Recombination events are concentrated in the spike protein region of Betacoronaviruses	50
Power analysis of transcriptome-wide association study: Implications for practical protocol choice	50
Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat	50
Steroid hormones regulate genome-wide epigenetic programming and gene transcription in human endometrial cells with marked aberrancies in endometriosis	49
Estimation of causal effects of a time-varying exposure at multiple time points through multivariable mendelian randomization	49
Brassinosteroids regulate root meristem development by mediating BIN2-UPB1 module in Arabidopsis	48
A powerful method for pleiotropic analysis under composite null hypothesis identifies novel shared loci between Type 2 Diabetes and Prostate Cancer	48
The membrane protein ANKH is crucial for bone mechanical performance by mediating cellular export of citrate and ATP	47
Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation	46
Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria	46
Identifying drug targets for neurological and psychiatric disease via genetics and the brain transcriptome	46
Steroid hormone ecdysone deficiency stimulates preparation for photoperiodic reproductive diapause	46
CSF1R-dependent macrophages control postnatal somatic growth and organ maturation	46
Gene regulatory effects of a large chromosomal inversion in highland maize	45
RNA editing at a limited number of sites is sufficient to prevent MDA5 activation in the mouse brain	45
Long noncoding RNA functionality in imprinted domain regulation	45
An Africa-wide genomic evolution of insecticide resistance in the malaria vector Anopheles funestus involves selective sweeps, copy number variations, gene conversion and transposons	45
Fine-tuning autophagy maximises lifespan and is associated with changes in mitochondrial gene expression in Drosophila	45
Innate immune signaling in Drosophila shifts anabolic lipid metabolism from triglyceride storage to phospholipid synthesis to support immune function	45
Significant sparse polygenic risk scores across 813 traits in UK Biobank	44
Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm	44
Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2	43
ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing	43
Accounting for long-range correlations in genome-wide simulations of large cohorts	43
MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies	43

Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas	43
Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty	42
On the cross-population generalizability of gene expression prediction models	41
Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing	41
ARID1A regulates R-loop associated DNA replication stress	41
Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images	40
Overlapping functions and protein-protein interactions of LRR-extensins in Arabidopsis	40
Nicotinic acetylcholine receptor modulator insecticides act on diverse receptor subtypes with distinct subunit compositions	40
Impact of insertion sequences on convergent evolution of Shigella species	40
Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus	40
An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages	39
Identifying causal variants by fine mapping across multiple studies	38
Holocentric chromosomes	38
NF-κB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1	38
Inhibition of the de novo pyrimidine biosynthesis pathway limits ribosomal RNA transcription causing nucleolar stress in glioblastoma cells	38
Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia	38
Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link	38
Aurora kinase A is essential for meiosis in mouse oocytes	38
Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data	37
Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon	37
Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA	37
MreC and MreD balance the interaction between the elongasome proteins PBP2 and RodA	36
Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci	36
The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila	36
Sex-stratified genome-wide association study of multisite chronic pain in UK Biobank	36
On cross-ancestry cancer polygenic risk scores	36
Diverse LXG toxin and antitoxin systems specifically mediate intraspecies competition in Bacillus subtilis biofilms	36
CRISPR gRNA phenotypic screening in zebrafish reveals pro-regenerative genes in spinal cord injury	36
Novel Variance-Component TWAS method for studying complex human diseases with applications to Alzheimer’s dementia	35
A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics	35
Meiotic cohesins mediate initial loading of HORMAD1 to the chromosomes and coordinate SC formation during meiotic prophase	35
Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improves the power of transcriptome-wide association studies	35
A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)	34
The helper NLR immune protein NRC3 mediates the hypersensitive cell death caused by the cell-surface receptor Cf-4	34
The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression	34
Scalable probabilistic PCA for large-scale genetic variation data	33
A neuroendocrine pathway modulating osmotic stress in Drosophila	33
Causal inference for heritable phenotypic risk factors using heterogeneous genetic instruments	33
Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis	33
All three mammalian MutL complexes are required for repeat expansion in a mouse cell model of the Fragile X-related disorders	33
Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus	33
Regulation of GSTu1-mediated insecticide resistance in Plutella xylostella by miRNA and lncRNA	33
ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing	32
PRSet: Pathway-based polygenic risk score analyses and software	32
Repeated evolution of circadian clock dysregulation in cavefish populations	32
Indole-3-acetic acid is a physiological inhibitor of TORC1 in yeast	32
A Rad51-independent pathway promotes single-strand template repair in gene editing	32
Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster	32
A subset of broadly responsive Type III taste cells contribute to the detection of bitter, sweet and umami stimuli	32
Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering	31
Mosquito genomes are frequently invaded by transposable elements through horizontal transfer	31
A viral guide RNA delivery system for CRISPR-based transcriptional activation and heritable targeted DNA demethylation in Arabidopsis thaliana	31
Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma	31
Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology	31
TaTLP1 interacts with TaPR1 to contribute to wheat defense responses to leaf rust fungus	31
The causal effect of obesity on prediabetes and insulin resistance reveals the important role of adipose tissue in insulin resistance	31
The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic	31
Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology	31
Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution	31
Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment	30
Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves	30
Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen	30
Disruption of the ERLIN–TM6SF2–APOB complex destabilizes APOB and contributes to non-alcoholic fatty liver disease	30
The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication	30
Systematic identification of functional SNPs interrupting 3’UTR polyadenylation signals	30
Loss of hepatocyte cell division leads to liver inflammation and fibrosis	30
Genetic sensitivity analysis: Adjusting for genetic confounding in epidemiological associations	30
Identification of a gustatory receptor tuned to sinigrin in the cabbage butterfly Pieris rapae	30
Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility	30
Human genetic admixture	30
Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum	29
Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation	29
ANGPTL8 protein-truncating variant associated with lower serum triglycerides and risk of coronary disease	29
Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon	29
Adaptation of codon usage to tRNA I34 modification controls translation kinetics and proteome landscape	29
Genetic analysis of the septal peptidoglycan synthase FtsWI complex supports a conserved activation mechanism for SEDS-bPBP complexes	29
Thyroid hormone receptor beta mutations alter photoreceptor development and function in Danio rerio (zebrafish)	28
Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans	28
PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer’s disease	28
Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei	28

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago	28
Super-resolution imaging of RAD51 and DMC1 in DNA repair foci reveals dynamic distribution patterns in meiotic prophase	28
Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea	28
Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription–replication conflict regions	28
Absence of YhdP, TamB, and YdbH leads to defects in glycerophospholipid transport and cell morphology in Gram-negative bacteria	28
UVR8-mediated inhibition of shade avoidance involves HFR1 stabilization in Arabidopsis	27
Multivariable G-E interplay in the prediction of educational achievement	27
The capacity of origins to load MCM establishes replication timing patterns	27
A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis	27
UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin	27
Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics	27
CRISPR/Cas9 modified An. gambiae carrying kdr mutation L1014F functionally validate its contribution in insecticide resistance and combined effect with metabolic enzymes	27
Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis	27
Bidirectional crosstalk between Hypoxia-Inducible Factor and glucocorticoid signalling in zebrafish larvae	27
IgaA negatively regulates the Rcs Phosphorelay via contact with the RcsD Phosphotransfer Protein	27
The genomics of rapid climatic adaptation and parallel evolution in North American house mice	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
Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals	26
A high-fat diet induces a microbiota-dependent increase in stem cell activity in the Drosophila intestine	26
Tetrahymena meiosis: Simple yet ingenious	26
To “Z” or not to “Z”: Z-RNA, self-recognition, and the MDA5 helicase	26
In vivo modeling of metastatic human high-grade serous ovarian cancer in mice	26
Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies	26
MAPK-mediated transcription factor GATAd contributes to Cry1Ac resistance in diamondback moth by reducing PxmALP expression	26
Pch2 orchestrates the meiotic recombination checkpoint from the cytoplasm	26
A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata	26
3D genome evolution and reorganization in the Drosophila melanogaster species group	26
Alpha- and beta-adrenergic octopamine receptors in muscle and heart are required for Drosophila exercise adaptations	26
Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits	26
Integrins regulate epithelial cell shape by controlling the architecture and mechanical properties of basal actomyosin networks	26
Functional information from clinically-derived drug resistant forms of the Candida glabrata Pdr1 transcription factor	26
Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites	26
Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation	25
Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease	25
Diversity and determinants of recombination landscapes in flowering plants	25
Lotus japonicus karrikin receptors display divergent ligand-binding specificities and organ-dependent redundancy	25
Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens	25
Age-of-onset information helps identify 76 genetic variants associated with allergic disease	25
Opposing functions of Fng1 and the Rpd3 HDAC complex in H4 acetylation in Fusarium graminearum	25
A conserved role for AMP-activated protein kinase in NGLY1 deficiency	25
A Novel Recessive Mutation in SPEG Causes Early Onset Dilated Cardiomyopathy	25
Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles	24
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis	24
Translational repression of NMD targets by GIGYF2 and EIF4E2	24
Genome-wide association study of fish oil supplementation on lipid traits in 81,246 individuals reveals new gene-diet interaction loci	24
RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays	24
A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle	24
Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies	24
Maize adaptation across temperate climates was obtained via expression of two florigen genes	24
DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress	24
MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity	24
Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination	24
The Species-Specific Acquisition and Diversification of a K1-like Family of Killer Toxins in Budding Yeasts of the Saccharomycotina	24
Trehalose and α-glucan mediate distinct abiotic stress responses in Pseudomonas aeruginosa	24
High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest	24
Distinct and sequential re-replication barriers ensure precise genome duplication	24
A genome-wide association study identifies 5 loci associated with frozen shoulder and implicates diabetes as a causal risk factor	23
Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome	23
Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae	23
A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster	23
The roles of replication-transcription conflict in mutagenesis and evolution of genome organization	23
Xrp1 and Irbp18 trigger a feed-forward loop of proteotoxic stress to induce the loser status	23
Genome-scale CRISPR screening for modifiers of cellular LDL uptake	23
Hypomodified tRNA in evolutionarily distant yeasts can trigger rapid tRNA decay to activate the general amino acid control response, but with different consequences	23
The defense island repertoire of the Escherichia coli pan-genome	23
The conserved transmembrane protein TMEM-39 coordinates with COPII to promote collagen secretion and regulate ER stress response	23
A novel type of colistin resistance genes selected from random sequence space	23
A new neuropeptide insect parathyroid hormone iPTH in the red flour beetle Tribolium castaneum	23
Chromosome number evolves at equal rates in holocentric and monocentric clades	23
HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation	23
Natural variation in the sequestosome-related gene, sqst-5, underlies zinc homeostasis in Caenorhabditis elegans	23
Reciprocal regulation between nicotinamide adenine dinucleotide metabolism and abscisic acid and stress response pathways in Arabidopsis	23
The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection	23
Nuclear lipid droplets and nuclear damage in Caenorhabditis elegans	23
Regulation of olfactory-based sex behaviors in the silkworm by genes in the sex-determination cascade	23
Indian genetic heritage in Southeast Asian populations	22
Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes	22
Replication of the Salmonella Genomic Island 1 (SGI1) triggered by helper IncC conjugative plasmids promotes incompatibility and plasmid loss	22
DNA methylation-mediated modulation of rapid desiccation tolerance acquisition and dehydration stress memory in the resurrection plant Boea hygrometrica	22
Cell competition is driven by Xrp1-mediated phosphorylation of eukaryotic initiation factor 2α	22
A mega-analysis of expression quantitative trait loci in retinal tissue	22
Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies	22
The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)	22
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	22
Split versions of Cleave and Rescue selfish genetic elements for measured self limiting gene drive	22
Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity	22
Proteome-wide Mendelian randomization identifies causal links between blood proteins and severe COVID-19	22
Resistance to a CRISPR-based gene drive at an evolutionarily conserved site is revealed by mimicking genotype fixation	22
miRNA-mediated loss of m6A increases nascent translation in glioblastoma	22
Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle	22
Circadian control of heparan sulfate levels times phagocytosis of amyloid beta aggregates	22
Tau, XMAP215/Msps and Eb1 co-operate interdependently to regulate microtubule polymerisation and bundle formation in axons	22
Endogenization and excision of human herpesvirus 6 in human genomes	22
Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers	22