PLoS Genetics

Article	Citations
Contribution of the eye and of opn4xa function to circadian photoentrainment in the diurnal zebrafish	808596525
Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses	170
RNA-directed DNA Methylation	161
Phylogenetic background and habitat drive the genetic diversification of Escherichia coli	127
MicroRNAs are minor constituents of extracellular vesicles that are rarely delivered to target cells	123
A more accurate method for colocalisation analysis allowing for multiple causal variants	122
Beyond SNP heritability: Polygenicity and discoverability of phenotypes estimated with a univariate Gaussian mixture model	116
Osteocalcin is necessary for the alignment of apatite crystallites, but not glucose metabolism, testosterone synthesis, or muscle mass	114
Evaluation of polygenic prediction methodology within a reference-standardized framework	92
Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits	88
What is ancestry?	87
Horizontal transmission and recombination maintain forever young bacterial symbiont genomes	85
A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease	84
Stability of SARS-CoV-2 phylogenies	83
Fine-mapping from summary data with the “Sum of Single Effects” model	82
Genotype imputation using the Positional Burrows Wheeler Transform	80
An osteocalcin-deficient mouse strain without endocrine abnormalities	80
Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements	78
A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank	71
Deleterious mutation accumulation and the long-term fate of chromosomal inversions	71
Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph	70
Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish	69
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism	69
Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance	69
Combining the strengths of inverse-variance weighting and Egger regression in Mendelian randomization using a mixture of regressions model	69

Tracking human population structure through time from whole genome sequences	67
OsMADS23 phosphorylated by SAPK9 confers drought and salt tolerance by regulating ABA biosynthesis in rice	65
Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution	63
Runx2 is essential for the transdifferentiation of chondrocytes into osteoblasts	63
Nationwide germline whole genome sequencing of 198 consecutive pediatric cancer patients reveals a high incidence of cancer prone syndromes	61
Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes	61
Introns mediate post-transcriptional enhancement of nuclear gene expression in the green microalga Chlamydomonas reinhardtii	60
Osteocalcin promotes bone mineralization but is not a hormone	60
Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress	57
Creating artificial human genomes using generative neural networks	57
VolcanoFinder: Genomic scans for adaptive introgression	57
Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae	55
­­­­­­Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods	55
Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study	54
Selection of GmSWEET39 for oil and protein improvement in soybean	53
The impact of age on genetic risk for common diseases	53
Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals	53
Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)	53
The genomic ecosystem of transposable elements in maize	52
Runx1 is a central regulator of osteogenesis for bone homeostasis by orchestrating BMP and WNT signaling pathways	52
Estimating FST and kinship for arbitrary population structures	51
The alarmones (p)ppGpp are part of the heat shock response of Bacillus subtilis	50
Recombination events are concentrated in the spike protein region of Betacoronaviruses	50
Elevated exopolysaccharide levels in Pseudomonas aeruginosa flagellar mutants have implications for biofilm growth and chronic infections	50
Changes in both trans- and cis-regulatory elements mediate insecticide resistance in a lepidopteron pest, Spodoptera exigua	49
Defects in the cytoplasmic assembly of axonemal dynein arms cause morphological abnormalities and dysmotility in sperm cells leading to male infertility	49
TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage	49
WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat	49
A cross-disorder PRS-pheWAS of 5 major psychiatric disorders in UK Biobank	49
Dual function of perivascular fibroblasts in vascular stabilization in zebrafish	48
Steroid hormones regulate genome-wide epigenetic programming and gene transcription in human endometrial cells with marked aberrancies in endometriosis	48
The evolution and functional divergence of the histone H2B family in plants	48
Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension in Drosophila	48
α-synuclein impairs autophagosome maturation through abnormal actin stabilization	48
Placental imprinting: Emerging mechanisms and functions	48
Selective sorting of ancestral introgression in maize and teosinte along an elevational cline	47
Brassinosteroids regulate root meristem development by mediating BIN2-UPB1 module in Arabidopsis	47
Power analysis of transcriptome-wide association study: Implications for practical protocol choice	46
Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus	46
Gene regulatory effects of a large chromosomal inversion in highland maize	45
The membrane protein ANKH is crucial for bone mechanical performance by mediating cellular export of citrate and ATP	45
Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria	45
Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat	45
Estimation of causal effects of a time-varying exposure at multiple time points through multivariable mendelian randomization	45
Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation	44
Long noncoding RNA functionality in imprinted domain regulation	43
CSF1R-dependent macrophages control postnatal somatic growth and organ maturation	43
Fine-tuning autophagy maximises lifespan and is associated with changes in mitochondrial gene expression in Drosophila	43
A powerful method for pleiotropic analysis under composite null hypothesis identifies novel shared loci between Type 2 Diabetes and Prostate Cancer	43
Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm	43

Reciprocal c-di-GMP signaling: Incomplete flagellum biogenesis triggers c-di-GMP signaling pathways that promote biofilm formation	42
Identifying drug targets for neurological and psychiatric disease via genetics and the brain transcriptome	42
An Africa-wide genomic evolution of insecticide resistance in the malaria vector Anopheles funestus involves selective sweeps, copy number variations, gene conversion and transposons	42
MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies	42
A fly model establishes distinct mechanisms for synthetic CRISPR/Cas9 sex distorters	41
ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing	41
RNA editing at a limited number of sites is sufficient to prevent MDA5 activation in the mouse brain	41
Steroid hormone ecdysone deficiency stimulates preparation for photoperiodic reproductive diapause	41
Innate immune signaling in Drosophila shifts anabolic lipid metabolism from triglyceride storage to phospholipid synthesis to support immune function	40
Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell	40
ARID1A regulates R-loop associated DNA replication stress	40
Accounting for long-range correlations in genome-wide simulations of large cohorts	40
Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing	39
Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty	39
Nicotinic acetylcholine receptor modulator insecticides act on diverse receptor subtypes with distinct subunit compositions	39
Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas	39
Impact of insertion sequences on convergent evolution of Shigella species	39
Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2	39
Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: Evidence for coevolution?	39
Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images	39
Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus	38
Inhibition of the de novo pyrimidine biosynthesis pathway limits ribosomal RNA transcription causing nucleolar stress in glioblastoma cells	38
Drosophila insulin-like peptide 2 mediates dietary regulation of sleep intensity	38
Bayesian network analysis incorporating genetic anchors complements conventional Mendelian randomization approaches for exploratory analysis of causal relationships in complex data	38
Overlapping functions and protein-protein interactions of LRR-extensins in Arabidopsis	38
On the cross-population generalizability of gene expression prediction models	37
Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon	37
NF-κB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1	36
Significant sparse polygenic risk scores across 813 traits in UK Biobank	36
CRISPR gRNA phenotypic screening in zebrafish reveals pro-regenerative genes in spinal cord injury	36
Technical and social issues influencing the adoption of preprints in the life sciences	36
Sex-stratified genome-wide association study of multisite chronic pain in UK Biobank	36
Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA	35
Loss of FOXM1 in macrophages promotes pulmonary fibrosis by activating p38 MAPK signaling pathway	35
Holocentric chromosomes	35
Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improves the power of transcriptome-wide association studies	35
Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia	35
Variants encoding a restricted carboxy-terminal domain of SLC12A2 cause hereditary hearing loss in humans	34
An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages	34
Novel Variance-Component TWAS method for studying complex human diseases with applications to Alzheimer’s dementia	34
Diverse LXG toxin and antitoxin systems specifically mediate intraspecies competition in Bacillus subtilis biofilms	33
The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression	33
Aurora kinase A is essential for meiosis in mouse oocytes	33
Causal inference for heritable phenotypic risk factors using heterogeneous genetic instruments	33
MreC and MreD balance the interaction between the elongasome proteins PBP2 and RodA	33
The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila	33
Identifying causal variants by fine mapping across multiple studies	33
Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data	32
DNA methylation-mediated repression of exosomal miR-652-5p expression promotes oesophageal squamous cell carcinoma aggressiveness by targeting PARG and VEGF pathways	32
A Rad51-independent pathway promotes single-strand template repair in gene editing	32
A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics	32
The helper NLR immune protein NRC3 mediates the hypersensitive cell death caused by the cell-surface receptor Cf-4	32
All three mammalian MutL complexes are required for repeat expansion in a mouse cell model of the Fragile X-related disorders	32
On cross-ancestry cancer polygenic risk scores	32
ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing	32
Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids	31
Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster	31
A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)	31
Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology	31
Scalable probabilistic PCA for large-scale genetic variation data	31
Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus	31
Waking up quiescent neural stem cells: Molecular mechanisms and implications in neurodevelopmental disorders	30
Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci	30
Indole-3-acetic acid is a physiological inhibitor of TORC1 in yeast	30
TaTLP1 interacts with TaPR1 to contribute to wheat defense responses to leaf rust fungus	30
High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements	30
Systematic identification of functional SNPs interrupting 3’UTR polyadenylation signals	30
Pleiotropy facilitates local adaptation to distant optima in common ragweed (Ambrosia artemisiifolia)	30
GLP-1 Notch—LAG-1 CSL control of the germline stem cell fate is mediated by transcriptional targets lst-1 and sygl-1	30
UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize	30
Deconstructing cerebellar development cell by cell	30
A neuroendocrine pathway modulating osmotic stress in Drosophila	30
Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link	30
A viral guide RNA delivery system for CRISPR-based transcriptional activation and heritable targeted DNA demethylation in Arabidopsis thaliana	30
Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen	30
Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering	29
Mosquito genomes are frequently invaded by transposable elements through horizontal transfer	29
The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic	29
Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution	29
Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves	29

A subset of broadly responsive Type III taste cells contribute to the detection of bitter, sweet and umami stimuli	29
Loss of hepatocyte cell division leads to liver inflammation and fibrosis	29
Global mistranslation increases cell survival under stress in Escherichia coli	29
Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin	29
Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis	29
Regulation of GSTu1-mediated insecticide resistance in Plutella xylostella by miRNA and lncRNA	29
Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma	29
Meiotic cohesins mediate initial loading of HORMAD1 to the chromosomes and coordinate SC formation during meiotic prophase	29
Adaptation of codon usage to tRNA I34 modification controls translation kinetics and proteome landscape	28
Disruption of the ERLIN–TM6SF2–APOB complex destabilizes APOB and contributes to non-alcoholic fatty liver disease	28
Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology	28
The causal effect of obesity on prediabetes and insulin resistance reveals the important role of adipose tissue in insulin resistance	28
Genetic sensitivity analysis: Adjusting for genetic confounding in epidemiological associations	28
Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum	28
E2f5 is a versatile transcriptional activator required for spermatogenesis and multiciliated cell differentiation in zebrafish	28
Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment	28
ANGPTL8 protein-truncating variant associated with lower serum triglycerides and risk of coronary disease	27
Human genetic admixture	27
The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication	27
Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation	27
Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon	27
Thyroid hormone receptor beta mutations alter photoreceptor development and function in Danio rerio (zebrafish)	27
Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago	27
Super-resolution imaging of RAD51 and DMC1 in DNA repair foci reveals dynamic distribution patterns in meiotic prophase	27
Identification of a gustatory receptor tuned to sinigrin in the cabbage butterfly Pieris rapae	27
Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei	26
Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans	26
IgaA negatively regulates the Rcs Phosphorelay via contact with the RcsD Phosphotransfer Protein	26
Absence of YhdP, TamB, and YdbH leads to defects in glycerophospholipid transport and cell morphology in Gram-negative bacteria	26
Alpha- and beta-adrenergic octopamine receptors in muscle and heart are required for Drosophila exercise adaptations	26
UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin	26
Bidirectional crosstalk between Hypoxia-Inducible Factor and glucocorticoid signalling in zebrafish larvae	26
Dynamic localization of SPO11-1 and conformational changes of meiotic axial elements during recombination initiation of maize meiosis	26
Genetic analysis of the septal peptidoglycan synthase FtsWI complex supports a conserved activation mechanism for SEDS-bPBP complexes	26
UVR8-mediated inhibition of shade avoidance involves HFR1 stabilization in Arabidopsis	26
Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics	26
The genomics of rapid climatic adaptation and parallel evolution in North American house mice	26
Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages	26
Functional information from clinically-derived drug resistant forms of the Candida glabrata Pdr1 transcription factor	25
Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription–replication conflict regions	25
PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer’s disease	25
The clarifying role of time series data in the population genetics of HIV	25
Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis	25
Repeated evolution of circadian clock dysregulation in cavefish populations	25
Multivariable G-E interplay in the prediction of educational achievement	25
A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata	25
Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites	25
PRSet: Pathway-based polygenic risk score analyses and software	25
In vivo modeling of metastatic human high-grade serous ovarian cancer in mice	25
A conserved role for AMP-activated protein kinase in NGLY1 deficiency	25
Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits	25
Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease	25
Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility	25
Age-of-onset information helps identify 76 genetic variants associated with allergic disease	25
Leveraging gene co-expression patterns to infer trait-relevant tissues in genome-wide association studies	25
3D genome evolution and reorganization in the Drosophila melanogaster species group	25
Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development	25
Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea	25
A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis	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
Integrins regulate epithelial cell shape by controlling the architecture and mechanical properties of basal actomyosin networks	24
Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering	24
Lotus japonicus karrikin receptors display divergent ligand-binding specificities and organ-dependent redundancy	24
Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies	24
A high-fat diet induces a microbiota-dependent increase in stem cell activity in the Drosophila intestine	24
Translational repression of NMD targets by GIGYF2 and EIF4E2	24
CRISPR/Cas9 modified An. gambiae carrying kdr mutation L1014F functionally validate its contribution in insecticide resistance and combined effect with metabolic enzymes	24
A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle	24
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis	24
pH-dependent activation of cytokinesis modulates Escherichia coli cell size	24
Genome-wide association study of fish oil supplementation on lipid traits in 81,246 individuals reveals new gene-diet interaction loci	24
Genome-scale CRISPR screening for modifiers of cellular LDL uptake	23
Natural variation in the sequestosome-related gene, sqst-5, underlies zinc homeostasis in Caenorhabditis elegans	23
Maize adaptation across temperate climates was obtained via expression of two florigen genes	23
Opposing functions of Fng1 and the Rpd3 HDAC complex in H4 acetylation in Fusarium graminearum	23
Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome	23
MAPK-mediated transcription factor GATAd contributes to Cry1Ac resistance in diamondback moth by reducing PxmALP expression	23
Pch2 orchestrates the meiotic recombination checkpoint from the cytoplasm	23
High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest	23
Distinct and sequential re-replication barriers ensure precise genome duplication	23
A new neuropeptide insect parathyroid hormone iPTH in the red flour beetle Tribolium castaneum	23
Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination	23
Tetrahymena meiosis: Simple yet ingenious	23
Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies	23
To “Z” or not to “Z”: Z-RNA, self-recognition, and the MDA5 helicase	23
DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress	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
RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays	22
Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers	22
Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae	22
Reciprocal regulation between nicotinamide adenine dinucleotide metabolism and abscisic acid and stress response pathways in Arabidopsis	22
Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome	22
A novel type of colistin resistance genes selected from random sequence space	22