PeerJ

Article	Citations
The timing mega-study: comparing a range of experiment generators, both lab-based and online	235
Impact of COVID-19 outbreak on the mental health status of undergraduate medical students in a COVID-19 treating medical college: a prospective longitudinal study	221
Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection	136
BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains	115
Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities	113
partR2: partitioning R2 in generalized linear mixed models	112
Computational bioacoustics with deep learning: a review and roadmap	105
Comparing multiple comparisons: practical guidance for choosing the best multiple comparisons test	101
Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach	99
Transfection types, methods and strategies: a technical review	95
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture	80
Deep learning prediction of likelihood of ICU admission and mortality in COVID-19 patients using clinical variables	79
Applications and limitations of current markerless motion capture methods for clinical gait biomechanics	77
Air transportation, population density and temperature predict the spread of COVID-19 in Brazil	77
No one-size-fits-all solution to clean GBIF	76
Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies	74
Plastic additives: challenges in ecotox hazard assessment	68
A comparison of COVID-19, SARS and MERS	67
Potential role of cellular miRNAs in coronavirus-host interplay	67
Utilization of brewery wastes in food industry	66
A potential role for Galectin-3 inhibitors in the treatment of COVID-19	65
Effectiveness of topical antibiotics in treating corals affected by Stony Coral Tissue Loss Disease	63
Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study	62
Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems	60
Identifying potential threats to soil biodiversity	60

Purpureocillium lilacinum and Metarhizium marquandii as plant growth-promoting fungi	59
A game-theoretic model of Monkeypox to assess vaccination strategies	59
Predicting CoVID-19 community mortality risk using machine learning and development of an online prognostic tool	59
eDNAir: proof of concept that animal DNA can be collected from air sampling	58
Current and future trends in socio-economic, demographic and governance factors affecting global primate conservation	56
Assessment of activities of daily living in patients post COVID-19: a systematic review	56
Perils and pitfalls of mixed-effects regression models in biology	55
The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma	55
Melatonin improves the germination rate of cotton seeds under drought stress by opening pores in the seed coat	55
Altered gut microbiota associated with symptom severity in schizophrenia	54
Evaluation of knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic	52
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation	51
Drought stress strengthens the link between chlorophyll fluorescence parameters and photosynthetic traits	50
Combined application of biochar and nitrogen fertilizer improves rice yield, microbial activity and N-metabolism in a pot experiment	49
Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure	49
RdRp mutations are associated with SARS-CoV-2 genome evolution	49
Global expansion of COVID-19 pandemic is driven by population size and airport connections	48
Publication rate and citation counts for preprints released during the COVID-19 pandemic: the good, the bad and the ugly	48
Recent advances in biochar application for water and wastewater treatment: a review	48
Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and	46
Syncmers are more sensitive than minimizers for selecting conserved k‑mers in biological sequences	46
Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function	46
Evolution ofWolbachiamutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas	46
A community perspective on the concept of marine holobionts: current status, challenges, and future directions	45
COVID-19: exploring impacts of the pandemic and lockdown on mental health of Pakistani students	44
Contamination and oxidative stress biomarkers in estuarine fish following a mine tailing disaster	44
Exogenous melatonin improves salt stress adaptation of cotton seedlings by regulating active oxygen metabolism	44
The role of textiles as fomites in the healthcare environment: a review of the infection control risk	44
Should I use fixed effects or random effects when I have fewer than five levels of a grouping factor in a mixed-effects model?	43
A high-resolution growth series ofTyrannosaurus rexobtained from multiple lines of evidence	43
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager	43
Beyond loot boxes: a variety of gambling-like practices in video games are linked to both problem gambling and disordered gaming	43
Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs	43
Harmful effects of the microplastic pollution on animal health: a literature review	43
Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach	43
PCAtest: testing the statistical significance of Principal Component Analysis in R	42
MULTI-DEEP: A novel CAD system for coronavirus (COVID-19) diagnosis from CT images using multiple convolution neural networks	42
Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study	41
Resampling-based methods for biologists	41
Open Access uptake by universities worldwide	40
Modelling fatality curves of COVID-19 and the effectiveness of intervention strategies	40
Integrated analysis of lymphocyte infiltration-associated lncRNA for ovarian cancer via TCGA, GTEx and GEO datasets	40
The effectiveness of the Peyton’s 4-step teaching approach on skill acquisition of procedures in health professions education: A systematic review and meta-analysis with integrated meta-regression	40
A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research	39
Geographic potential of the world’s largest hornet,Vespa mandariniaSmith (Hymenoptera: Vespidae), worldwide and particularly in North America	39
Effect of storage conditions on SARS-CoV-2 RNA quantification in wastewater solids	39
The efficacy of IL-6 inhibitor Tocilizumab in reducing severe COVID-19 mortality: a systematic review	39
Exosomes derived from M0, M1 and M2 macrophages exert distinct influences on the proliferation and differentiation of mesenchymal stem cells	38
Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)	38
Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries	37

Effects of Origanum vulgare essential oil and its two main components, carvacrol and thymol, on the plant pathogen Botrytis cinerea	37
Co-application of bio-fertilizer and salicylic acid improves growth, photosynthetic pigments and stress tolerance in wheat under drought stress	37
Effects of plastic mulching on the accumulation and distribution of macro and micro plastics in soils of two farming systems in Northwest China	36
Mutational spectra of SARS-CoV-2 isolated from animals	36
Macrel: antimicrobial peptide screening in genomes and metagenomes	36
Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load	35
Arthropod IGF, relaxin and gonadulin, putative orthologs of Drosophila insulin-like peptides 6, 7 and 8, likely originated from an ancient gene triplication	35
Taxonomic revision of the threatened African genus Pseudohydrosme Engl. (Araceae), with P. ebo, a new, critically endangered species from Ebo, Cameroon	35
COL1A1 is a prognostic biomarker and correlated with immune infiltrates in lung cancer	35
Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis	34
Isolation and identification of flavonoid-producing endophytic fungi from medicinal plant Conyza blinii H.Lév that exhibit higher antioxidant and antibacterial activities	34
Perception and practices during the COVID-19 pandemic in an urban community in Nigeria: a cross-sectional study	34
A validation of Emotiv EPOC Flex saline for EEG and ERP research	34
Polylactic acid as a suitable material for 3D printing of protective masks in times of COVID-19 pandemic	34
The biomarkers of key miRNAs and target genes associated with acute myocardial infarction	34
iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC	34
Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem	34
Potential of rice straw biochar, sulfur and ryegrass (Lolium perenne L.) in remediating soil contaminated with nickel through irrigation with untreated wastewater	33
Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease	33
Liraglutide-induced structural modulation of the gut microbiota in patients with type 2 diabetes mellitus	33
Lactobacillus reuteri TSR332 and Lactobacillus fermentum TSF331 stabilize serum uric acid levels and prevent hyperuricemia in rats	33
CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments	32
Production of cupcake-like dessert containing microbial biosurfactant as an emulsifier	32
CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content	32
Uncovering the species diversity of subterranean rodents at the end of the World: three new species of Patagonian tuco-tucos (Rodentia, Hystricomorpha,Ctenomys)	31
Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues	31
Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters	31
Air quality improvement during triple-lockdown in the coastal city of Kannur, Kerala to combat Covid-19 transmission	31
Prophet forecasting model: a machine learning approach to predict the concentration of air pollutants (PM2.5, PM10, O3, NO2, SO2, CO) in Seoul, S	31
Biases in genome reconstruction from metagenomic data	31
The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies	30
Revisiting food-sourced vitamins for consumer diet and health needs: a perspective review, from vitamin classification, metabolic functions, absorption, utilization, to balancing nutritional requireme	30
The linkages of plant, litter and soil C:N:P stoichiometry and nutrient stock in different secondary mixed forest types in the Qinling Mountains, China	30
Effects of self-isolation and quarantine on loot box spending and excessive gaming—results of a natural experiment	30
Deep-learning convolutional neural networks with transfer learning accurately classify COVID-19 lung infection on portable chest radiographs	30
Luteolin attenuates doxorubicin-induced cardiotoxicity by modulating the PHLPP1/AKT/Bcl-2 signalling pathway	30
Clinical applicability of the Feline Grimace Scale: real-time versus image scoring and the influence of sedation and surgery	29
Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment	29
SARS-CoV-2 seroprevalence study in Lambayeque, Peru. June–July 2020	29
Desulfovibrio is not always associated with adverse health effects in the Guangdong Gut Microbiome Project	29
The reuse of public datasets in the life sciences: potential risks and rewards	29
Blue carbon of Mexico, carbon stocks and fluxes: a systematic review	29
Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios	29
The phylogenetics of Teleosauroidea (Crocodylomorpha, Thalattosuchia) and implications for their ecology and evolution	29
Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns	29
A fresh look at an old concept: home-range estimation in a tidy world	29
Nitrogen eutrophication particularly promotes turf algae in coral reefs of the central Red Sea	29
Omics approaches inAlliumresearch: Progress and way ahead	29
A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genusMicrohyla(Amphibia: Microhylidae)	29
Predicting continuous ground reaction forces from accelerometers during uphill and downhill running: a recurrent neural network solution	28
Sharing for science: high-resolution trophic interactions revealed rapidly by social media	28
Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)	28
Insight into the kinematics of blue whale surface foraging through drone observations and prey data	28
Alien plants of Europe: introduction pathways, gateways and time trends	28
Polarity and epithelial-mesenchymal transition of retinal pigment epithelial cells in proliferative vitreoretinopathy	28
Zonula occludens and nasal epithelial barrier integrity in allergic rhinitis	28
Effect of calcium on relieving berry cracking in grape (Vitis viniferaL.) ‘Xiangfei’	28
Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions	28
Adaptive Metropolis-coupled MCMC for BEAST 2	28
Nitrogen fertilization affects maize grain yield through regulating nitrogen uptake, radiation and water use efficiency, photosynthesis and root distribution	28
Combination of circulating miR-145-5p/miR-191-5p as biomarker for breast cancer detection	28
Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture	27
COVID-19: molecular and serological detection methods	27
The phylogeny and systematics of Xiphosura	27
COVID-19 mortality in cancer patients: a report from a tertiary cancer centre in India	27
Temperature alters the shape of predator–prey cycles through effects on underlying mechanisms	27
The effects of humic substances on DNA isolation from soils	27
The frequency of combined IFITM3 haplotype involving the reference alleles of both rs12252 and rs34481144 is in line with COVID-19 standardized mortality ratio of ethnic groups in England	27
The m6A reader protein YTHDC2 is a potential biomarker and associated with immune infiltration in head and neck squamous cell carcinoma	27
Machine learning in dental, oral and craniofacial imaging: a review of recent progress	27
Validation of a general subjective well-being factor using Classical Test Theory	27
The phylogenetic nomenclature of ornithischian dinosaurs	27
Double lives: transfer of fungal endophytes from leaves to woody substrates	27
Exosomal hsa-miR-21-5p is a biomarker for breast cancer diagnosis	26
Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians	26
Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2	26
A review of the carotid artery and facial nerve canal systems in extant turtles	26
Evidence of transfer of miRNAs from the diet to the blood still inconclusive	26
Salmo salar fish waste oil: Fatty acids composition and antibacterial activity	26
A descriptive study of random forest algorithm for predicting COVID-19 patients outcome	26

A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19	26
IL-4/IL-13 axis as therapeutic targets in allergic rhinitis and asthma	26
ATR-FTIR, EDS and SEM evaluations of enamel structure after treatment with hydrogen peroxide bleaching agents loaded with nano-hydroxyapatite particles	26
In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococci	26
Antibacterial activity and mechanism of sanguinarine againstProvidencia rettgeriin vitro	25
Soil health and nutrient density: preliminary comparison of regenerative and conventional farming	25
Exogenous melatonin improves growth in hulless barley seedlings under cold stress by influencing the expression rhythms of circadian clock genes	25
Changes in precipitation amounts and extremes across Xinjiang (northwest China) and their connection to climate indices	25
Exact integer linear programming solvers outperform simulated annealing for solving conservation planning problems	25
Agreement between the GAITRite® System and the Wearable Sensor BTS G-Walk® for measurement of gait parameters in healthy adults and Parkinson’s disease patients	25
Assessment and simulation of land use and land cover change impacts on the land surface temperature of Chaoyang District in Beijing, China	25
Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements	25
Entomopathogenic fungi decreaseRhizoctoniadisease in potato in field conditions	25
Phosphate solubilizing bacteria stimulate wheat rhizosphere and endosphere biological nitrogen fixation by improving phosphorus content	25
The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genusAurelia(Cnidaria: Scyphozoa)	25
Repurposing FDA-approved phytomedicines, natural products, antivirals and cell protectives against SARS-CoV-2 (COVID-19) RNA-dependent RNA polymerase	25
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets	24
Clinical validation of the short and long UNESP-Botucatu scales for feline pain assessment	24
Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress	24
Measuring recognition memory in zebrafish larvae: issues and limitations	24
High microphone signal-to-noise ratio enhances acoustic sampling of wildlife	24
Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma	24
An eye for a tooth:Thylacosmiluswas not a marsupial “saber-tooth predator”	24
Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)	24
Silicon induces hormetic dose-response effects on growth and concentrations of chlorophylls, amino acids and sugars in pepper plants during the early developmental stage	24
The regulation of immune checkpoints by the hypoxic tumor microenvironment	24
Estimation of soil salt content by combining UAV-borne multispectral sensor and machine learning algorithms	24
Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation	24
Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil	24
Comparative transcriptome analyses of maize seedling root responses to salt stress	24
Beyond polyphagy and opportunism: natural prey of hunting spiders in the canopy of apple trees	24
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly	24
Identification of areas of very high biodiversity value to achieve the EU Biodiversity Strategy for 2030 key commitments	24
Comparison of gut microbiota between adults with autism spectrum disorder and obese adults	23
Healthcare applications of single camera markerless motion capture: a scoping review	23
Association between serum and dietary antioxidant micronutrients and advanced liver fibrosis in non-alcoholic fatty liver disease: an observational study	23
Enhanced soluble sugar content in tomato fruit using CRISPR/Cas9-mediated SlINVINH1 and SlVPE5 gene editing	23
Lots of movement, little progress: a review of reptile home range literature	23
healthcareCOVID: a national cross-sectional observational study identifying risk factors for developing suspected or confirmed COVID-19 in UK healthcare workers	23
Transcriptomic analysis highlights cochlear inflammation associated with age-related hearing loss in C57BL/6 mice using next generation sequencing	23
Cranial osteology of the Early Cretaceous turtlePleurosternon bullockii(Paracryptodira: Pleurosternidae)	23
The metabolism and role of free fatty acids in key physiological processes in insects of medical, veterinary and forensic importance	23
The effect of brewery spent grain application on biogas yields and kinetics in co-digestion with sewage sludge	23
Public perspectives and media reporting of wolf reintroduction in Colorado	23
Settling taxonomic and nomenclatural problems in brine shrimps,Artemia(Crustacea: Branchiopoda: Anostraca), by integrating mitogenomics, marker discordances and nomenclature rules	23
Osmotic stress in banana is relieved by exogenous nitric oxide	23
The utility of MEWS for predicting the mortality in the elderly adults with COVID-19: a retrospective cohort study with comparison to other predictive clinical scores	23
The association between serum uric acid and diabetic complications in patients with type 2 diabetes mellitus by gender: a cross-sectional study	23
Fast sequence-based microsatellite genotyping development workflow	23
miR-29a-3p directly targets Smad nuclear interacting protein 1 and inhibits the migration and proliferation of cervical cancer HeLa cells	22
Fecal microbiota transplantation mitigates bone loss by improving gut microbiome composition and gut barrier function in aged rats	22
Association between dietary mineral nutrient intake, body mass index, and waist circumference in U.S. adults using quantile regression analysis NHANES 2007–2014	22
Effectiveness of digital mental health interventions for university students: an umbrella review	22
Evaluation of the effective dose of amygdalin for the improvement of antioxidant gene expression and suppression of oxidative damage in mice	22
Prognostic implications of metabolism-associated gene signatures in colorectal cancer	22
A new phylogenetic hypothesis of Tanystropheidae (Diapsida, Archosauromorpha) and other “protorosaurs”, and its implications for the early evolution of stem archosaurs	22
Reducing publication delay to improve the efficiency and impact of conservation science	22
Assessing turbine passage effects on internal fish injury and delayed mortality using X-ray imaging	22
COVID-19: Taiwan’s epidemiological characteristics and public and hospital responses	22
Genome-wide analysis of growth-regulating factors (GRFs) inTriticum aestivum	22
Fear and stressing in predator–prey ecology: considering the twin stressors of predators and people on mammals	22
Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2	22
Changes in sprint performance and sagittal plane kinematics after heavy resisted sprint training in professional soccer players	22
Improving decolorization of dyes by laccase from Bacillus licheniformis by random and site-directed mutagenesis	22
Experiencing fear during the pandemic: validation of the fear of COVID-19 scale in Polish	22
Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)	22
Sugarcane/peanut intercropping system improves physicochemical properties by changing N and P cycling and organic matter turnover in root zone soil	22
Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide	22
Variation of soil microbial carbon use efficiency (CUE) and its Influence mechanism in the context of global environmental change: a review	22
The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review	22
Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome	22
VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature	22
Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance	22
Anti-inflammatory and antiaging properties of chlorogenic acid on UV-induced fibroblast cell	22
Generation of human liver organoids from pluripotent stem cell-derived hepatic endoderms	22
LCZ696 mitigates diabetic-induced nephropathy through inhibiting oxidative stress, NF-κB mediated inflammation and glomerulosclerosis in rats	22
KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept	22
Dung beetles as samplers of mammals in Malaysian Borneo—a test of high throughput metabarcoding of iDNA	22
Diversity of rhizosphere and endophytic fungi in Atractylodes macrocephala during continuous cropping	22
Prognostic significance of PI3K/AKT/ mTOR signaling pathway members in clear cell renal cell carcinoma	21
Quantifying local ecological knowledge to model historical abundance of long-lived, heavily-exploited fauna	21
Ribovirus classification by a polymerase barcode sequence	21
Prediction of state anxiety by machine learning applied to photoplethysmography data	21
Identification and expression analysis of the DREB transcription factor family in pineapple (Ananas comosus (L.) Merr.)	21
Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields	21
Shade effects on growth, photosynthesis and chlorophyll fluorescence parameters of three Paeonia species	21
Tetrandrine alleviates cerebral ischemia/reperfusion injury by suppressing NLRP3 inflammasome activation via Sirt-1	21
Serratia marcescens antibiotic resistance mechanisms of an opportunistic pathogen: a literature review	21
A scoping review of determinants of performance in dressage	21
Reliability and validity of an equanimity questionnaire: the two-factor equanimity scale (EQUA-S)	21
Effects of dry-wet cycles on nitrous oxide emissions in freshwater sediments: a synthesis	21
Using organic fertilizers to increase crop yield, economic growth, and soil quality in a temperate farmland	21
Integrated analysis of the transcriptome-wide m6A methylome in preeclampsia and healthy control placentas	21
Six complete mitochondrial genomes of mayflies from three genera of Ephemerellidae (Insecta: Ephemeroptera) with inversion and translocation oftrnIrearrangement and their phylogenetic relations	21
The evaluation of factors affecting antibody response after administration of the BNT162b2 vaccine: a prospective study in Japan	21