PeerJ

Papers
(The TQCC of PeerJ is 6. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-03-01 to 2024-03-01.)
ArticleCitations
The timing mega-study: comparing a range of experiment generators, both lab-based and online231
Impact of COVID-19 outbreak on the mental health status of undergraduate medical students in a COVID-19 treating medical college: a prospective longitudinal study220
Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection135
BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains111
Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities110
partR2: partitioning R2 in generalized linear mixed models107
Computational bioacoustics with deep learning: a review and roadmap99
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 approach99
Comparing multiple comparisons: practical guidance for choosing the best multiple comparisons test98
Transfection types, methods and strategies: a technical review92
Deep learning prediction of likelihood of ICU admission and mortality in COVID-19 patients using clinical variables79
Air transportation, population density and temperature predict the spread of COVID-19 in Brazil77
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture77
Applications and limitations of current markerless motion capture methods for clinical gait biomechanics71
A technical review and guide to RNA fluorescence in situ hybridization71
No one-size-fits-all solution to clean GBIF71
Shannon diversity index: a call to replace the original Shannon’s formula with unbiased estimator in the population genetics studies70
Potential role of cellular miRNAs in coronavirus-host interplay66
A comparison of COVID-19, SARS and MERS66
Plastic additives: challenges in ecotox hazard assessment65
Utilization of brewery wastes in food industry65
A potential role for Galectin-3 inhibitors in the treatment of COVID-1964
Effectiveness of topical antibiotics in treating corals affected by Stony Coral Tissue Loss Disease62
Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study62
Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems60
Identifying potential threats to soil biodiversity60
Predicting CoVID-19 community mortality risk using machine learning and development of an online prognostic tool59
A game-theoretic model of Monkeypox to assess vaccination strategies58
eDNAir: proof of concept that animal DNA can be collected from air sampling58
Let’s talk about pain catastrophizing measures: an item content analysis58
Purpureocillium lilacinum and Metarhizium marquandii as plant growth-promoting fungi57
Current and future trends in socio-economic, demographic and governance factors affecting global primate conservation56
The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma55
Perils and pitfalls of mixed-effects regression models in biology55
Altered gut microbiota associated with symptom severity in schizophrenia54
Assessment of activities of daily living in patients post COVID-19: a systematic review54
Melatonin improves the germination rate of cotton seeds under drought stress by opening pores in the seed coat51
Evaluation of knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic51
The altered gut microbiota of high-purine-induced hyperuricemia rats and its correlation with hyperuricemia50
RdRp mutations are associated with SARS-CoV-2 genome evolution49
Combined application of biochar and nitrogen fertilizer improves rice yield, microbial activity and N-metabolism in a pot experiment49
Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure49
Drought stress strengthens the link between chlorophyll fluorescence parameters and photosynthetic traits48
Global expansion of COVID-19 pandemic is driven by population size and airport connections48
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation48
Publication rate and citation counts for preprints released during the COVID-19 pandemic: the good, the bad and the ugly47
Syncmers are more sensitive than minimizers for selecting conserved k‑mers in biological sequences46
Recent advances in biochar application for water and wastewater treatment: a review46
Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and45
Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function45
The role of textiles as fomites in the healthcare environment: a review of the infection control risk44
Exogenous melatonin improves salt stress adaptation of cotton seedlings by regulating active oxygen metabolism44
Contamination and oxidative stress biomarkers in estuarine fish following a mine tailing disaster44
COVID-19: exploring impacts of the pandemic and lockdown on mental health of Pakistani students44
Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics43
Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach43
Beyond loot boxes: a variety of gambling-like practices in video games are linked to both problem gambling and disordered gaming43
Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs43
A community perspective on the concept of marine holobionts: current status, challenges, and future directions42
Identification of WRKY gene family and characterization of cold stress-responsive WRKY genes in eggplant42
Evolution ofWolbachiamutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas42
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager42
A high-resolution growth series ofTyrannosaurus rexobtained from multiple lines of evidence42
MULTI-DEEP: A novel CAD system for coronavirus (COVID-19) diagnosis from CT images using multiple convolution neural networks42
Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study41
Resampling-based methods for biologists41
Integrated analysis of lymphocyte infiltration-associated lncRNA for ovarian cancer via TCGA, GTEx and GEO datasets40
Modelling fatality curves of COVID-19 and the effectiveness of intervention strategies40
A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research39
Harmful effects of the microplastic pollution on animal health: a literature review39
Open Access uptake by universities worldwide39
The efficacy of IL-6 inhibitor Tocilizumab in reducing severe COVID-19 mortality: a systematic review39
Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)38
Diversity of fall armyworm, Spodoptera frugiperda and their gut bacterial community in Kenya38
Effect of storage conditions on SARS-CoV-2 RNA quantification in wastewater solids38
PCAtest: testing the statistical significance of Principal Component Analysis in R38
Geographic potential of the world’s largest hornet,Vespa mandariniaSmith (Hymenoptera: Vespidae), worldwide and particularly in North America38
Should I use fixed effects or random effects when I have fewer than five levels of a grouping factor in a mixed-effects model?38
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-regression38
Tumour-associated macrophages mediate the invasion and metastasis of bladder cancer cells through CXCL838
Exosomes derived from M0, M1 and M2 macrophages exert distinct influences on the proliferation and differentiation of mesenchymal stem cells37
Effects of Origanum vulgare essential oil and its two main components, carvacrol and thymol, on the plant pathogen Botrytis cinerea37
Co-application of bio-fertilizer and salicylic acid improves growth, photosynthetic pigments and stress tolerance in wheat under drought stress37
Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries37
Mutational spectra of SARS-CoV-2 isolated from animals36
Effects of plastic mulching on the accumulation and distribution of macro and micro plastics in soils of two farming systems in Northwest China35
Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load35
A validation of Emotiv EPOC Flex saline for EEG and ERP research34
Macrel: antimicrobial peptide screening in genomes and metagenomes34
Perception and practices during the COVID-19 pandemic in an urban community in Nigeria: a cross-sectional study34
Arthropod IGF, relaxin and gonadulin, putative orthologs of Drosophila insulin-like peptides 6, 7 and 8, likely originated from an ancient gene triplication34
Taxonomic revision of the threatened African genus Pseudohydrosme Engl. (Araceae), with P. ebo, a new, critically endangered species from Ebo, Cameroon34
Polylactic acid as a suitable material for 3D printing of protective masks in times of COVID-19 pandemic34
iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC34
Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease33
The biomarkers of key miRNAs and target genes associated with acute myocardial infarction33
Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem32
Molecular detection and genotyping of intestinal protozoa from different biogeographical regions of Colombia32
Production of cupcake-like dessert containing microbial biosurfactant as an emulsifier32
CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content32
Potential of rice straw biochar, sulfur and ryegrass (Lolium perenne L.) in remediating soil contaminated with nickel through irrigation with untreated wastewater32
Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis32
Uncovering the species diversity of subterranean rodents at the end of the World: three new species of Patagonian tuco-tucos (Rodentia, Hystricomorpha,Ctenomys)31
mHealth technology for ecological momentary assessment in physical activity research: a systematic review31
COL1A1 is a prognostic biomarker and correlated with immune infiltrates in lung cancer31
Lactobacillus reuteri TSR332 and Lactobacillus fermentum TSF331 stabilize serum uric acid levels and prevent hyperuricemia in rats31
Isolation and identification of flavonoid-producing endophytic fungi from medicinal plant Conyza blinii H.Lév that exhibit higher antioxidant and antibacterial activities31
Liraglutide-induced structural modulation of the gut microbiota in patients with type 2 diabetes mellitus31
Air quality improvement during triple-lockdown in the coastal city of Kannur, Kerala to combat Covid-19 transmission31
Biases in genome reconstruction from metagenomic data30
The linkages of plant, litter and soil C:N:P stoichiometry and nutrient stock in different secondary mixed forest types in the Qinling Mountains, China30
Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues30
Effects of self-isolation and quarantine on loot box spending and excessive gaming—results of a natural experiment30
The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies30
Self-concept in poor readers: a systematic review and meta-analysis30
Prophet forecasting model: a machine learning approach to predict the concentration of air pollutants (PM2.5, PM10, O3, NO2, SO2, CO) in Seoul, S30
CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments30
Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters30
Nitrogen eutrophication particularly promotes turf algae in coral reefs of the central Red Sea29
Luteolin attenuates doxorubicin-induced cardiotoxicity by modulating the PHLPP1/AKT/Bcl-2 signalling pathway29
Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns29
ClpP regulates breast cancer cell proliferation, invasion and apoptosis by modulating the Src/PI3K/Akt signaling pathway29
Blue carbon of Mexico, carbon stocks and fluxes: a systematic review29
Omics approaches inAlliumresearch: Progress and way ahead29
Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment29
SARS-CoV-2 seroprevalence study in Lambayeque, Peru. June–July 202029
Desulfovibrio is not always associated with adverse health effects in the Guangdong Gut Microbiome Project29
Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions28
Zonula occludens and nasal epithelial barrier integrity in allergic rhinitis28
Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios28
Insight into the kinematics of blue whale surface foraging through drone observations and prey data28
Polarity and epithelial-mesenchymal transition of retinal pigment epithelial cells in proliferative vitreoretinopathy28
A fresh look at an old concept: home-range estimation in a tidy world28
The phylogenetics of Teleosauroidea (Crocodylomorpha, Thalattosuchia) and implications for their ecology and evolution28
The reuse of public datasets in the life sciences: potential risks and rewards28
Clinical applicability of the Feline Grimace Scale: real-time versus image scoring and the influence of sedation and surgery28
Sharing for science: high-resolution trophic interactions revealed rapidly by social media28
Combination of circulating miR-145-5p/miR-191-5p as biomarker for breast cancer detection28
The m6A reader protein YTHDC2 is a potential biomarker and associated with immune infiltration in head and neck squamous cell carcinoma27
Temperature alters the shape of predator–prey cycles through effects on underlying mechanisms27
Alien plants of Europe: introduction pathways, gateways and time trends27
Characterization of cold stress responses in different rapeseed ecotypes based on metabolomics and transcriptomics analyses27
Nitrogen fertilization affects maize grain yield through regulating nitrogen uptake, radiation and water use efficiency, photosynthesis and root distribution27
Role of salicylic acid in regulating ethylene and physiological characteristics for alleviating salinity stress on germination, growth and yield of sweet pepper27
Revisiting food-sourced vitamins for consumer diet and health needs: a perspective review, from vitamin classification, metabolic functions, absorption, utilization, to balancing nutritional requireme27
COVID-19: molecular and serological detection methods27
Validation of a general subjective well-being factor using Classical Test Theory27
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 England27
COVID-19 mortality in cancer patients: a report from a tertiary cancer centre in India27
Effect of calcium on relieving berry cracking in grape (Vitis viniferaL.) ‘Xiangfei’27
Deep-learning convolutional neural networks with transfer learning accurately classify COVID-19 lung infection on portable chest radiographs27
Predicting continuous ground reaction forces from accelerometers during uphill and downhill running: a recurrent neural network solution27
Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)27
A review of the carotid artery and facial nerve canal systems in extant turtles26
The phylogenetic nomenclature of ornithischian dinosaurs26
Adaptive Metropolis-coupled MCMC for BEAST 226
Effects of outdoor ranging on external and internal health parameters for hens from different rearing enrichments26
A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genusMicrohyla(Amphibia: Microhylidae)26
A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-1926
The phylogeny and systematics of Xiphosura26
A descriptive study of random forest algorithm for predicting COVID-19 patients outcome26
Double lives: transfer of fungal endophytes from leaves to woody substrates26
Evidence of transfer of miRNAs from the diet to the blood still inconclusive26
Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians26
Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-226
In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococci26
Salmo salar fish waste oil: Fatty acids composition and antibacterial activity25
The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genusAurelia(Cnidaria: Scyphozoa)25
Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture25
Entomopathogenic fungi decreaseRhizoctoniadisease in potato in field conditions25
Exosomal hsa-miR-21-5p is a biomarker for breast cancer diagnosis25
Phosphate solubilizing bacteria stimulate wheat rhizosphere and endosphere biological nitrogen fixation by improving phosphorus content25
ATR-FTIR, EDS and SEM evaluations of enamel structure after treatment with hydrogen peroxide bleaching agents loaded with nano-hydroxyapatite particles25
Changes in precipitation amounts and extremes across Xinjiang (northwest China) and their connection to climate indices25
Detection and visualization of abnormality in chest radiographs using modality-specific convolutional neural network ensembles25
Agreement between the GAITRite® System and the Wearable Sensor BTS G-Walk® for measurement of gait parameters in healthy adults and Parkinson’s disease patients25
Soil health and nutrient density: preliminary comparison of regenerative and conventional farming25
Repurposing FDA-approved phytomedicines, natural products, antivirals and cell protectives against SARS-CoV-2 (COVID-19) RNA-dependent RNA polymerase25
Machine learning in dental, oral and craniofacial imaging: a review of recent progress25
Exact integer linear programming solvers outperform simulated annealing for solving conservation planning problems25
The effects of humic substances on DNA isolation from soils25
Potential of the economic valuation of soil-based ecosystem services to inform sustainable soil management and policy24
Identification of areas of very high biodiversity value to achieve the EU Biodiversity Strategy for 2030 key commitments24
Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation24
Assessment and simulation of land use and land cover change impacts on the land surface temperature of Chaoyang District in Beijing, China24
An eye for a tooth:Thylacosmiluswas not a marsupial “saber-tooth predator”24
Coupling effects of phosphorus fertilization source and rate on growth and ion accumulation of common bean under salinity stress24
Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)24
IL-4/IL-13 axis as therapeutic targets in allergic rhinitis and asthma24
Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil24
Clinical validation of the short and long UNESP-Botucatu scales for feline pain assessment24
Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements24
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly24
Antibacterial activity and mechanism of sanguinarine againstProvidencia rettgeriin vitro24
Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma24
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets24
Exogenous melatonin improves growth in hulless barley seedlings under cold stress by influencing the expression rhythms of circadian clock genes24
Beyond polyphagy and opportunism: natural prey of hunting spiders in the canopy of apple trees24
Estimation of soil salt content by combining UAV-borne multispectral sensor and machine learning algorithms23
The association between serum uric acid and diabetic complications in patients with type 2 diabetes mellitus by gender: a cross-sectional study23
Cranial osteology of the Early Cretaceous turtlePleurosternon bullockii(Paracryptodira: Pleurosternidae)23
Fast sequence-based microsatellite genotyping development workflow23
Comparative transcriptome analyses of maize seedling root responses to salt stress23
High microphone signal-to-noise ratio enhances acoustic sampling of wildlife23
healthcareCOVID: a national cross-sectional observational study identifying risk factors for developing suspected or confirmed COVID-19 in UK healthcare workers23
VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature22
Comparison of gut microbiota between adults with autism spectrum disorder and obese adults22
Evaluation of the effective dose of amygdalin for the improvement of antioxidant gene expression and suppression of oxidative damage in mice22
Settling taxonomic and nomenclatural problems in brine shrimps,Artemia(Crustacea: Branchiopoda: Anostraca), by integrating mitogenomics, marker discordances and nomenclature rules22
Generation of human liver organoids from pluripotent stem cell-derived hepatic endoderms22
Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)22
Silicon induces hormetic dose-response effects on growth and concentrations of chlorophylls, amino acids and sugars in pepper plants during the early developmental stage22
miR-29a-3p directly targets Smad nuclear interacting protein 1 and inhibits the migration and proliferation of cervical cancer HeLa cells22
Lots of movement, little progress: a review of reptile home range literature22
Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-222
Improving decolorization of dyes by laccase from Bacillus licheniformis by random and site-directed mutagenesis22
Prognostic implications of metabolism-associated gene signatures in colorectal cancer22
Measuring recognition memory in zebrafish larvae: issues and limitations22
Prognostic analysis of histopathological images using pre-trained convolutional neural networks: application to hepatocellular carcinoma22
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 scores22
Diversity of rhizosphere and endophytic fungi in Atractylodes macrocephala during continuous cropping22
Genome-wide analysis of growth-regulating factors (GRFs) inTriticum aestivum22
Public perspectives and media reporting of wolf reintroduction in Colorado22
Changes in sprint performance and sagittal plane kinematics after heavy resisted sprint training in professional soccer players22
Healthcare applications of single camera markerless motion capture: a scoping review22
Transcriptomic analysis highlights cochlear inflammation associated with age-related hearing loss in C57BL/6 mice using next generation sequencing22
Association between serum and dietary antioxidant micronutrients and advanced liver fibrosis in non-alcoholic fatty liver disease: an observational study22
Assessing turbine passage effects on internal fish injury and delayed mortality using X-ray imaging22
COVID-19: Taiwan’s epidemiological characteristics and public and hospital responses22
Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome22
Shade effects on growth, photosynthesis and chlorophyll fluorescence parameters of three Paeonia species21
Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide21
Association between dietary mineral nutrient intake, body mass index, and waist circumference in U.S. adults using quantile regression analysis NHANES 2007–201421
A new phylogenetic hypothesis of Tanystropheidae (Diapsida, Archosauromorpha) and other “protorosaurs”, and its implications for the early evolution of stem archosaurs21
LCZ696 mitigates diabetic-induced nephropathy through inhibiting oxidative stress, NF-κB mediated inflammation and glomerulosclerosis in rats21
Effects of dry-wet cycles on nitrous oxide emissions in freshwater sediments: a synthesis21
Using organic fertilizers to increase crop yield, economic growth, and soil quality in a temperate farmland21
The effect of brewery spent grain application on biogas yields and kinetics in co-digestion with sewage sludge21
Fecal microbiota transplantation mitigates bone loss by improving gut microbiome composition and gut barrier function in aged rats21
The regulation of immune checkpoints by the hypoxic tumor microenvironment21
Identification and expression analysis of the DREB transcription factor family in pineapple (Ananas comosus (L.) Merr.)21
Osmotic stress in banana is relieved by exogenous nitric oxide21
Tetrandrine alleviates cerebral ischemia/reperfusion injury by suppressing NLRP3 inflammasome activation via Sirt-121
The metabolism and role of free fatty acids in key physiological processes in insects of medical, veterinary and forensic importance21
Serratia marcescens antibiotic resistance mechanisms of an opportunistic pathogen: a literature review21
A scoping review of determinants of performance in dressage21
Prediction of state anxiety by machine learning applied to photoplethysmography data21
Experiencing fear during the pandemic: validation of the fear of COVID-19 scale in Polish21
The paleobiology and paleoecology of South African Lystrosaurus21
Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields21
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