| # | Title | Journal | Year | Citations |
|---|
| 1 | VSEARCH: a versatile open source tool for metagenomics | PeerJ | 2016 | 7,113 |
| 2 | scikit-image: image processing in Python | PeerJ | 2014 | 3,711 |
| 3 | Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction | PeerJ | 2014 | 2,224 |
| 4 | MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | PeerJ | 2019 | 1,704 |
| 5 | MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities | PeerJ | 2015 | 1,546 |
| 6 | Anvi’o: an advanced analysis and visualization platform for ‘omics data | PeerJ | 2015 | 1,488 |
| 7 | A brief introduction to mixed effects modelling and multi-model inference in ecology | PeerJ | 2018 | 1,277 |
| 8 | VirSorter: mining viral signal from microbial genomic data | PeerJ | 2015 | 949 |
| 9 | Swarm: robust and fast clustering method for amplicon-based studies | PeerJ | 2014 | 828 |
| 10 | Using observation-level random effects to model overdispersion in count data in ecology and evolution | PeerJ | 2014 | 818 |
| 11 | Compact graphical representation of phylogenetic data and metadata with GraPhlAn | PeerJ | 2015 | 701 |
| 12 | Analyzing mixing systems using a new generation of Bayesian tracer mixing models | PeerJ | 2018 | 676 |
| 13 | PhyloSift: phylogenetic analysis of genomes and metagenomes | PeerJ | 2014 | 633 |
| 14 | The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles | PeerJ | 2018 | 606 |
| 15 | SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses | PeerJ | 2017 | 581 |
| 16 | Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences | PeerJ | 2014 | 535 |
| 17 | AMAS: a fast tool for alignment manipulation and computing of summary statistics | PeerJ | 2016 | 535 |
| 18 | Swarm v2: highly-scalable and high-resolution amplicon clustering | PeerJ | 2015 | 528 |
| 19 | Hierarchical generalized additive models in ecology: an introduction with mgcv | PeerJ | 2019 | 522 |
| 20 | kuenm: an R package for detailed development of ecological niche models using Maxent | PeerJ | 2019 | 473 |
| 21 | Random forest as a generic framework for predictive modeling of spatial and spatio-temporal variables | PeerJ | 2018 | 469 |
| 22 | D-GENIES: dot plot large genomes in an interactive, efficient and simple way | PeerJ | 2018 | 462 |
| 23 | The impact of artificial intelligence in medicine on the future role of the physician | PeerJ | 2019 | 364 |
| 24 | Factors affecting the composition of the gut microbiota, and its modulation | PeerJ | 2019 | 360 |
| 25 | dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms | PeerJ | 2014 | 357 |
| 26 | Data reuse and the open data citation advantage | PeerJ | 2013 | 352 |
| 27 | Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons | PeerJ | 2017 | 325 |
| 28 | Linking pangenomes and metagenomes: the Prochlorococcus metapangenome | PeerJ | 2018 | 318 |
| 29 | Real-time bioacoustics monitoring and automated species identification | PeerJ | 2013 | 315 |
| 30 | Pre-trained convolutional neural networks as feature extractors toward improved malaria parasite detection in thin blood smear images | PeerJ | 2018 | 298 |
| 31 | Validation of the Emotiv EPOC®EEG gaming system for measuring research quality auditory ERPs | PeerJ | 2013 | 288 |
| 32 | A comparison of observation-level random effect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution | PeerJ | 2015 | 286 |
| 33 | Breast cancer detection using deep convolutional neural networks and support vector machines | PeerJ | 2019 | 279 |
| 34 | Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches | PeerJ | 2018 | 278 |
| 35 | MaxEnt’s parameter configuration and small samples: are we paying attention to recommendations? A systematic review | PeerJ | 2017 | 270 |
| 36 | The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes | PeerJ | 2014 | 265 |
| 37 | iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteineS-nitrosylation sites in proteins | PeerJ | 2013 | 259 |
| 38 | System wide analyses have underestimated protein abundances and the importance of transcription in mammals | PeerJ | 2014 | 255 |
| 39 | GroopM: an automated tool for the recovery of population genomes from related metagenomes | PeerJ | 2014 | 254 |
| 40 | Spider phylogenomics: untangling the Spider Tree of Life | PeerJ | 2016 | 253 |
| 41 | De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units | PeerJ | 2015 | 247 |
| 42 | Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext) | PeerJ | 2019 | 243 |
| 43 | 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 | PeerJ | 2020 | 242 |
| 44 | The timing mega-study: comparing a range of experiment generators, both lab-based and online | PeerJ | 2020 | 242 |
| 45 | Leopard (Panthera pardus) status, distribution, and the research efforts across its range | PeerJ | 2016 | 238 |
| 46 | Identification ofSalmonellafor public health surveillance using whole genome sequencing | PeerJ | 2016 | 236 |
| 47 | Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity | PeerJ | 2017 | 235 |
| 48 | Phage on tap–a quick and efficient protocol for the preparation of bacteriophage laboratory stocks | PeerJ | 2016 | 233 |
| 49 | The phylogenetic relationships of basal archosauromorphs, with an emphasis on the systematics of proterosuchian archosauriforms | PeerJ | 2016 | 233 |
| 50 | The relationship between mobile phone location sensor data and depressive symptom severity | PeerJ | 2016 | 229 |
