| # | Title | Journal | Year | Citations |
|---|
| 1 | Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences | F1000Research | 2015 | 2,612 |
| 2 | Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences | F1000Research | 2015 | 1,848 |
| 3 | FastQ Screen: A tool for multi-genome mapping and quality control | F1000Research | 2018 | 905 |
| 4 | FastQ Screen: A tool for multi-genome mapping and quality control | F1000Research | 2018 | 865 |
| 5 | A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor | F1000Research | 2016 | 822 |
| 6 | Leishmaniasis: a review | F1000Research | 2017 | 699 |
| 7 | Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses | F1000Research | 2016 | 664 |
| 8 | A step-by-step workflow for low-level analysis of single-cell RNA-seq data | F1000Research | 2016 | 654 |
| 9 | Sustainable data analysis with Snakemake | F1000Research | 2021 | 642 |
| 10 | Epidemiology of mental health problems in COVID-19: a review | F1000Research | 2020 | 633 |
| 11 | Current understanding of Alzheimer’s disease diagnosis and treatment | F1000Research | 2018 | 619 |
| 12 | BlobTools: Interrogation of genome assemblies | F1000Research | 0 | 600 |
| 13 | GFF Utilities: GffRead and GffCompare | F1000Research | 2020 | 579 |
| 14 | Plant adaptation to drought stress | F1000Research | 2016 | 538 |
| 15 | From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline | F1000Research | 2016 | 497 |
| 16 | HiCUP: pipeline for mapping and processing Hi-C data | F1000Research | 2015 | 485 |
| 17 | GFF Utilities: GffRead and GffCompare | F1000Research | 2020 | 469 |
| 18 | Bioconductor workflow for microbiome data analysis: from raw reads to community analyses | F1000Research | 2016 | 466 |
| 19 | taxize: taxonomic search and retrieval in R | F1000Research | 2013 | 407 |
| 20 | From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline | F1000Research | 2016 | 399 |
| 21 | CoNet app: inference of biological association networks using Cytoscape | F1000Research | 2016 | 398 |
| 22 | RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR | F1000Research | 2016 | 394 |
| 23 | Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues | F1000Research | 2013 | 372 |
| 24 | RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR | F1000Research | 2016 | 368 |
| 25 | Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CLpro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates | F1000Research | 2020 | 368 |
| 26 | Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis | F1000Research | 2017 | 366 |
| 27 | The khmer software package: enabling efficient nucleotide sequence analysis | F1000Research | 2015 | 362 |
| 28 | Recent advances in (therapeutic protein) drug development | F1000Research | 2017 | 348 |
| 29 | gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler | F1000Research | 2020 | 331 |
| 30 | CoNet app: inference of biological association networks using Cytoscape | F1000Research | 2016 | 331 |
| 31 | CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets | F1000Research | 2017 | 312 |
| 32 | RNA-Seq workflow: gene-level exploratory analysis and differential expression | F1000Research | 2015 | 304 |
| 33 | FreeSASA: An open source C library for solvent accessible surface area calculations | F1000Research | 2016 | 294 |
| 34 | Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues | F1000Research | 2013 | 293 |
| 35 | The academic, economic and societal impacts of Open Access: an evidence-based review | F1000Research | 2016 | 284 |
| 36 | Members of the genus Burkholderia: good and bad guys | F1000Research | 2016 | 280 |
| 37 | Dietary assessment methods in epidemiological research: current state of the art and future prospects | F1000Research | 2017 | 274 |
| 38 | MinION Analysis and Reference Consortium: Phase 1 data release and analysis | F1000Research | 2015 | 270 |
| 39 | Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China | F1000Research | 2020 | 251 |
| 40 | AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations | F1000Research | 2016 | 249 |
| 41 | CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets | F1000Research | 2017 | 244 |
| 42 | mTOR as a central regulator of lifespan and aging | F1000Research | 2019 | 244 |
| 43 | Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CLpro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates | F1000Research | 2020 | 242 |
| 44 | GeneMANIA: Fast gene network construction and function prediction for Cytoscape | F1000Research | 2014 | 242 |
| 45 | mTOR inhibitors in cancer therapy | F1000Research | 2016 | 228 |
| 46 | Tumour necrosis factor signalling in health and disease | F1000Research | 2019 | 228 |
| 47 | All disease begins in the (leaky) gut: role of zonulin-mediated gut permeability in the pathogenesis of some chronic inflammatory diseases | F1000Research | 2020 | 221 |
| 48 | taxize: taxonomic search and retrieval in R | F1000Research | 2013 | 219 |
| 49 | Noise-induced and age-related hearing loss: new perspectives and potential therapies | F1000Research | 2017 | 216 |
| 50 | Improving data transparency in clinical trials using blockchain smart contracts | F1000Research | 2016 | 215 |
