| SCANPY: large-scale single-cell gene expression data analysis |
233 |
| OrthoFinder: phylogenetic orthology inference for comparative genomics |
143 |
| Improved metagenomic analysis with Kraken 2 |
119 |
| Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data |
112 |
| Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression |
110 |
| PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells |
86 |
| Ten things you should know about transposable elements |
82 |
| From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy |
69 |
| Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics |
64 |
| Performance of neural network basecalling tools for Oxford Nanopore sequencing |
63 |
| Cytoscape Automation: empowering workflow-based network analysis |
63 |
| Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion |
63 |
| Translation of the circular RNA circ-catenin promotes liver cancer cell growth through activation of the Wnt pathway |
62 |
| A novel long noncoding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding to YBX1 |
58 |
| The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions |
54 |
| SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation |
53 |
| Exosomal miR-196a derived from cancer-associated fibroblasts confers cisplatin resistance in head and neck cancer through targeting CDKN1B and ING5 |
52 |
| DNA methylation aging clocks: challenges and recommendations |
50 |
| Current status and applications of genome-scale metabolic models |
50 |
| RNA virus interference via CRISPR/Cas13a system in plants |
48 |
| Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants |
46 |
| A novel FLI1 exonic circular RNA promotes metastasis in breast cancer by coordinately regulating TET1 and DNMT1 |
46 |
| EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data |
45 |
| Ythdf2-mediated m(6)A mRNA clearance modulates neural development in mice |
41 |
| SKESA: strategic k-mer extension for scrupulous assemblies |
41 |
| Identification of transcription factor binding sites using ATAC-seq |
40 |
| A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice |
39 |
| DeepCRISPR: optimized CRISPR guide RNA design by deep learning |
39 |
| Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data |
39 |
| Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing |
36 |
| Epigenetic modifications of histones in cancer |
36 |
| An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar |
35 |
| SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions |
34 |
| Applications and potential of genome editing in crop improvement |
32 |
| CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise |
31 |
| HiGlass: web-based visual exploration and analysis of genome interaction maps |
31 |
| Interaction between the microbiome and TP53 in human lung cancer |
31 |
| Analysis of error profiles in deep next-generation sequencing data |
30 |
| A comparison of automatic cell identification methods for single-cell RNA sequencing data |
30 |
| RNA m(6)A methylation participates in regulation of postnatal development of the mouse cerebellum |
29 |
| RaGOO: fast and accurate reference-guided scaffolding of draft genomes |
29 |
| Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods |
29 |
| KrakenUniq: confident and fast metagenomics classification using unique k-mer counts |
28 |
| Transcriptome assembly from long-read RNA-seq alignments with StringTie2 |
28 |
| Impact of transposable elements on genome structure and evolution in bread wheat |
28 |
| Chromosome evolution at the origin of the ancestral vertebrate genome |
27 |
| Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat |
25 |
| Livestock 2.0-genome editing for fitter, healthier, and more productive farmed animals |
24 |
| Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome |
24 |
| Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications |
24 |
