| Maftools: efficient and comprehensive analysis of somatic variants in cancer |
178 |
| GrapeTree: visualization of core genomic relationships among 000 bacterial pathogens |
57 |
| Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid |
43 |
| SvABA: genome-wide detection of structural variants and indels by local assembly |
33 |
| Selective maternal seeding and environment shape the human gut microbiome |
33 |
| Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses |
33 |
| Human papillomavirus and the landscape of secondary genetic alterations in oral cancers |
31 |
| High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics |
31 |
| CRISPR RNAs trigger innate immune responses in human cells |
29 |
| Nucleosomes and DNA methylation shape meiotic DSB frequency in &ITArabidopsis thaliana&IT transposons and gene regulatory regions |
28 |
| Benchmark and integration of resources for the estimation of human transcription factor activities |
28 |
| RNA editing in nascent RNA affects pre-mRNA splicing |
26 |
| Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome |
25 |
| Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis |
25 |
| Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis |
23 |
| Enduring epigenetic landmarks define the cancer microenvironment |
23 |
| Fast and flexible bacterial genomic epidemiology with PopPUNK |
22 |
| Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin |
22 |
| A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci |
22 |
| The circular RNome of primary breast cancer |
21 |
| Sequential regulatory activity prediction across chromosomes with convolutional neural networks |
21 |
| Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome |
21 |
| The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting |
21 |
| Human proteins that interact with RNA/DNA hybrids |
20 |
| Structural variants in 3000 rice genomes |
20 |
| Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis |
20 |
| Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes |
19 |
| Decrypting noncoding RNA interactions, structures, and functional networks |
19 |
| In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors |
19 |
| Recompleting the Caenorhabditis elegans genome |
19 |
| An atlas of chromatin accessibility in the adult human brain |
19 |
| Resolving the full spectrum of human genome variation using Linked-Reads |
19 |
| Repeat associated mechanisms of genome evolution and function revealed by the &ITMus caroli&IT and &ITMus pahari&IT genomes |
18 |
| Epigenetic activation of meiotic recombination near&IT Arabidopsis thaliana&IT centromeres via loss of H3K9me2 and non-CG DNA methylation |
18 |
| A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection |
18 |
| A chromosome-scale assembly of the axolotl genome |
18 |
| MinION-based long-read sequencing and assembly extends the &ITCaenorhabditis elegans&IT reference genome |
18 |
| Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line |
17 |
| Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data |
17 |
| A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing |
17 |
| In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors |
16 |
| Genome-reconstruction for eukaryotes from complex natural microbial communities |
16 |
| Human contamination in bacterial genomes has created thousands of spurious proteins |
16 |
| The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes |
16 |
| A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs |
16 |
| Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly |
16 |
| Long-read sequencing of nascent RNA reveals coupling among RNA processing events |
16 |
| Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations |
16 |
| High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity |
16 |
| 3 ' UTR lengthening as a novel mechanism in regulating cellular senescence |
16 |
