Minimap2: pairwise alignment for nucleotide sequences
Abstract Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic cont...
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1,686 publications
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets
A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Succe...
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood....
Reflecting on reflexive thematic analysis
Since initially writing on thematic analysis in 2006, the popularity of the method we outlined has exploded, the variety of TA approaches have expanded, and, not least, our thin...
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for...
Integrating single-cell transcriptomic data across different conditions, technologies, and species
Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and defin...
The Sequence of the Human Genome
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp ...
Global, regional, and national incidence, prevalence, and years lived with disability for 354 diseases and injuries for 195 countries and territories, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017
The Global Burden of Diseases, Injuries, and Risk Factors Study 2017 (GBD 2017) includes a comprehensive assessment of incidence, prevalence, and years lived with disability (YL...
Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis
Antimicrobial resistance (AMR) poses a major threat to human health around the world. Previous publications have estimated the effect of AMR on incidence, deaths, hospital lengt...
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexib...
Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation
Spatial pyramid pooling module or encode-decoder structure are used in deep neural networks for semantic segmentation task. The former networks are able to encode multi-scale co...
APACHE II
This paper presents the form and validation results of APACHE II, a severity of disease classification system. APACHE II uses a point score based upon initial values of 12 routi...