New approaches for metagenome assembly with short reads
M Ayling, MD Clark, RM Leggett - Briefings in bioinformatics, 2020 - academic.oup.com
In recent years, the use of longer range read data combined with advances in assembly
algorithms has stimulated big improvements in the contiguity and quality of genome …
algorithms has stimulated big improvements in the contiguity and quality of genome …
Perspective on taxonomic classification of uncultivated viruses
Historically, virus taxonomy has been limited to describing viruses that were readily
cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single …
cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single …
Cancer‐associated fibroblast‐mediated cellular crosstalk supports hepatocellular carcinoma progression
M Song, J He, QZ Pan, J Yang, J Zhao, YJ Zhang… - …, 2021 - Wiley Online Library
Background and Aims Cancer‐associated fibroblasts (CAFs) are key players in multicellular,
stromal‐dependent alterations leading to HCC pathogenesis. However, the intricate …
stromal‐dependent alterations leading to HCC pathogenesis. However, the intricate …
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
Sequence analyses of RNA virus genomes remain challenging owing to the exceptional
genetic plasticity of these viruses. Because of high mutation and recombination rates …
genetic plasticity of these viruses. Because of high mutation and recombination rates …
A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events
Genome-wide association study (GWAS) methods applied to bacterial genomes have
shown promising results for genetic marker discovery or detailed assessment of marker …
shown promising results for genetic marker discovery or detailed assessment of marker …
Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques
Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter
the ongoing pandemic. Predicting lineage abundance from wastewater, however, is …
the ongoing pandemic. Predicting lineage abundance from wastewater, however, is …
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data
S Posada-Céspedes, D Seifert, I Topolsky… - …, 2021 - academic.oup.com
Motivation High-throughput sequencing technologies are used increasingly not only in viral
genomics research but also in clinical surveillance and diagnostics. These technologies …
genomics research but also in clinical surveillance and diagnostics. These technologies …
Bioinformatics resources for SARS-CoV-2 discovery and surveillance
T Hu, J Li, H Zhou, C Li, EC Holmes… - Briefings in …, 2021 - academic.oup.com
In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia
outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and …
outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and …
Strainberry: automated strain separation in low-complexity metagenomes using long reads
High-throughput short-read metagenomics has enabled large-scale species-level analysis
and functional characterization of microbial communities. Microbiomes often contain multiple …
and functional characterization of microbial communities. Microbiomes often contain multiple …
Computational graph pangenomics: a tutorial on data structures and their applications
Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …
computer scientists are facing challenges in biological sequence analysis. In past decades …