Next-generation sequencing: insights to advance clinical investigations of the microbiome
CR Wensel, JL Pluznick, SL Salzberg… - The Journal of clinical …, 2022 - Am Soc Clin Investig
Next-generation sequencing (NGS) technology has advanced our understanding of the
human microbiome by allowing for the discovery and characterization of unculturable …
human microbiome by allowing for the discovery and characterization of unculturable …
Next-generation sequencing technologies: An overview
T Hu, N Chitnis, D Monos, A Dinh - Human Immunology, 2021 - Elsevier
Since the days of Sanger sequencing, next-generation sequencing technologies have
significantly evolved to provide increased data output, efficiencies, and applications. These …
significantly evolved to provide increased data output, efficiencies, and applications. These …
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological
studies. It becomes routine to utilize multiple genes on mitogenome or the entire …
studies. It becomes routine to utilize multiple genes on mitogenome or the entire …
[HTML][HTML] Integrated proteogenomic characterization of HBV-related hepatocellular carcinoma
We performed the first proteogenomic characterization of hepatitis B virus (HBV)-related
hepatocellular carcinoma (HCC) using paired tumor and adjacent liver tissues from 159 …
hepatocellular carcinoma (HCC) using paired tumor and adjacent liver tissues from 159 …
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently
available microbial genomes. This is being addressed by advances in sequencing …
available microbial genomes. This is being addressed by advances in sequencing …
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are
increasingly used in high-throughput sequencing experiments. Through a UMI, identical …
increasingly used in high-throughput sequencing experiments. Through a UMI, identical …
A survey of best practices for RNA-seq data analysis
Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
E Becht, NA Giraldo, L Lacroix, B Buttard, N Elarouci… - Genome biology, 2016 - Springer
Abstract We introduce the Microenvironment Cell Populations-counter (MCP-counter)
method, which allows the robust quantification of the absolute abundance of eight immune …
method, which allows the robust quantification of the absolute abundance of eight immune …
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data
Motivation: Detection of random errors and systematic biases is a crucial step of a robust
pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software …
pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software …
Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing
The human microbiome has emerged as a major player in regulating human health and
disease. Translational studies of the microbiome have the potential to indicate clinical …
disease. Translational studies of the microbiome have the potential to indicate clinical …