The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we a...
BACKGROUND: Quantifying gene expression by RNA-Seq has several advantages over microarrays, including greater dynamic range and gene expression estimates on an absolute, rather than a relative scale. Nevertheless, microarrays remain in widespread use...
Journal of bioinformatics and computational biology
Aug 24, 2015
Sequence alignment/map (SAM) formatted sequences [Li H, Handsaker B, Wysoker A et al., Bioinformatics 25(16):2078-2079, 2009.] have taken on a main role in bioinformatics since the development of massive parallel sequencing. However, because misalign...
BACKGROUND: People with an autistic spectrum disorder (ASD) display a variety of characteristic behavioral traits, including impaired social interaction, communication difficulties and repetitive behavior. This complex neurodevelopment disorder is kn...
BACKGROUND: High throughput sequencing technologies are able to identify the whole genomic variation of an individual. Gene-targeted and whole-exome experiments are mainly focused on coding sequence variants related to a single or multiple nucleotide...
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtai...
BACKGROUND: Microsatellite instability (MSI) has emerged as a predictive biomarker for immunotherapy response in various cancers, but its role in non-small cell lung cancer (NSCLC) is not fully understood.
The rapid advancement of next-generation sequencing (NGS) technology and the expanding availability of NGS datasets have led to a significant surge in biomedical research. To better understand the molecular processes, underlying cancer and to support...
MOTIVATION: Single-cell RNA sequencing (scRNA-seq) enables high-throughput transcriptomic profiling at single-cell resolution. The inherent spatial location is crucial for understanding how single cells orchestrate multicellular functions and drive d...
RNA sequencing (RNA-seq) is widely adopted for transcriptome analysis but has inherent biases that hinder the comprehensive detection and quantification of alternative splicing. To address this, we present an efficient targeted RNA-seq method that gr...