Analysis Pipelines

With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which ...

Transfer of genetic material from microbes or viruses into the host genome is known as horizontal gene transfer (HGT). The integration of viruses into the human genome is associated with multiple...

A CRISPR locus, defined by an array of repeat and spacer elements, constitutes a genetic record of the ceaseless battle between bacteria and viruses, showcasing the genomic integration of spacers acquired from invasive DNA. In particular, iterative...

To comprehensively study extracellular small RNAs (sRNA) by sequencing (sRNA-seq), researchers at the Vanderbilt University Medical Center developed a novel pipeline to overcome current limitations in analysis entitled, "Tools for Integrative Genome analysis...

Discovering new long non-coding RNAs (lncRNAs) has been a fundamental step in lncRNA-related research. Nowadays, many machine learning-based tools have been developed for lncRNA identification. However, many methods predict lncRNAs using sequence-derived features alone, which tend to display unstable performances ...

The field of small RNA is one of the most investigated research areas since they were shown to regulate transposable elements and gene...

Recently, long noncoding RNA molecules (lncRNA) captured widespread attentions for its critical roles in diverse biological process and important implications in variety of human diseases and cancers...

Assay for Transposase-Accessible Chromatin (ATAC)-cap-seq is a high-throughput sequencing method that combines ATAC-seq with targeted nucleic acid enrichment of precipitated DNA fragments. There are increased analytical difficulties arising from working with a set of regions of interest that may be ...

Although different quality controls have been applied at different stages of the sample preparation and data analysis to ensure both reproducibility and reliability of RNA-seq results, there are still limitations and bias on the detectability for certain differentially expressed genes ...

Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing...