Current advances in next-generation sequencing techniques have allowed researchers to conduct comprehensive research on the microbiome and human diseases, with recent studies identifying associations between the human microbiome and health outcomes f...
Deep learning algorithms have been utilized to achieve enhanced performance in pattern-recognition tasks. The ability to learn complex patterns in data has tremendous implications in immunogenomics. T-cell receptor (TCR) sequencing assesses the diver...
Controlling quality of next-generation sequencing (NGS) data files is a necessary but complex task. To address this problem, we statistically characterize common NGS quality features and develop a novel quality control procedure involving tree-based ...
The presence of pathogen-specific antibodies in an individual's blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achie...
The identification of SARS-CoV-2-specific T cell receptor (TCR) sequences is critical for understanding T cell responses to SARS-CoV-2. Accordingly, we reanalyze publicly available data from SARS-CoV-2-recovered patients who had low-severity disease ...
Retrotransposons can cause somatic genome variation in the human nervous system, which is hypothesized to have relevance to brain development and neuropsychiatric disease. However, the detection of individual somatic mobile element insertions present...
Genotype plays a significant role in determining characteristics in an organism and genotype calling has been greatly accelerated by sequencing technologies. Furthermore, most parametric statistical models are unable to effectively call genotype, whi...
Small non-coding RNAs (ncRNAs) are short non-coding sequences involved in gene regulation in many biological processes and diseases. The lack of a complete comprehension of their biological functionality, especially in a genome-wide scenario, has dem...
In research and clinical genomics laboratories today, sample preparation is the bottleneck of experiments, particularly when it comes to high-throughput next generation sequencing (NGS). More genomics laboratories are now considering liquid-handling ...
Next-generation sequencing (NGS) methods lie at the heart of large parts of biological and medical research. Their fundamental importance has created a continuously increasing demand for processing and analysis methods of the data sets produced, addr...