MOTIVATION: Structural variants (SVs) play an important role in genetic research and precision medicine. As existing SV detection methods usually contain a substantial number of false positive calls, approaches to filter the detection results are nee...
Next-generation DNA sequencing has shown that the great plate count anomaly, that is, the difference between bacteria present in the environment and those that can be obtained in culture from that environment, is even greater and more persisting than...
Recent advancements in high-throughput sequencing technologies have significantly enhanced our ability to unravel the intricacies of gene regulatory processes. A critical challenge in this endeavor is the identification of variant effects, a key fact...
High-throughput DNA sequencing technologies decode tremendous amounts of microbial protein-coding gene sequences. However, accurately assigning protein functions to novel gene sequences remain a challenge. To this end, we developed FunGeneTyper, an e...
The advent of high-throughput sequencing technologies has not only revolutionized the field of bioinformatics but has also heightened the demand for efficient taxonomic classification. Despite technological advancements, efficiently processing and an...
MOTIVATION: Structural variants (SVs) play a causal role in numerous diseases but can be difficult to detect and accurately genotype (determine zygosity) with short-read genome sequencing data (SRS). Improving SV genotyping accuracy in SRS data, part...
A powerful adaptive immune system, which includes cellular (T lymphocytes) and humoral (B lymphocytes) immunity, depends on its ability to recognize and protect against millions of different foreign antigens. It does so through an enormous diverse ar...
High throughput sequencing of B cell receptors (BCRs) is increasingly applied to study the immense diversity of antibodies. Learning biologically meaningful embeddings of BCR sequences is beneficial for predictive modeling. Several embedding methods ...
Proteins play an important role in life activities and are the basic units for performing functions. Accurately annotating functions to proteins is crucial for understanding the intricate mechanisms of life and developing effective treatments for com...
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