A fundamental prerequisite for the efficacy of cancer immunotherapy is the presence of
functional, antigen-specific T cells within the tumor. Neoantigen-directed therapy is a …

Unraveling of the HLA-related immunogenetic basis of several immune disorders is complex
due to the extensive HLA polymorphism and strong linkage-disequilibrium between HLA …

Motivation The human leukocyte antigen (HLA) locus plays a critical role in tissue
compatibility and regulates the host response to many diseases, including cancers and …

There is growing interest in using genetic variants to augment the reference genome into a
graph genome, with alternative sequences, to improve read alignment accuracy and reduce …

Aligning DNA sequences to an annotated reference is a key step for genoty** in biology.
Recent scientific studies have demonstrated improved inference by aligning reads to a …

Motivation Variation graph representations are projected to either replace or supplement
conventional single genome references due to their ability to capture population genetic …

Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as
cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and …

In March 2019, 45 scientists and software engineers from around the world converged at the
University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the …

Graph-based genome representations have proven to be a powerful tool in genomic
analysis due to their ability to encode variations found in multiple haplotypes and capture …

Infections with Salmonella enterica serovars Typhi and Paratyphi A cause an estimated 14
million cases of enteric fever annually. Here, the controlled nature of challenge studies is …