Aligning sequencing reads onto a reference is an essential step of the majority of genomic
analysis pipelines. Computational algorithms for read alignment have evolved in …

We now need more than ever to make genome analysis more intelligent. We need to read,
analyze, and interpret our genomes not only quickly, but also accurately and efficiently …

Background Tumor-infiltrating immune cells have been linked to prognosis and response to
immunotherapy; however, the levels of distinct immune cell subsets and the signals that …

Immune evasion is a hallmark of cancer and therapies that restore immune surveillance
have proven highly effective in cancers with high tumor mutation burden (TMB)(for example …

The CD155/TIGIT axis can be co-opted during immune evasion in chronic viral infections
and cancer. Pancreatic adenocarcinoma (PDAC) is a highly lethal malignancy, and immune …

Clonal evolution of a tumor ecosystem depends on different selection pressures that are
principally immune and treatment mediated. We integrate RNA-seq, DNA sequencing, TCR …

Read alignment is an ongoing challenge for the analysis of data from sequencing
technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and …

Long-read, single-molecule real-time (SMRT) sequencing is routinely used to finish
microbial genomes, but available assembly methods have not scaled well to larger …

Motivation: The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive
immunity and is thus relevant in many biomedical applications. While next-generation …

CD8+ T cell reactivity towards tumor mutation-derived neoantigens is widely believed to
facilitate the antitumor immunity induced by immune checkpoint blockade (ICB). Here we …