In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts
present in each cell are sequenced. This leads to unreliable quantification of genes with low …

Abstract Knowledge of cell type composition in disease relevant tissues is an important step
towards the identification of cellular targets of disease. We present MuSiC, a method that …

In the analysis of data generated by change-point processes, one critical challenge is to
determine the number of change-points. The classic Bayes information criterion (BIC) statistic …

The intestine is a complex organ that promotes digestion, extracts nutrients, participates in
immune surveillance, maintains critical symbiotic relationships with microbiota and affects …

Interferon-gamma (IFNG) augments immune function yet promotes T cell exhaustion through
PDL1. How these opposing effects are integrated to impact immune checkpoint blockade (…

Complete loss of BRCA1 or BRCA2 function is associated with sensitivity to DNA damaging
agents. However, not all BRCA1 and BRCA2 germline mutation-associated tumors respond. …

Cancer is a disease driven by evolutionary selection on somatic genetic and epigenetic
alterations. Here, we propose Canopy, a method for inferring the evolutionary phylogeny of a …

… We follow the approach suggested in Zhang, Wildermuth, and Speed (2008) and use the
scores of the first principal component of the data, the loadings of which are plotted versus time …

… One is a multi-sequence version of the Bayesian information criterion for model selection
that we used for single sequence analysis (Zhang & Siegmund, 2007). This has the potential to …

Interferon-gamma (IFN-γ) has pleiotropic effects on cancer immune checkpoint blockade (ICB),
including roles in ICB resistance. We analyzed gene expression in ICB-sensitive versus …