By exerting pro-and anti-tumorigenic actions, tumor-infiltrating immune cells can profoundly
influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the …

Methodological breakthroughs over the past four decades have repeatedly revolutionized
transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to …

Single-cell RNA-sequencing has emerged as a powerful technique for characterizing
cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be …

CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance
and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With …

Gene expression profiling is nowadays routinely performed on clinically relevant samples
(eg, from tumor specimens). Such measurements are often obtained from bulk samples …

Immune cells infiltrating tumors can have important impact on tumor progression and
response to therapy. We present an efficient algorithm to simultaneously estimate the …

There is substantial heterogeneity among primary prostate cancers, evident in the spectrum
of molecular abnormalities and its variable clinical course. As part of The Cancer Genome …

Invasive lobular carcinoma (ILC) is the second most prevalent histologic subtype of invasive
breast cancer. Here, we comprehensively profiled 817 breast tumors, including 127 ILC, 490 …

Single-cell RNA sequencing studies have suggested that total mRNA content correlates with
tumor phenotypes. Technical and analytical challenges, however, have so far impeded at …

Gene expression analyses of bulk tissues often ignore cell type composition as an important
confounding factor, resulting in a loss of signal from lowly abundant cell types. In this review …