Computational genomics tools for dissecting tumour–immune cell interactions
Recent breakthroughs in cancer immunotherapy and decreasing costs of high-throughput
technologies have sparked intensive research into tumour–immune cell interactions using …
technologies have sparked intensive research into tumour–immune cell interactions using …
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA …
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 …
immunotherapy; however, the levels of distinct immune cell subsets and the signals that …
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
E Becht, NA Giraldo, L Lacroix, B Buttard, N Elarouci… - Genome biology, 2016 - Springer
Abstract We introduce the Microenvironment Cell Populations-counter (MCP-counter)
method, which allows the robust quantification of the absolute abundance of eight immune …
method, which allows the robust quantification of the absolute abundance of eight immune …
High-throughput genomic profiling of tumor-infiltrating leukocytes
AM Newman, AA Alizadeh - Current opinion in immunology, 2016 - Elsevier
Highlights•Tumor infiltrating leukocytes (TILs) critically influence cancer clinical
outcomes.•Classical techniques for studying TILs have important limitations.•TILs can be …
outcomes.•Classical techniques for studying TILs have important limitations.•TILs can be …
The genetic regulatory signature of type 2 diabetes in human skeletal muscle
Abstract Type 2 diabetes (T2D) results from the combined effects of genetic and
environmental factors on multiple tissues over time. Of the> 100 variants associated with …
environmental factors on multiple tissues over time. Of the> 100 variants associated with …
A transcriptome-based global map of signaling pathways in the ovarian cancer microenvironment associated with clinical outcome
S Reinartz, F Finkernagel, T Adhikary, V Rohnalter… - Genome biology, 2016 - Springer
Background Soluble protein and lipid mediators play essential roles in the tumor
environment, but their cellular origins, targets, and clinical relevance are only partially …
environment, but their cellular origins, targets, and clinical relevance are only partially …
Inferring regulatory change from gene expression: the confounding effects of tissue scaling
SH Montgomery, JE Mank - Molecular ecology, 2016 - Wiley Online Library
Comparative studies of gene expression are often designed with the aim of identifying
regulatory changes associated with phenotypic variation. In recent years, large‐scale …
regulatory changes associated with phenotypic variation. In recent years, large‐scale …
Disease-specific classification using deconvoluted whole blood gene expression
Blood-based biomarker assays have an advantage in being minimally invasive. Diagnostic
and prognostic models built on peripheral blood gene expression have been reported for …
and prognostic models built on peripheral blood gene expression have been reported for …
Searching for convergent pathways in autism spectrum disorders: insights from human brain transcriptome studies
A Gokoolparsadh, GJ Sutton, A Charamko… - Cellular and molecular …, 2016 - Springer
Autism spectrum disorder (ASD) is one of the most heritable neuropsychiatric conditions.
The complex genetic landscape of the disorder includes both common and rare variants at …
The complex genetic landscape of the disorder includes both common and rare variants at …
contamDE: differential expression analysis of RNA-seq data for contaminated tumor samples
Motivation: Accurate detection of differentially expressed genes between tumor and normal
samples is a primary approach of cancer-related biomarker identification. Due to the …
samples is a primary approach of cancer-related biomarker identification. Due to the …