TIMER2. 0 for analysis of tumor-infiltrating immune cells

T Li, J Fu, Z Zeng, D Cohen, J Li, Q Chen… - Nucleic acids …, 2020 - academic.oup.com
Tumor progression and the efficacy of immunotherapy are strongly influenced by the
composition and abundance of immune cells in the tumor microenvironment. Due to the …

TIMER: a web server for comprehensive analysis of tumor-infiltrating immune cells

T Li, J Fan, B Wang, N Traugh, Q Chen, JS Liu, B Li… - Cancer research, 2017 - AACR
Recent clinical successes of cancer immunotherapy necessitate the investigation of the
interaction between malignant cells and the host immune system. However, elucidation of …

[HTML][HTML] Quantifying tumor-infiltrating immune cells from transcriptomics data

F Finotello, Z Trajanoski - Cancer Immunology, Immunotherapy, 2018 - Springer
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 …

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

G Sturm, F Finotello, F Petitprez, JD Zhang… - …, 2019 - academic.oup.com
Motivation The composition and density of immune cells in the tumor microenvironment
(TME) profoundly influence tumor progression and success of anti-cancer therapies. Flow …

[HTML][HTML] Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

J Racle, K de Jonge, P Baumgaertner, DE Speiser… - elife, 2017 - elifesciences.org
Immune cells infiltrating tumors can have important impact on tumor progression and
response to therapy. We present an efficient algorithm to simultaneously estimate the …

Deconvoluting tumor-infiltrating immune cells from RNA-seq data using quanTIseq

C Plattner, F Finotello, D Rieder - Methods in enzymology, 2020 - Elsevier
Tumor-infiltrating immune cells comprise various cells of the innate and the adaptive
immune system, which influence tumor growth and response to immunotherapy by exerting …

A single-cell tumor immune atlas for precision oncology

P Nieto, M Elosua-Bayes, JL Trincado… - Genome …, 2021 - genome.cshlp.org
The tumor immune microenvironment is a main contributor to cancer progression and a
promising therapeutic target for oncology. However, immune microenvironments vary …

[HTML][HTML] Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

B Li, E Severson, JC Pignon, H Zhao, T Li, J Novak… - Genome biology, 2016 - Springer
Background Understanding the interactions between tumor and the host immune system is
critical to finding prognostic biomarkers, reducing drug resistance, and developing new …

RNA sequencing of the tumor microenvironment in precision cancer immunotherapy

D Lau, AM Bobe, AA Khan - Trends in cancer, 2019 - cell.com
RNA sequencing (RNA-seq) provides an efficient high-throughput technique to robustly
characterize the tumor immune microenvironment (TME). The increasing use of RNA-seq in …

[HTML][HTML] 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 …