HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD)

Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells

(2021) Shang Liu et al.   Scientific Reports

Not-so-opposite ends of the spectrum: CD8+ T cell dysfunction across chronic infection, cancer and autoimmunity

(2021) Jenna L. Collier et al.   NATURE IMMUNOLOGY

Tumor-associated hematopoietic stem and progenitor cells positively linked to glioblastoma progression

(2021) I-Na Lu et al.   Nature Communications

Efficient and precise single-cell reference atlas mapping with Symphony

(2021) Joyce B. Kang et al.   Nature Communications

Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies

(2020) Enrique Martin-Gayo et al.   Cell Reports

Deep learning–based cell composition analysis from tissue expression profiles

(2020) Kevin Menden et al.   Science Advances

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

Tumor-infiltrating CD8+ T-cell density is an independent prognostic marker for oral squamous cell carcinoma

(2019) Shota Shimizu et al.   Cancer Medicine

Regulatory T (Treg) cells in cancer: can Treg cells be a new therapeutic target?

(2019) Yoshihiro Ohue et al.   CANCER SCIENCE

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

(2019) Francesca Finotello et al.   Genome Medicine

Accurate estimation of cell-type composition from gene expression data

(2019) Daphne Tsoucas et al.   Nature Communications

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases

(2018) Francesco Vallania et al.   Nature Communications

A new cancer ecosystem

(2017) Sandra J. Horning   SCIENCE

Regulatory T cells, especially ICOS+ FOXP3+ regulatory T cells, are increased in the hepatocellular carcinoma microenvironment and predict reduced survival

(2016) Jian-Fei Tu et al.   Scientific Reports

RNA-Seq methods for transcriptome analysis

(2016) Radmila Hrdlickova et al.   Wiley Interdisciplinary Reviews-RNA

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Tumor-Associated Macrophages: From Mechanisms to Therapy

(2014) Roy Noy et al.   IMMUNITY

A high M1/M2 ratio of tumor-associated macrophages is associated with extended survival in ovarian cancer patients

(2014) Meiying Zhang et al.   Journal of Ovarian Research

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS