The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression

Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease

(2020) David Gate et al.   NATURE

PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins

(2020) Patryk Jarnot et al.   NUCLEIC ACIDS RESEARCH

The cis-Regulatory Atlas of the Mouse Immune System

(2019) Hideyuki Yoshida et al.   CELL

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

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

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

(2019) Gregor Sturm et al.   BIOINFORMATICS

Sensitization to immune checkpoint blockade through activation of a STAT1/NK axis in the tumor microenvironment

(2019) Rachael M. Zemek et al.   Science Translational Medicine

Next-generation computational tools for interrogating cancer immunity

(2019) Francesca Finotello et al.   NATURE REVIEWS GENETICS

Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer

(2018) Ana Costa et al.   CANCER CELL

Quantifying tumor-infiltrating immune cells from transcriptomics data

(2018) Francesca Finotello et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data

(2018) Ziyi Chen et al.   Frontiers in Immunology

Quantitative Analyses of the Tumor Microenvironment Composition and Orientation in the Era of Precision Medicine

(2018) Florent Petitprez et al.   Frontiers in Oncology

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Trial watch: The clinical trial landscape for PD1/PDL1 immune checkpoint inhibitors

(2018) Jun Tang et al.   NATURE REVIEWS DRUG DISCOVERY

Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans

(2018) Jarny Choi et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Francesco Vallania et al.   Nature Communications

Microglia in Alzheimer’s disease

(2017) David V. Hansen et al.   JOURNAL OF CELL BIOLOGY

Mouse models of atherosclerosis: a historical perspective and recent advances

(2017) Yee Ting Lee et al.   Lipids in Health and Disease

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

The immune contexture in cancer prognosis and treatment

(2017) Wolf H. Fridman et al.   Nature Reviews Clinical Oncology

Inference of immune cell composition on the expression profiles of mouse tissue

(2017) Ziyi Chen et al.   Scientific Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

GATA-3 Function in Innate and Adaptive Immunity

(2014) Irma Tindemans et al.   IMMUNITY

Digital cell quantification identifies global immune cell dynamics during influenza infection

(2014) Z. Altboum et al.   Molecular Systems Biology

The Tumor Microenvironment Shapes Lineage, Transcriptional, and Functional Diversity of Infiltrating Myeloid Cells

(2014) K. G. Elpek et al.   Cancer Immunology Research

Identification of transcriptional regulators in the mouse immune system

(2013) Vladimir Jojic et al.   NATURE IMMUNOLOGY

Murine Models of Inflammatory Bowel Disease (IBD)

(2013) Jason DeVoss et al.   TOXICOLOGIC PATHOLOGY

Animal Models in Autoimmune Diseases: Lessons Learned from Mouse Models for Sjögren’s Syndrome

(2011) Byung Ha Lee et al.   CLINICAL REVIEWS IN ALLERGY & IMMUNOLOGY

Interaction of tumor cells and lymphatic vessels in cancer progression

(2011) A Alitalo et al.   ONCOGENE

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

Evidence of angiogenic vessels in Alzheimer’s disease

(2009) Brinda S. Desai et al.   JOURNAL OF NEURAL TRANSMISSION

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY