Cell composition analysis of bulk genomics using single-cell data

Computational deconvolution of transcriptomics data from mixed cell populations

(2018) Francisco Avila Cobos et al.   BIOINFORMATICS

The Cancer Genome Atlas: Creating Lasting Value beyond Its Data

(2018) Carolyn Hutter et al.   CELL

Inflammatory Monocytes Drive Influenza A Virus–Mediated Lung Injury in Juvenile Mice

(2018) Bria M. Coates et al.   JOURNAL OF IMMUNOLOGY

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

(2018) Carsten Krieg et al.   NATURE MEDICINE

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing

(2018) Yael Steuerman et al.   Cell Systems

Computational approaches for interpreting scRNA-seq data

(2017) Raghd Rostom et al.   FEBS LETTERS

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

(2017) Barbara E Stranger et al.   NATURE GENETICS

Single-cell analyses to tailor treatments

(2017) Alex K. Shalek et al.   Science Translational Medicine

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data

(2017) Max Schelker et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Flow-cytometric method for simultaneous analysis of mouse lung epithelial, endothelial, and hematopoietic lineage cells

(2016) Benjamin D. Singer et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

ImmQuant: a user-friendly tool for inferring immune cell-type composition from gene-expression data

(2016) Amit Frishberg et al.   BIOINFORMATICS

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

A Protocol for the Comprehensive Flow Cytometric Analysis of Immune Cells in Normal and Inflamed Murine Non-Lymphoid Tissues

(2016) Yen-Rei A. Yu et al.   PLoS One

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Digital cell quantification identifies global immune cell dynamics during influenza infection

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

Cellular Changes in Blood Indicate Severe Respiratory Disease during Influenza Infections in Mice

(2014) Leonie Dengler et al.   PLoS One

Computational deconvolution: extracting cell type-specific information from heterogeneous samples

(2013) Shai S Shen-Orr et al.   CURRENT OPINION IN IMMUNOLOGY

Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross

(2013) Martin T. Ferris et al.   PLoS Pathogens

Status and access to the Collaborative Cross population

(2012) Catherine E. Welsh et al.   MAMMALIAN GENOME

Expression Quantitative Trait Loci for Extreme Host Response to Influenza A in Pre-Collaborative Cross Mice

(2012) Daniel Bottomly et al.   G3-Genes Genomes Genetics

Cell type–specific gene expression differences in complex tissues

(2010) Shai S Shen-Orr et al.   NATURE METHODS