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

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

(2017) Ziyi Chen et al.   Scientific Reports

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

(2017) Pornpimol Charoentong et al.   Cell Reports

Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease

(2017) Christopher A. Odhams et al.   PLoS Genetics

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

(2017) Julien Racle et al.   eLife

Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism

(2016) Jennifer Tisoncik-Go et al.   Cell Host & Microbe

Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells

(2016) Marco De Simone et al.   IMMUNITY

Resistance Mechanisms to Immune-Checkpoint Blockade in Cancer: Tumor-Intrinsic and -Extrinsic Factors

(2016) Jonathan M. Pitt et al.   IMMUNITY

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits

(2016) Raul Aguirre-Gamboa et al.   Cell Reports

A pathway-centric view of spatial proximity in the 3D nucleome across cell lines

(2016) Hiren Karathia et al.   Scientific Reports

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

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples

(2013) David A. Liebner et al.   BIOINFORMATICS

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

(2013) Ting Gong et al.   BIOINFORMATICS

SRAdb: query and use public next-generation sequencing data from within R

(2013) Yuelin Zhu et al.   BMC BIOINFORMATICS

From a gene-centric to whole-proteome view of differentiation of T helper cell subsets

(2013) T. Lonnberg et al.   Briefings in Functional Genomics

Genotype to phenotype via network analysis

(2013) Hannah Carter et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Tumor-Infiltrating FoxP3+ Tregs and CD8+ T Cells Affect the Prognosis of Hepatocellular Carcinoma Patients

(2012) Yong Huang et al.   DIGESTION

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

(2012) Wenlian Qiao et al.   PLoS Computational Biology

Optimal Deconvolution of Transcriptional Profiling Data Using Quadratic Programming with Application to Complex Clinical Blood Samples

(2011) Ting Gong et al.   PLoS One

Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus

(2009) Alexander R. Abbas et al.   PLoS One