Visualizing the structure of RNA-seq expression data using grade of membership models

Differential effects of myelin basic protein-activated Th1 and Th2 cells on the local immune microenvironment of injured spinal cord

(2016) Jian-Guo Hu et al.   EXPERIMENTAL NEUROLOGY

Assessing the consistency of public human tissue RNA-seq data sets

(2015) F. Danielsson et al.   BRIEFINGS IN BIOINFORMATICS

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures

(2015) Yuichi Shiraishi et al.   PLoS Genetics

UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples

(2014) Niya Wang et al.   BIOINFORMATICS

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

DeMix: deconvolution for mixed cancer transcriptomes using raw measured data

(2013) Jaeil Ahn et al.   BIOINFORMATICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction

(2013) Gerald Quon et al.   Genome Medicine

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Wenlian Qiao et al.   PLoS Computational Biology

Sparse Bayesian infinite factor models

(2011) A. Bhattacharya et al.   BIOMETRIKA

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape

(2010) Konstantin Pentchev et al.   BIOINFORMATICS

Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach

(2010) Dirk Repsilber et al.   BMC BIOINFORMATICS

Applying unmixing to gene expression data for tumor phylogeny inference

(2010) Russell Schwartz et al.   BMC BIOINFORMATICS

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Cell type–specific gene expression differences in complex tissues

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

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis

(2010) Barbara E. Engelhardt et al.   PLoS Genetics

Role of Bcl2-like 10 (Bcl2l10) in Regulating Mouse Oocyte Maturation1

(2009) Se-Jin Yoon et al.   BIOLOGY OF REPRODUCTION

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse

(2009) J. Rossant et al.   DEVELOPMENT

Gene expression during the oocyte-to-embryo transition in mammals

(2009) Alexei V. Evsikov et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Horseshoes in multidimensional scaling and local kernel methods

(2008) Persi Diaconis et al.   Annals of Applied Statistics

Interpreting principal component analyses of spatial population genetic variation

(2008) John Novembre et al.   NATURE GENETICS