Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

The contribution of cell cycle to heterogeneity in single-cell RNA-seq data

(2016) Andrew McDavid et al.   NATURE BIOTECHNOLOGY

Biased Allelic Expression in Human Primary Fibroblast Single Cells

(2015) Christelle Borel et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation

(2015) Björn Reinius et al.   NATURE REVIEWS GENETICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

(2015) Jong Kyoung Kim et al.   Nature Communications

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

(2015) Catalina A. Vallejos et al.   PLoS Computational Biology

A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data

(2015) Amanda J. Lea et al.   PLoS Genetics

The genetic architecture of gene expression levels in wild baboons

(2015) Jenny Tung et al.   eLife

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

(2015) Kyu-Tae Kim et al.   GENOME BIOLOGY

Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single-Cell Resolution

(2014) Robert Durruthy-Durruthy et al.   CELL

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Efficient multivariate linear mixed model algorithms for genome-wide association studies

(2014) Xiang Zhou et al.   NATURE METHODS

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing

(2014) M.-C. W. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping

(2013) Can Yang et al.   BIOINFORMATICS

Poisson factor models with applications to non-normalized microRNA profiling

(2013) Seonjoo Lee et al.   BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Comparison of software packages for detecting differential expression in RNA-seq studies

(2013) F. Seyednasrollah et al.   BRIEFINGS IN BIOINFORMATICS

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Multiple hypothesis testing adjusted for latent variables, with an application to the AGEMAP gene expression data

(2012) Yunting Sun et al.   Annals of Applied Statistics

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Using control genes to correct for unwanted variation in microarray data

(2011) J. A. Gagnon-Bartsch et al.   BIOSTATISTICS

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes

(2011) Leopold Parts et al.   PLoS Genetics

A factor model to analyze heterogeneity in gene expression

(2010) Yuna Blum et al.   BMC BIOINFORMATICS

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Correction for hidden confounders in the genetic analysis of gene expression

(2010) J. Listgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Latent Factor Analysis to Discover Pathway-Associated Putative Segmental Aneuploidies in Human Cancers

(2010) Joseph E. Lucas et al.   PLoS Computational Biology

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics

(2009) Carlos M. Carvalho et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients

(2008) Wynn L Walker et al.   BMC GENOMICS

Accurate Discovery of Expression Quantitative Trait Loci Under Confounding From Spurious and Genuine Regulatory Hotspots

(2008) H. M. Kang et al.   GENETICS