A fast and efficient count-based matrix factorization method for detecting cell types from single-cell RNAseq data

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

(2018) Zhun Miao et al.   BIOINFORMATICS

Heritability Estimation and Differential Analysis with Generalized Linear Mixed Models in Genomic Sequencing Studies

(2018) Shiquan Sun et al.   BIOINFORMATICS

Higher-order partial least squares for predicting gene expression levels from chromatin states

(2018) Shiquan Sun et al.   BMC BIOINFORMATICS

An accurate and robust imputation method scImpute for single-cell RNA-seq data

(2018) Wei Vivian Li et al.   Nature Communications

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Normalizing single-cell RNA sequencing data: challenges and opportunities

(2017) Catalina A Vallejos et al.   NATURE METHODS

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

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

(2017) Mengjie Chen et al.   Scientific Reports

Robust classification of single-cell transcriptome data by nonnegative matrix factorization

(2016) Chunxuan Shao et al.   BIOINFORMATICS

pcaReduce: hierarchical clustering of single cell transcriptional profiles

(2016) Justina žurauskienė et al.   BMC BIOINFORMATICS

Global feature selection from microarray data using Lagrange multipliers

(2016) Shiquan Sun et al.   KNOWLEDGE-BASED SYSTEMS

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

(2016) Andrew McDavid et al.   NATURE BIOTECHNOLOGY

Normalization and noise reduction for single cell RNA-seq experiments

(2015) Bo Ding et al.   BIOINFORMATICS

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Abstract IA14: Single-cell sequencing in cancer genomics

(2015) J. Christopher Love   CANCER RESEARCH

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

(2015) Evan Z. Macosko et al.   CELL

Single‐cell transcriptomes reveal characteristic features of human pancreatic islet cell types

(2015) Jin Li et al.   EMBO REPORTS

Application of single-cell genomics in cancer: promise and challenges

(2015) Quin F. Wills et al.   HUMAN MOLECULAR GENETICS

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

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How deep is enough in single-cell RNA-seq?

(2014) Aaron M Streets et al.   NATURE BIOTECHNOLOGY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A Kernel-Based Multivariate Feature Selection Method for Microarray Data Classification

(2014) Shiquan Sun et al.   PLoS One

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

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

(2013) Philip Brennecke et al.   NATURE METHODS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS