Revealing dynamics of gene expression variability in cell state space

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

(2018) Josip S Herman et al.   NATURE METHODS

Population snapshots predict early haematopoietic and erythroid hierarchies

(2018) Betsabeh Khoramian Tusi et al.   NATURE

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

(2018) Hui Hu et al.   NUCLEIC ACIDS RESEARCH

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

(2018) Nils Eling et al.   Cell Systems

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Hepatic Leukemia Factor Maintains Quiescence of Hematopoietic Stem Cells and Protects the Stem Cell Pool during Regeneration

(2017) Karolina Komorowska et al.   Cell Reports

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

(2016) Guangchuang Yu et al.   Molecular BioSystems

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

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

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

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

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

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

(2013) Philip Brennecke et al.   NATURE METHODS

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY