SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Studying Lineage Decision-Making In Vitro: Emerging Concepts and Novel Tools

(2015) Stefan Semrau et al.   Annual Review of Cell and Developmental Biology

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR 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

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

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

(2015) A. Zeisel et al.   SCIENCE

Detecting Adaptive Evolution in Phylogenetic Comparative Analysis Using the Ornstein–Uhlenbeck Model

(2015) Clayton E. Cressler et al.   SYSTEMATIC BIOLOGY

Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear

(2015) Joseph C. Burns et al.   Nature Communications

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

Transcriptional mechanisms of cell fate decisions revealed by single cell expression profiling

(2014) Victoria Moignard et al.   BIOESSAYS

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

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

(2014) Barbara Treutlein et al.   NATURE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

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

(2013) Zhigang Xue et al.   NATURE

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Temporal dynamics and transcriptional control using single-cell gene expression analysis

(2013) Tsukasa Kouno et al.   GENOME BIOLOGY

Sufficient statistics and expectation maximization algorithms in phylogenetic tree models

(2011) Hisanori Kiryu   BIOINFORMATICS

TLR signalling regulated antigen presentation in dendritic cells

(2010) Colin Watts et al.   CURRENT OPINION IN IMMUNOLOGY

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

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Sequestosome-1/p62 Is the Key Intracellular Target of Innate Defense Regulator Peptide

(2009) Hong Bing Yu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

ITFP: an integrated platform of mammalian transcription factors

(2008) G. Zheng et al.   BIOINFORMATICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH