CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data

Pseudotime estimation: deconfounding single cell time series

(2016) John E. Reid et al.   BIOINFORMATICS

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq: Fig. 1.

(2015) Miguel Juliá et al.   BIOINFORMATICS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

The brain's identity crisis

(2015) E. Underwood   SCIENCE

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

(2015) A. Zeisel et al.   SCIENCE

Smurf2 regulates hematopoietic stem cell self-renewal and aging

(2014) Charusheila Ramkumar et al.   AGING CELL

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

(2014) Sean C. Bendall et al.   CELL

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Q. Deng et al.   SCIENCE

How big is the myelinating orchestra? Cellular diversity within the oligodendrocyte lineage: facts and hypotheses

(2014) Giulio Srubek Tomassy et al.   Frontiers in Cellular Neuroscience

The antral follicle: a microenvironment for oocyte differentiation

(2013) Margo l. Hennet et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Interactive topic modeling

(2013) Yuening Hu et al.   MACHINE LEARNING

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

(2013) Zhigang Xue et al.   NATURE

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

(2013) Victoria Moignard et al.   NATURE CELL BIOLOGY

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

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

Integration of GABAergic Interneurons into Cortical Cell Assemblies: Lessons from Embryos and Adults

(2013) Giorgia Bartolini et al.   NEURON

Statistical significance of combinatorial regulations

(2013) A. Terada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Matrix Remodeling Maintains Embryonic Stem Cell Self-Renewal by Activating Stat3

(2013) Laralynne M. Przybyla et al.   STEM CELLS

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

(2013) Tsukasa Kouno et al.   GENOME BIOLOGY

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

Tracking the progression of the human inner cell mass during embryonic stem cell derivation

(2012) Thomas O'Leary et al.   NATURE BIOTECHNOLOGY

Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion

(2012) Cyrille Girard et al.   Nature Communications

STIM Proteins and the Endoplasmic Reticulum-Plasma Membrane Junctions

(2011) Silvia Carrasco et al.   Annual Review of Biochemistry

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Virus-Host Coevolution in a Persistently Coxsackievirus B3-Infected Cardiomyocyte Cell Line

(2011) S. Pinkert et al.   JOURNAL OF VIROLOGY

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

Glee for Glia

(2010) P. Stern   SCIENCE

Wnt signal transduction pathways

(2010) Yuko Komiya et al.   Organogenesis

Gradients in the Brain: The Control of the Development of Form and Function in the Cerebral Cortex

(2009) S. N. Sansom et al.   Cold Spring Harbor Perspectives in Biology