TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data

Reconstructing differentiation networks and their regulation from time series single-cell expression data

(2018) Jun Ding et al.   GENOME RESEARCH

Constructing cell lineages from single-cell transcriptomes

(2018) Jinmiao Chen et al.   MOLECULAR ASPECTS OF MEDICINE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Topological Data Analysis

(2018) Larry Wasserman   Annual Review of Statistics and Its Application

Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency

(2018) Steffen Rulands et al.   Cell Systems

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty 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

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Sox2 Acts in a Dose-Dependent Fashion to Regulate Proliferation of Cortical Progenitors

(2014) Daniel W. Hagey et al.   Cell Reports

Post-transcriptional regulation of wnt8a is essential to zebrafish axis development

(2013) Annika D. Wylie et al.   DEVELOPMENTAL BIOLOGY

Oscillatory gene expression and somitogenesis

(2012) Ryoichiro Kageyama et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Community Structure in Time-Dependent, Multiscale, and Multiplex Networks

(2010) P. J. Mucha et al.   SCIENCE