SLICE: determining cell differentiation and lineage based on single cell entropy

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Alveolar Development and Disease

(2015) Jeffrey A. Whitsett et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

‘LungGENS’: a web-based tool for mapping single-cell gene expression in the developing lung: Figure 1

(2015) Yina Du et al.   THORAX

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

(2015) Minzhe Guo et al.   PLoS Computational Biology

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

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Statistical Mechanics of Pluripotency

(2013) Ben D. MacArthur et al.   CELL

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

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

Cellular network entropy as the energy potential in Waddington's differentiation landscape

(2013) Christopher R. S. Banerji et al.   Scientific Reports

Regulated Noise in the Epigenetic Landscape of Development and Disease

(2012) Elisabet Pujadas et al.   CELL

Quantifying cellular differentiation by physical phenotype using digital holographic microscopy

(2012) Kevin J. Chalut et al.   Integrative Biology

Tumor cell differentiation by label-free fluorescence microscopy

(2012) Petra Weber   JOURNAL OF BIOMEDICAL OPTICS

Transcriptional Programs Controlling Perinatal Lung Maturation

(2012) Yan Xu et al.   PLoS One

Epithelial Progenitor Cells in Lung Development, Maintenance, Repair, and Disease

(2011) Jason R. Rock et al.   Annual Review of Cell and Developmental Biology

BioNet: an R-Package for the functional analysis of biological networks

(2010) D. Beisser et al.   BIOINFORMATICS

Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models

(2010) Simon N. Wood   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Coexistence of Quiescent and Active Adult Stem Cells in Mammals

(2010) L. Li et al.   SCIENCE

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

(2009) Da Wei Huang et al.   Nature Protocols

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

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

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