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

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

(2016) Andre Olsson et al.   NATURE

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

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

(2016) Minzhe Guo et al.   NUCLEIC ACIDS RESEARCH

Creb1 regulates late stage mammalian lung development via respiratory epithelial and mesenchymal-independent mechanisms

(2016) N. Antony et al.   Scientific Reports

Hypoxia-Inducible Factor-1 Stimulates Postnatal Lung Development but Does Not Prevent O2-Induced Alveolar Injury

(2015) Jeroen Tibboel et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Alveolar Development and Disease

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

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

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

High mobility group protein-mediated transcription requires DNA damage marker γ-H2AX

(2015) Indrabahadur Singh et al.   CELL RESEARCH

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

(2015) Jaehoon Shin et al.   Cell Stem Cell

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

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

‘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

TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles

(2014) Ashwini Patil et al.   BMC Systems Biology

Fast Bayesian inference for gene regulatory networks using ScanBMA

(2014) William Young et al.   BMC Systems Biology

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

(2014) Sean C. Bendall et al.   CELL

Lung development: orchestrating the generation and regeneration of a complex organ

(2014) M. Herriges et al.   DEVELOPMENT

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

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

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 transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Sox9 plays multiple roles in the lung epithelium during branching morphogenesis

(2013) B. E. Rockich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RFX3 Modulation of FOXJ1 regulation of cilia genes in the human airway epithelium

(2013) Lukas Didon et al.   RESPIRATORY RESEARCH

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

(2012) Marcel H Schulz et al.   BMC Systems Biology

Airway epithelial cell differentiation during lung organogenesis requires C/EBPα and C/EBPβ

(2012) Abraham B. Roos et al.   DEVELOPMENTAL DYNAMICS

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Genome-Wide Analyses of Nkx2-1 Binding to Transcriptional Target Genes Uncover Novel Regulatory Patterns Conserved in Lung Development and Tumors

(2012) Jean-Bosco Tagne et al.   PLoS One

A survey on unsupervised outlier detection in high-dimensional numerical data

(2012) Arthur Zimek et al.   Statistical Analysis and Data Mining

HIF and the Lung

(2011) Larissa A. Shimoda et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Conditional hypoxia inducible factor-1α induction in embryonic pulmonary epithelium impairs maturation and augments lymphangiogenesis

(2011) James P. Bridges et al.   DEVELOPMENTAL BIOLOGY

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

cAMP Response Element Binding Protein Is Required for Differentiation of Respiratory Epithelium during Murine Development

(2011) A. Daniel Bird et al.   PLoS One

Maternal Synchronization of Gestational Length and Lung Maturation

(2011) Valérie Besnard et al.   PLoS One

The rate of cell growth is governed by cell cycle stage

(2009) A. I. Goranov et al.   GENES & DEVELOPMENT

HMGA2 Participates in Transformation in Human Lung Cancer

(2008) F. Di Cello et al.   MOLECULAR CANCER RESEARCH