Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development

(2017) Abbas H Rizvi et al.   NATURE BIOTECHNOLOGY

Gene regulatory networks and network models in development and evolution

(2017) Neil Shubin   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage

(2017) Ben W. Dulken et al.   Cell Reports

Beta-Poisson model for single-cell RNA-seq data analyses

(2016) Trung Nghia Vu et al.   BIOINFORMATICS

Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure

(2016) Xuyu Qian et al.   CELL

Midbrain-like Organoids from Human Pluripotent Stem Cells Contain Functional Dopaminergic and Neuromelanin-Producing Neurons

(2016) Junghyun Jo et al.   Cell Stem Cell

Engineering Stem Cell Organoids

(2016) Xiaolei Yin et al.   Cell Stem Cell

A comprehensive transcriptional map of primate brain development

(2016) Trygve E. Bakken et al.   NATURE

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

(2016) Andre Olsson et al.   NATURE

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone 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

Disentangling neural cell diversity using single-cell transcriptomics

(2016) Jean-Francois Poulin et al.   NATURE NEUROSCIENCE

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

Prediction of disease–gene–drug relationships following a differential network analysis

(2016) S Zickenrott et al.   Cell Death & Disease

Inferring single-cell gene expression mechanisms using stochastic simulation

(2015) Bernie J. Daigle et al.   BIOINFORMATICS

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

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

(2015) Jaehoon Shin et al.   Cell Stem Cell

Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury

(2015) Enric Llorens-Bobadilla et al.   Cell Stem Cell

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

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

Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes

(2015) János Fuzik et al.   NATURE BIOTECHNOLOGY

Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex

(2015) Matthew B Johnson et al.   NATURE NEUROSCIENCE

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

(2015) J. Gray Camp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) A. Zeisel et al.   SCIENCE

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

(2015) F. Notta et al.   SCIENCE

Each cell counts: Hematopoiesis and immunity research in the era of single cell genomics

(2015) Diego Adhemar Jaitin et al.   SEMINARS IN IMMUNOLOGY

Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

(2015) Gautham Nair et al.   Scientific Reports

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Sean C. Bendall et al.   CELL

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

Deconstructing transcriptional heterogeneity in pluripotent stem cells

(2014) Roshan M. Kumar et al.   NATURE

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

(2014) Barbara Treutlein et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen 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

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

A High-Resolution Spatiotemporal Atlas of Gene Expression of the Developing Mouse Brain

(2014) Carol L. Thompson et al.   NEURON

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

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

(2014) Q. Deng et al.   SCIENCE

Organogenesis in a dish: Modeling development and disease using organoid technologies

(2014) M. A. Lancaster et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Generation of Induced Neuronal Cells by the Single Reprogramming Factor ASCL1

(2014) Soham Chanda et al.   Stem Cell Reports

Endogenous WNT Signaling Regulates hPSC-Derived Neural Progenitor Cell Heterogeneity and Specifies Their Regional Identity

(2014) Noel Moya et al.   Stem Cell Reports

Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks

(2013) Isaac Crespo et al.   BMC Systems Biology

Functional Maturation of hPSC-Derived Forebrain Interneurons Requires an Extended Timeline and Mimics Human Neural Development

(2013) Cory R. Nicholas et al.   Cell Stem Cell

Human pluripotent stem cells: an emerging model in developmental biology

(2013) Z. Zhu et al.   DEVELOPMENT

Gene Regulatory Networks Governing Pancreas Development

(2013) H. Efsun Arda et al.   DEVELOPMENTAL CELL

The Long Noncoding RNA RMST Interacts with SOX2 to Regulate Neurogenesis

(2013) Shi-Yan Ng et al.   MOLECULAR CELL

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

(2013) Esteban O Mazzoni et al.   NATURE NEUROSCIENCE

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

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

Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells

(2013) Yingsha Zhang et al.   NEURON

Hox Genes: Choreographers in Neural Development, Architects of Circuit Organization

(2013) Polyxeni Philippidou et al.   NEURON

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

(2013) Jong Kim et al.   GENOME BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Inferring rules of lineage commitment in haematopoiesis

(2012) Cristina Pina et al.   NATURE CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states

(2012) Isaac Crespo et al.   NUCLEIC ACIDS RESEARCH

The Master Negative Regulator REST/NRSF Controls Adult Neurogenesis by Restraining the Neurogenic Program in Quiescent Stem Cells

(2011) Z. Gao et al.   JOURNAL OF NEUROSCIENCE

Induction of human neuronal cells by defined transcription factors

(2011) Zhiping P. Pang et al.   NATURE

Adult Neurogenesis in the Mammalian Brain: Significant Answers and Significant Questions

(2011) Guo-li Ming et al.   NEURON

Rapid induction and long-term self-renewal of primitive neural precursors from human embryonic stem cells by small molecule inhibitors

(2011) W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene regulatory networks governing haematopoietic stem cell development and identity

(2010) John E. Pimanda et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Neurod1 is essential for the survival and maturation of adult-born neurons

(2009) Zhengliang Gao et al.   NATURE NEUROSCIENCE

Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells

(2009) Tibor Kalmar et al.   PLOS BIOLOGY

Concise Review: Pax6 Transcription Factor Contributes to both Embryonic and Adult Neurogenesis as a Multifunctional Regulator

(2008) Noriko Osumi et al.   STEM CELLS