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

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Direct Lineage Reprogramming: Strategies, Mechanisms, and Applications

(2015) Jun Xu et al.   Cell Stem Cell

Early reprogramming regulators identified by prospective isolation and mass cytometry

(2015) Ernesto Lujan 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

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

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

(2015) A. Zeisel et al.   SCIENCE

Brains in metamorphosis: reprogramming cell identity within the central nervous system

(2014) Paola Arlotta et al.   CURRENT OPINION IN NEUROBIOLOGY

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

(2014) Y. Zhang et al.   JOURNAL OF NEUROSCIENCE

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

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 highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Generation of Induced Neuronal Cells by the Single Reprogramming Factor ASCL1

(2014) Soham Chanda et al.   Stem Cell Reports

Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons

(2013) Orly L. Wapinski et al.   CELL

Modeling Human Disease with Pluripotent Stem Cells: from Genome Association to Function

(2013) Florian T. Merkle et al.   Cell Stem Cell

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

(2013) Alex K. Shalek et al.   NATURE

C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells

(2013) Bruno Di Stefano et al.   NATURE

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Historical Origins of Transdifferentiation and Reprogramming

(2011) Thomas Graf   Cell Stem Cell

Direct Reprogramming of Adult Human Fibroblasts to Functional Neurons under Defined Conditions

(2011) Rajesh Ambasudhan et al.   Cell Stem Cell

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

MicroRNA-mediated conversion of human fibroblasts to neurons

(2011) Andrew S. Yoo et al.   NATURE

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts

(2011) Massimiliano Caiazzo et al.   NATURE

AnimalTFDB: a comprehensive animal transcription factor database

(2011) H.-M. Zhang et al.   NUCLEIC ACIDS RESEARCH

Direct conversion of human fibroblasts to dopaminergic neurons

(2011) U. Pfisterer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Da Wei Huang et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY