Cross-lineage potential of Ascl1 uncovered by comparing diverse reprogramming regulatomes

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(2021) Haofei Wang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

YAP and TAZ Mediators at the Crossroad between Metabolic and Cellular Reprogramming

(2021) Giorgia Di Benedetto et al.   Metabolites

Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID

(2021) Akira Cortal et al.   NATURE BIOTECHNOLOGY

CellProfiler 4: improvements in speed, utility and usability

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Integrated analysis of multimodal single-cell data

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Delineating chromatin accessibility re-patterning at single cell level during early stage of direct cardiac reprogramming

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JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

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Trajectory-based differential expression analysis for single-cell sequencing data

(2020) Koen Van den Berge et al.   Nature Communications

The Dynamics of Transcriptional Activation by Hepatic Reprogramming Factors

(2020) Kenichi Horisawa et al.   MOLECULAR CELL

Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers

(2019) Hisayuki Hashimoto et al.   Cell Stem Cell

Comprehensive Integration of Single-Cell Data

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Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming

(2019) Nicole R. Stone et al.   Cell Stem Cell

Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming

(2019) Yang Zhou et al.   Cell Stem Cell

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

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AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection

(2017) Thomas Vierbuchen et al.   MOLECULAR CELL

Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte

(2017) Ziqing Liu et al.   NATURE

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

DNA-binding mechanism of the Hippo pathway transcription factor TEAD4

(2017) Z Shi et al.   ONCOGENE

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

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

(2016) Barbara Treutlein et al.   NATURE

deepTools2: a next generation web server for deep-sequencing data analysis

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Re-patterning of H3K27me3, H3K4me3 and DNA methylation during fibroblast conversion into induced cardiomyocytes

(2016) Ziqing Liu et al.   Stem Cell Research

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(2015) Guangchuang Yu et al.   BIOINFORMATICS

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Landscape of Cardiomyocyte Maturation

(2015) Hideki Uosaki et al.   Cell Reports

Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet

(2014) Samantha A. Morris et al.   CELL

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons

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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Cellular Alchemy and the Golden Age of Reprogramming

(2012) George Q. Daley   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Pioneer transcription factors: establishing competence for gene expression

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Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors

(2011) Sayaka Sekiya et al.   NATURE

Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors

(2010) Masaki Ieda et al.   CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Social isolation stress induces ATF-7 phosphorylation and impairs silencing of the 5-HT 5B receptor gene

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Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY