Single Cell Transcriptomics Reconstructs Fate Conversion from Fibroblast to Cardiomyocyte

[1]  C. Hodgkinson,et al.  Demethylation of H3K27 Is Essential for the Induction of Direct Cardiac Reprogramming by miR Combo , 2017, Circulation research.

[2]  D. Srivastava,et al.  Chemical Enhancement of In Vitro and In Vivo Direct Cardiac Reprogramming , 2017, Circulation.

[3]  C. Yin,et al.  Generation of an inducible fibroblast cell line for studying direct cardiac reprogramming , 2016, Genesis.

[4]  Eric C. Rouchka,et al.  rMAPS: RNA map analysis and plotting server for alternative exon regulation , 2016, Nucleic Acids Res..

[5]  Li Qian,et al.  SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data , 2016, Genome Biology.

[6]  Greg G. Wang,et al.  Bmi1 Is a Key Epigenetic Barrier to Direct Cardiac Reprogramming. , 2016, Cell stem cell.

[7]  C. Yin,et al.  Re-patterning of H3K27me3, H3K4me3 and DNA methylation during fibroblast conversion into induced cardiomyocytes. , 2016, Stem cell research.

[8]  F. Conlon,et al.  The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation. , 2016, Developmental cell.

[9]  C. Yin,et al.  Improved Generation of Induced Cardiomyocytes Using a Polycistronic Construct Expressing Optimal Ratio of Gata4, Mef2c and Tbx5. , 2015, Journal of visualized experiments : JoVE.

[10]  C. Yin,et al.  In vivo cardiac reprogramming using an optimal single polycistronic construct. , 2015, Cardiovascular research.

[11]  Kenneth L. Jones,et al.  High-efficiency reprogramming of fibroblasts into cardiomyocytes requires suppression of pro-fibrotic signalling , 2015, Nature Communications.

[12]  E. Olson,et al.  Akt1/protein kinase B enhances transcriptional reprogramming of fibroblasts to functional cardiomyocytes , 2015, Proceedings of the National Academy of Sciences.

[13]  David W. Nauen,et al.  Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. , 2015, Cell stem cell.

[14]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[15]  N. Bursac,et al.  Stoichiometry of Gata4, Mef2c, and Tbx5 Influences the Efficiency and Quality of Induced Cardiac Myocyte Reprogramming , 2015, Circulation research.

[16]  Lan Lin,et al.  rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data , 2014, Proceedings of the National Academy of Sciences.

[17]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[18]  M. Ares,et al.  Context-dependent control of alternative splicing by RNA-binding proteins , 2014, Nature Reviews Genetics.

[19]  D. Dube,et al.  Translational Control of Tropomyosin Expression in Vertebrate Hearts , 2014, Anatomical record.

[20]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[21]  Keiichi Fukuda,et al.  MiR‐133 promotes cardiac reprogramming by directly repressing Snai1 and silencing fibroblast signatures , 2014, The EMBO journal.

[22]  C. Fan,et al.  Prolyl hydroxylation by EglN2 destabilizes FOXO3a by blocking its interaction with the USP9x deubiquitinase , 2014, Genes & development.

[23]  N. Neff,et al.  Reconstructing lineage hierarchies of the distal lung epithelium using single cell RNA-seq , 2014, Nature.

[24]  Cole Trapnell,et al.  The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.

[25]  J. Epstein,et al.  Inhibition of TGFβ Signaling Increases Direct Conversion of Fibroblasts to Induced Cardiomyocytes , 2014, PloS one.

[26]  N. Neff,et al.  Quantitative assessment of single-cell RNA-sequencing methods , 2013, Nature Methods.

[27]  Aleksandra A. Kolodziejczyk,et al.  Accounting for technical noise in single-cell RNA-seq experiments , 2013, Nature Methods.

[28]  Eric T. Wang,et al.  MBNL proteins repress ES-cell-specific alternative splicing and reprogramming , 2013, Nature.

[29]  D. Srivastava,et al.  Reprogramming of mouse fibroblasts into cardiomyocyte-like cells in vitro , 2013, Nature Protocols.

[30]  S. Ramaswamy,et al.  A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells , 2012, Cell.

[31]  R. Crystal,et al.  In Vivo Cardiac Cellular Reprogramming Efficacy Is Enhanced by Angiogenic Preconditioning of the Infarcted Myocardium With Vascular Endothelial Growth Factor , 2012, Journal of the American Heart Association.

[32]  E. Finch,et al.  MicroRNA-Mediated In Vitro and In Vivo Direct Reprogramming of Cardiac Fibroblasts to Cardiomyocytes , 2012, Circulation research.

[33]  N. Rosenthal,et al.  An Abundant Tissue Macrophage Population in the Adult Murine Heart with a Distinct Alternatively-Activated Macrophage Profile , 2012, PloS one.

[34]  Xiaoxia Qi,et al.  Heart repair by reprogramming non-myocytes with cardiac transcription factors , 2012, Nature.

[35]  Li Qian,et al.  In vivo reprogramming of murine cardiac fibroblasts into induced cardiomyocytes , 2011, Nature.

[36]  Aibin He,et al.  Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart , 2011, Proceedings of the National Academy of Sciences.

[37]  Chunyu Liu,et al.  Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods , 2011, PloS one.

[38]  V. Vedantham,et al.  Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors , 2010, Cell.

[39]  A. Ladd,et al.  Conserved developmental alternative splicing of muscleblind-like (MBNL) transcripts regulates MBNL localization and activity , 2010, RNA biology.

[40]  C. Gooding,et al.  Tropomyosin exons as models for alternative splicing. , 2008, Advances in experimental medicine and biology.

[41]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.

[42]  C. Ball,et al.  Identification of genes periodically expressed in the human cell cycle and their expression in tumors. , 2002, Molecular biology of the cell.