Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.

[1]  B. Hadland,et al.  Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells , 2016, Nature Protocols.

[2]  Kyoung-Jae Won,et al.  Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts , 2015, Science.

[3]  I. Simon,et al.  Reconstructing dynamic regulatory maps , 2007, Molecular systems biology.

[4]  R. Moon,et al.  Biphasic role for Wnt/β-catenin signaling in cardiac specification in zebrafish and embryonic stem cells , 2007, Proceedings of the National Academy of Sciences.

[5]  Ann B. Lee,et al.  Geometric diffusions as a tool for harmonic analysis and structure definition of data: multiscale methods. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Grace X. Y. Zheng,et al.  Massively parallel digital transcriptional profiling of single cells , 2016, Nature Communications.

[7]  Gordon Keller,et al.  Differentiation of Embryonic Stem Cells to Clinically Relevant Populations: Lessons from Embryonic Development , 2008, Cell.

[8]  M. Suematsu,et al.  Distinct metabolic flow enables large-scale purification of mouse and human pluripotent stem cell-derived cardiomyocytes. , 2013, Cell stem cell.

[9]  J. Seidman,et al.  Single-Cell Resolution of Temporal Gene Expression during Heart Development. , 2016, Developmental cell.

[10]  R. Passier,et al.  Transcriptome of human foetal heart compared with cardiomyocytes from pluripotent stem cells , 2015, Development.

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

[12]  Barbara Di Camillo,et al.  Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods , 2017, Front. Genet..

[13]  H. Akaike,et al.  Information Theory and an Extension of the Maximum Likelihood Principle , 1973 .

[14]  Adam A. Margolin,et al.  Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis. , 2017, Cell reports.

[15]  Kumaraswamy Nanthakumar,et al.  Design and formulation of functional pluripotent stem cell-derived cardiac microtissues , 2013, Proceedings of the National Academy of Sciences.

[16]  B. Hadland,et al.  Transmembrane protein 88: a Wnt regulatory protein that specifies cardiomyocyte development , 2013, Development.

[17]  K. Sawada,et al.  Low-density plating is sufficient to induce cardiac hypertrophy and electrical remodeling in highly purified human iPS cell-derived cardiomyocytes. , 2014, Journal of pharmacological and toxicological methods.

[18]  Fabian J Theis,et al.  Decoding the Regulatory Network for Blood Development from Single-Cell Gene Expression Measurements , 2015, Nature Biotechnology.

[19]  M. Ramialison,et al.  Multicellular Transcriptional Analysis of Mammalian Heart Regeneration , 2017, Circulation.

[20]  Bin Zhou,et al.  Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells. , 2016, Developmental cell.

[21]  Davis J. McCarthy,et al.  A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor , 2016, F1000Research.

[22]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[23]  David E James,et al.  Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest , 2017, Proceedings of the National Academy of Sciences.

[24]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[25]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[26]  R. Schwartz,et al.  Hop Is an Unusual Homeobox Gene that Modulates Cardiac Development , 2002, Cell.

[27]  P. Wolf,et al.  Heart disease and stroke statistics--2006 update: a report from the American Heart Association Statistics Committee and Stroke Statistics Subcommittee. , 2006, Circulation.

[28]  J. Epstein,et al.  Cardiac hypertrophy and histone deacetylase-dependent transcriptional repression mediated by the atypical homeodomain protein Hop. , 2003, The Journal of clinical investigation.

[29]  N. Bowles,et al.  Non-synonymous variants in pre-B cell leukemia homeobox (PBX) genes are associated with congenital heart defects. , 2012, European journal of medical genetics.

[30]  J. Han,et al.  Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo. , 2016, Developmental cell.

[31]  Thomas Lengauer,et al.  Improved scoring of functional groups from gene expression data by decorrelating GO graph structure , 2006, Bioinform..

[32]  Thomas M. Harris,et al.  Modulation of Cardiac Growth and Development by HOP, an Unusual Homeodomain Protein , 2002, Cell.

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

[34]  Ziv Bar-Joseph,et al.  DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data , 2012, BMC Systems Biology.

[35]  Joseph E Powell,et al.  Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations , 2018, Genome research.

[36]  Gordon Keller,et al.  SIRPA is a specific cell-surface marker for isolating cardiomyocytes derived from human pluripotent stem cells , 2011, Nature Biotechnology.

[37]  C. Schreurs,et al.  Dual Reporter MESP1mCherry/w‐NKX2‐5eGFP/w hESCs Enable Studying Early Human Cardiac Differentiation , 2015, Stem cells.

[38]  J. Powell,et al.  Determining cell fate specification and genetic contribution to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution , 2017, bioRxiv.

[39]  Joshua W. K. Ho,et al.  CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data , 2016, Genome Biology.

[40]  Kavitha T. Kuppusamy,et al.  Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes , 2015, Proceedings of the National Academy of Sciences.

[41]  Lil Pabon,et al.  Engineering Adolescence: Maturation of Human Pluripotent Stem Cell–Derived Cardiomyocytes , 2014, Circulation research.

[42]  Rowland Mosbergen,et al.  Stemformatics: visualisation and sharing of stem cell gene expression. , 2013, Stem cell research.

[43]  D. Mozaffarian,et al.  Heart disease and stroke statistics--2009 update: a report from the American Heart Association Statistics Committee and Stroke Statistics Subcommittee. , 2009, Circulation.

[44]  B. Cui,et al.  Chemically Defined and Small Molecule-Based Generation of Human Cardiomyocytes , 2014, Nature methods.

[45]  Nevan J Krogan,et al.  CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. , 2016, Cell stem cell.

[46]  Donald W. Bouldin,et al.  A Cluster Separation Measure , 1979, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[47]  P. Rousseeuw Silhouettes: a graphical aid to the interpretation and validation of cluster analysis , 1987 .

[48]  Luke T. Dang,et al.  First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor , 2017, Proceedings of the National Academy of Sciences.

[49]  Z. Bar-Joseph,et al.  Reconstructing differentiation networks and their regulation from time series single-cell expression data , 2018, Genome research.

[50]  Xin Mei,et al.  ascend: R package for analysis of single-cell RNA-seq data , 2017, bioRxiv.

[51]  Sean P. Palecek,et al.  Robust cardiomyocyte differentiation from human pluripotent stem cells via temporal modulation of canonical Wnt signaling , 2012, Proceedings of the National Academy of Sciences.