Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J et al (2017) SCENIC: single-cell regulatory network inference and clustering. Nat Methods 14:1083–1086

CAS  PubMed  PubMed Central  Article  Google Scholar 

Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106

CAS  PubMed  PubMed Central  Article  Google Scholar 

Angerer P, Haghverdi L, Büttner M, Theis FJ, Marr C, Buettner F (2016) destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics 32:1241–1243

CAS  PubMed  Article  PubMed Central  Google Scholar 

Arimura T, Bos JM, Sato A, Kubo T, Okamoto H, Nishi H, Harada H, Koga Y, Moulik M, Doi YL et al (2009) Cardiac ankyrin repeat protein gene (ANKRD1) mutations in hypertrophic cardiomyopathy. J Am Coll Cardiol 54:334–342

Bassat E, Mutlak YE, Genzelinakh A, Shadrin IY, Baruch Umansky K, Yifa O, Kain D, Rajchman D, Leach J, Riabov Bassat D et al (2017) The extracellular matrix protein agrin promotes heart regeneration in mice. Nature 547:179–184

CAS  PubMed  PubMed Central  Article  Google Scholar 

Becker RA, Chambers JM, Wilks AR (1988) The new S language, Wadsworth & Brooks/Cole, Monterey

Google Scholar 

Butler A, Hoffman P, Smibert P, Papalexi E, Satija R (2018) Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 36:411–420

CAS  PubMed  PubMed Central  Article  Google Scholar 

Del Monte-Nieto G, Ramialison M, Adam AAS, Wu B, Aharonov A, D’Uva G, Bourke LM, Pitulescu ME, Chen H, de la Pompa JL et al (2018) Control of cardiac jelly dynamics by NOTCH1 and NRG1 defines the building plan for trabeculation. Nature 557:439–445

PubMed  Article  CAS  PubMed Central  Google Scholar 

DeLaughter DM, Bick AG, Wakimoto H, McKean D, Gorham JM, Kathiriya IS, Hinson JT, Homsy J, Gray J, Pu W et al (2016) Single-cell resolution of temporal gene expression during heart development. Dev Cell 39:480–490

CAS  PubMed  PubMed Central  Article  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21

CAS  PubMed  Article  PubMed Central  Google Scholar 

Eulalio A, Mano M, Dal Ferro M, Zentilin L, Sinagra G, Zacchigna S, Giacca M (2012) Functional screening identifies miRNAs inducing cardiac regeneration. Nature 492:376–381

CAS  PubMed  Article  PubMed Central  Google Scholar 

Gan J, Sonntag HJ, Tang MK, Cai D, Lee KK (2015) Integrative analysis of the developing postnatal mouse heart transcriptome. PLoS ONE 10:e0133288

PubMed  PubMed Central  Article  CAS  Google Scholar 

Gilsbach R, Preissl S, Gruning BA, Schnick T, Burger L, Benes V, Wurch A, Bonisch U, Gunther S, Backofen R et al (2014) Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease. Nat Commun 5:5288

CAS  PubMed  Article  PubMed Central  Google Scholar 

Gilsbach R, Schwaderer M, Preissl S, Gruning BA, Kranzhofer D, Schneider P, Nuhrenberg TG, Mulero-Navarro S, Weichenhan D, Braun C et al (2018) Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo. Nat Commun 9:391

PubMed  PubMed Central  Article  CAS  Google Scholar 

Gladka MM, Molenaar B, de Ruiter H, van der Elst S, Tsui H, Versteeg D, Lacraz GPA, Huibers MMH, van Oudenaarden A, van Rooij E (2018) Single-cell sequencing of the healthy and diseased heart reveals cytoskeleton-associated protein 4 as a new modulator of fibroblasts activation. Circulation 138:166–180

CAS  PubMed  Article  PubMed Central  Google Scholar 

Goldstein LD, Chen YJ, Dunne J, Mir A, Hubschle H, Guillory J, Yuan W, Zhang J, Stinson J, Jaiswal B et al (2017) Massively parallel nanowell-based single-cell gene expression profiling. BMC Genom 18:519

Article  CAS  Google Scholar 

Gupta V, Poss KD (2012) Clonally dominant cardiomyocytes direct heart morphogenesis. Nature 484:479–484

CAS  PubMed  PubMed Central  Article  Google Scholar 

Heallen T, Zhang M, Wang J, Bonilla-Claudio M, Klysik E, Johnson RL, Martin JF (2011) Hippo pathway inhibits Wnt signaling to restrain cardiomyocyte proliferation and heart size. Science 332:458–461

CAS  PubMed  PubMed Central  Article  Google Scholar 

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38:576–589

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hirose K, Payumo AY, Cutie S, Hoang A, Zhang H, Guyot R, Lunn D, Bigley RB, Yu H, Wang J et al (2019) Evidence for hormonal control of heart regenerative capacity during endothermy acquisition. Science 364:184–188

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hsieh PC, Segers VF, Davis ME, MacGillivray C, Gannon J, Molkentin JD, Robbins J, Lee RT (2007) Evidence from a genetic fate-mapping study that stem cells refresh adult mammalian cardiomyocytes after injury. Nat Med 13:970–974

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hu P, Liu J, Zhao J, Wilkins BJ, Lupino K, Wu H, Pei L (2018) Single-nucleus transcriptomic survey of cell diversity and functional maturation in postnatal mammalian hearts. Genes Dev 32:1344–1357

CAS  PubMed  PubMed Central  Article  Google Scholar 

Jopling C, Sleep E, Raya M, Marti M, Raya A, Izpisua Belmonte JC (2010) Zebrafish heart regeneration occurs by cardiomyocyte dedifferentiation and proliferation. Nature 464:606–609

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kikuchi K, Holdway JE, Werdich AA, Anderson RM, Fang Y, Egnaczyk GF, Evans T, Macrae CA, Stainier DY, Poss KD (2010) Primary contribution to zebrafish heart regeneration by gata4(+) cardiomyocytes. Nature 464:601–605

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kim C, Gao R, Sei E, Brandt R, Hartman J, Hatschek T, Crosetto N, Foukakis T, Navin NE (2018) Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell 173:879–893

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ (2015) Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. Cell Stem Cell 16:88–101

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kwapiszewska G, Wygrecka M, Marsh LM, Schmitt S, Trosser R, Wilhelm J, Helmus K, Eul B, Zakrzewicz A, Ghofrani HA et al (2008) Fhl-1, a new key protein in pulmonary hypertension. Circulation 118:1183–1194

Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

CAS  PubMed  PubMed Central  Article  Google Scholar 

Law CW, Alhamdoosh M, Su S, Smyth GK, Ritchie ME (2016) RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Res 5:1408

Article  CAS  Google Scholar 

Lee TI, Young RA (2013) Transcriptional regulation and its misregulation in disease. Cell 152:1237–1251

CAS  PubMed  PubMed Central  Article  Google Scholar 

Liao Y, Smyth GK, Shi W (2013) The subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res 41:e108

PubMed  PubMed Central  Article  CAS  Google Scholar 

Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930

CAS  PubMed  Article  PubMed Central  Google Scholar 

Litvinukova M, Talavera-Lopez C, Maatz H, Reichart D, Worth CL, Lindberg EL, Kanda M, Polanski K, Heinig M, Lee M et al (2020) Cells of the adult human heart. Nature 588:466–472

CAS  PubMed  PubMed Central  Article  Google Scholar 

Mahdavi V, Periasamy M, Nadal-Ginard B (1982) Molecular characterization of two myosin heavy chain genes expressed in the adult heart. Nature 297:659–664

CAS  PubMed  Article  PubMed Central  Google Scholar 

Mahmoud AI, Kocabas F, Muralidhar SA, Kimura W, Koura AS, Thet S, Porrello ER, Sadek HA (2013) Meis1 regulates postnatal cardiomyocyte cell cycle arrest. Nature 497:249–253

CAS  PubMed  PubMed Central  Article  Google Scholar 

Mohamed TMA, Ang YS, Radzinsky E, Zhou P, Huang Y, Elfenbein A, Foley A, Magnitsky S, Srivastava D (2018) Regulation of cell cycle to stimulate adult cardiomyocyte proliferation and cardiac regeneration. Cell 173:104–116

CAS  PubMed  PubMed Central  Article  Google Scholar 

Mojtahedi M, Skupin A, Zhou J, Castano IG, Leong-Quong RY, Chang H, Trachana K, Giuliani A, Huang S (2016) Cell fate decision as high-dimensional critical state transition. PLoS Biol 14:e2000640

PubMed  PubMed Central  Article  CAS  Google Scholar 

Morikawa Y, Heallen T, Leach J, Xiao Y, Martin JF (2017) Dystrophin-glycoprotein complex sequesters Yap to inhibit cardiomyocyte proliferation. Nature 547:227–231

CAS