{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,8]],"date-time":"2026-11-08T04:02:16Z","timestamp":1794110536842,"version":"4.8.0"},"reference-count":63,"publisher":"Springer Science and Business Media LLC","issue":"7921","license":[{"start":{"date-parts":[[2022,6,22]],"date-time":"2022-06-22T00:00:00Z","timestamp":1655856000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,6,22]],"date-time":"2022-06-22T00:00:00Z","timestamp":1655856000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2022,8,4]]},"DOI":"10.1038\/s41586-022-04989-3","type":"journal-article","created":{"date-parts":[[2022,6,22]],"date-time":"2022-06-22T16:37:07Z","timestamp":1655915827000},"page":"181-191","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":144,"title":["Integrated multi-omic characterization of congenital heart disease"],"prefix":"10.1038","volume":"608","author":[{"given":"Matthew C.","family":"Hill","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1254-377X","authenticated-orcid":false,"given":"Zachary A.","family":"Kadow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hali","family":"Long","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4571-8409","authenticated-orcid":false,"given":"Yuka","family":"Morikawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas J.","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma J.","family":"Birks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5615-5958","authenticated-orcid":false,"given":"Kenneth S.","family":"Campbell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8334-8499","authenticated-orcid":false,"given":"Jeanne","family":"Nerbonne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1948-9945","authenticated-orcid":false,"given":"Kory","family":"Lavine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lalita","family":"Wadhwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6874-9331","authenticated-orcid":false,"given":"Jun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diwakar","family":"Turaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iki","family":"Adachi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7842-9857","authenticated-orcid":false,"given":"James F.","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,6,22]]},"reference":[{"key":"4989_CR1","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1161\/CIRCULATIONAHA.114.011190","volume":"131","author":"A Raissadati","year":"2015","unstructured":"Raissadati, A., Nieminen, H., Jokinen, E. & Sairanen, H. Progress in late results among pediatric cardiac surgery patients: a population-based 6-decade study with 98% follow-up. Circulation 131, 347\u2013353 (2015).","journal-title":"Circulation"},{"key":"4989_CR2","doi-asserted-by":"publisher","first-page":"2118","DOI":"10.1161\/CIRCULATIONAHA.115.017202","volume":"132","author":"GP Diller","year":"2015","unstructured":"Diller, G. P. et al. Survival prospects and circumstances of death in contemporary adult congenital heart disease patients under follow-up at a large tertiary centre. Circulation 132, 2118\u20132125 (2015).","journal-title":"Circulation"},{"key":"4989_CR3","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1161\/CIRCHEARTFAILURE.109.856229","volume":"2","author":"DT Hsu","year":"2009","unstructured":"Hsu, D. T. & Pearson, G. D. Heart failure in children: part II: diagnosis, treatment, and future directions. Circ. Heart. Fail. 2, 490\u2013498 (2009).","journal-title":"Circ. Heart. Fail."},{"key":"4989_CR4","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1097\/MOP.0000000000000804","volume":"31","author":"MK Friedberg","year":"2019","unstructured":"Friedberg, M. K. & Reddy, S. Right ventricular failure in congenital heart disease. Curr. Opin. Pediatr. 31, 604\u2013610 (2019).","journal-title":"Curr. Opin. Pediatr."},{"key":"4989_CR5","doi-asserted-by":"publisher","first-page":"1956","DOI":"10.1016\/j.jacc.2016.01.062","volume":"67","author":"M Gurvitz","year":"2016","unstructured":"Gurvitz, M. et al. Emerging research directions in adult congenital heart disease: A report from an NHLBI\/ACHA working group. J. Am. Coll. Cardiol. 67, 1956\u20131964 (2016).","journal-title":"J. Am. Coll. Cardiol."},{"key":"4989_CR6","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/j.ijcard.2016.05.046","volume":"218","author":"D Ntiloudi","year":"2016","unstructured":"Ntiloudi, D. et al. Adult congenital heart disease: a paradigm of epidemiological change. Int. J. Cardiol. 218, 269\u2013274 (2016).","journal-title":"Int. J. Cardiol."},{"key":"4989_CR7","doi-asserted-by":"publisher","first-page":"1520","DOI":"10.1161\/01.CIR.81.5.1520","volume":"81","author":"F Fontan","year":"1990","unstructured":"Fontan, F. et al. Outcome after a \u201cperfect\u201d Fontan operation. Circulation 81, 1520\u20131536 (1990).","journal-title":"Circulation"},{"key":"4989_CR8","doi-asserted-by":"publisher","first-page":"1152","DOI":"10.1038\/ng.3870","volume":"49","author":"X Liu","year":"2017","unstructured":"Liu, X. et al. The complex genetics of hypoplastic left heart syndrome. Nat. Genet. 49, 1152\u20131159 (2017).","journal-title":"Nat. Genet."},{"key":"4989_CR9","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1542\/peds.2011-0134","volume":"129","author":"AR Brisson","year":"2012","unstructured":"Brisson, A. R., Matsui, D., Rieder, M. J. & Fraser, D. D. Translational research in pediatrics: tissue sampling and biobanking. Pediatrics 129, 153\u2013162 (2012).","journal-title":"Pediatrics"},{"key":"4989_CR10","doi-asserted-by":"publisher","first-page":"1614","DOI":"10.1161\/CIRCULATIONAHA.120.051921","volume":"143","author":"CB Sim","year":"2021","unstructured":"Sim, C. B. et al. Sex-specific control of human heart maturation by the progesterone receptor. Circulation 143, 1614\u20131628 (2021).","journal-title":"Circulation"},{"key":"4989_CR11","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1038\/s41586-020-2797-4","volume":"588","author":"M Litvi\u0148ukov\u00e1","year":"2020","unstructured":"Litvi\u0148ukov\u00e1, M. et al. Cells of the adult human heart. Nature 588, 466\u2013472 (2020).","journal-title":"Nature"},{"key":"4989_CR12","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1161\/CIRCULATIONAHA.119.045401","volume":"142","author":"NR Tucker","year":"2020","unstructured":"Tucker, N. R. et al. Transcriptional and cellular diversity of the human heart. Circulation 142, 466\u2013482 (2020).","journal-title":"Circulation"},{"key":"4989_CR13","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/s41587-021-01033-z","volume":"40","author":"E Dann","year":"2022","unstructured":"Dann, E., Henderson, N. C., Teichmamnn, S. A., Morgan, M. D. & Marioni, J. C. Differential abundance testing on single-cell data using k-nearest neighbor graphs. Nat. Biotechnol. 40, 245\u2013253 (2022).","journal-title":"Nat. Biotechnol."},{"key":"4989_CR14","doi-asserted-by":"publisher","first-page":"eaaw6419","DOI":"10.1126\/scitranslmed.aaw6419","volume":"11","author":"H Liu","year":"2019","unstructured":"Liu, H. et al. Control of cytokinesis by \u03b2-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment. Sci. Transl. Med. 11, eaaw6419 (2019).","journal-title":"Sci. Transl. Med."},{"key":"4989_CR15","doi-asserted-by":"publisher","first-page":"864","DOI":"10.1161\/CIRCULATIONAHA.118.038944","volume":"140","author":"K van Duijvenboden","year":"2019","unstructured":"van Duijvenboden, K. et al. Conserved NPPB+ border zone switches from MEF2- to AP-1-driven gene program. Circulation 140, 864\u2013879 (2019).","journal-title":"Circulation"},{"key":"4989_CR16","doi-asserted-by":"publisher","first-page":"e001104","DOI":"10.1161\/JAHA.114.001104","volume":"3","author":"R Lee","year":"2014","unstructured":"Lee, R. et al. Regulated inositol-requiring protein 1-dependent decay as a mechanism of corin RNA and protein deficiency in advanced human systolic heart failure. J. Am. Heart Assoc. 3, e001104 (2014).","journal-title":"J. Am. Heart Assoc."},{"key":"4989_CR17","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1038\/s41569-020-0381-0","volume":"17","author":"JP Goetze","year":"2020","unstructured":"Goetze, J. P. et al. Cardiac natriuretic peptides. Nat. Rev. Cardiol. 17, 698\u2013717 (2020).","journal-title":"Nat. Rev. Cardiol."},{"key":"4989_CR18","doi-asserted-by":"publisher","first-page":"e008157","DOI":"10.1161\/JAHA.117.008157","volume":"7","author":"SF Yang","year":"2018","unstructured":"Yang, S. F., Chou, R. H., Li, S. Y., Huang, S. S. & Huang, P. H. Serum corin level is associated with subsequent decline in renal function in patients with suspected coronary artery disease. J. Am. Heart Assoc. 7, e008157 (2018).","journal-title":"J. Am. Heart Assoc."},{"key":"4989_CR19","doi-asserted-by":"publisher","first-page":"214","DOI":"10.3109\/1354750X.2014.896946","volume":"19","author":"E Eleuteri","year":"2014","unstructured":"Eleuteri, E. et al. Fibrosis markers and CRIM1 increase in chronic heart failure of increasing severity. Biomarkers 19, 214\u2013221 (2014).","journal-title":"Biomarkers"},{"key":"4989_CR20","first-page":"276","volume":"24","author":"EJ Beckman","year":"2019","unstructured":"Beckman, E. J. Management of the pediatric organ donor. J. Pediatr. Pharmacol. Ther. 24, 276\u2013289 (2019).","journal-title":"J. Pediatr. Pharmacol. Ther."},{"key":"4989_CR21","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1038\/nrcardio.2017.57","volume":"14","author":"MD Tallquist","year":"2017","unstructured":"Tallquist, M. D. & Molkentin, J. D. Redefining the identity of cardiac fibroblasts. Nat. Rev. Cardiol. 14, 484\u2013491 (2017).","journal-title":"Nat. Rev. Cardiol."},{"key":"4989_CR22","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1002\/path.826","volume":"193","author":"M Corbel","year":"2001","unstructured":"Corbel, M. et al. Inhibition of bleomycin-induced pulmonary fibrosis in mice by the matrix metalloproteinase inhibitor batimastat. J. Pathol. 193, 538\u2013545 (2001).","journal-title":"J. Pathol."},{"key":"4989_CR23","doi-asserted-by":"publisher","first-page":"601","DOI":"10.3389\/fendo.2018.00601","volume":"9","author":"XX Nguyen","year":"2018","unstructured":"Nguyen, X. X., Muhammad, L., Nietert, P. J. & Feghali-Bostwick, C. IGFBP-5 promotes fibrosis via increasing its own expression and that of other pro-fibrotic mediators. Front. Endocrinol. 9, 601 (2018).","journal-title":"Front. Endocrinol."},{"key":"4989_CR24","doi-asserted-by":"publisher","DOI":"10.1038\/srep39383","volume":"6","author":"T Numaga-Tomita","year":"2016","unstructured":"Numaga-Tomita, T. et al. TRPC3\u2013GEF\u2013H1 axis mediates pressure overload-induced cardiac fibrosis. Sci. Rep. 6, 39383 (2016).","journal-title":"Sci. Rep."},{"key":"4989_CR25","doi-asserted-by":"publisher","first-page":"1491","DOI":"10.1101\/gad.329763.119","volume":"33","author":"Y Xiao","year":"2019","unstructured":"Xiao, Y. et al. Hippo pathway deletion in adult resting cardiac fibroblasts initiates a cell state transition with spontaneous and self-sustaining fibrosis. Genes Dev. 33, 1491\u20131505 (2019).","journal-title":"Genes Dev."},{"key":"4989_CR26","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1016\/j.bbrc.2020.05.115","volume":"528","author":"F Long","year":"2020","unstructured":"Long, F. et al. Targeting JMJD3 histone demethylase mediates cardiac fibrosis and cardiac function following myocardial infarction. Biochem. Biophys. Res. Commun. 528, 671\u2013677 (2020).","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"4989_CR27","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1016\/j.cell.2020.01.015","volume":"180","author":"J Kalucka","year":"2020","unstructured":"Kalucka, J. et al. Single-cell transcriptome atlas of murine endothelial cells. Cell 180, 764\u2013779.e720 (2020).","journal-title":"Cell"},{"key":"4989_CR28","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1038\/s41586-018-0288-7","volume":"559","author":"T Su","year":"2018","unstructured":"Su, T. et al. Single-cell analysis of early progenitor cells that build coronary arteries. Nature 559, 356\u2013362 (2018).","journal-title":"Nature"},{"key":"4989_CR29","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-017-0381-7","volume":"15","author":"A Thiriot","year":"2017","unstructured":"Thiriot, A. et al. Differential DARC\/ACKR1 expression distinguishes venular from non-venular endothelial cells in murine tissues. BMC Biol. 15, 45 (2017).","journal-title":"BMC Biol."},{"key":"4989_CR30","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1038\/nature25739","volume":"554","author":"M Vanlandewijck","year":"2018","unstructured":"Vanlandewijck, M. et al. A molecular atlas of cell types and zonation in the brain vasculature. Nature 554, 475\u2013480 (2018).","journal-title":"Nature"},{"key":"4989_CR31","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1007\/s00380-019-01463-5","volume":"35","author":"X Jiang","year":"2020","unstructured":"Jiang, X. et al. Elevated lymphatic vessel density measured by Lyve-1 expression in areas of replacement fibrosis in the ventricular septum of patients with hypertrophic obstructive cardiomyopathy (HOCM). Heart Vessels 35, 78\u201385 (2020).","journal-title":"Heart Vessels"},{"key":"4989_CR32","doi-asserted-by":"publisher","first-page":"165803","DOI":"10.1016\/j.bbadis.2020.165803","volume":"1866","author":"E Bertero","year":"2020","unstructured":"Bertero, E., Kutschka, I., Maack, C. & Dudek, J. Cardiolipin remodeling in Barth syndrome and other hereditary cardiomyopathies. Biochim. Biophys. Acta 1866, 165803 (2020).","journal-title":"Biochim. Biophys. Acta"},{"key":"4989_CR33","doi-asserted-by":"publisher","first-page":"48043","DOI":"10.1074\/jbc.M205324200","volume":"277","author":"AH Salehi","year":"2002","unstructured":"Salehi, A. H., Xanthoudakis, S. & Barker, P. A. NRAGE, a p75 neurotrophin receptor-interacting protein, induces caspase activation and cell death through a JNK-dependent mitochondrial pathway. J. Biol. Chem. 277, 48043\u201348050 (2002).","journal-title":"J. Biol. Chem."},{"key":"4989_CR34","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1126\/science.291.5502.319","volume":"291","author":"H Nishimura","year":"2001","unstructured":"Nishimura, H. et al. Autoimmune dilated cardiomyopathy in PD-1 receptor-deficient mice. Science 291, 319\u2013322 (2001).","journal-title":"Science"},{"key":"4989_CR35","doi-asserted-by":"publisher","first-page":"6407","DOI":"10.1158\/0008-5472.CAN-10-1544","volume":"70","author":"B Zhang","year":"2010","unstructured":"Zhang, B. CD73: a novel target for cancer immunotherapy. Cancer Res. 70, 6407\u20136411 (2010).","journal-title":"Cancer Res."},{"key":"4989_CR36","doi-asserted-by":"publisher","first-page":"7007","DOI":"10.1002\/cam4.3360","volume":"9","author":"SY Hyun","year":"2020","unstructured":"Hyun, S. Y. et al. Immunosuppressive role of CD11b+ CD33+ HLA-DR\u2212 myeloid-derived suppressor cells-like blast subpopulation in acute myeloid leukemia. Cancer Med. 9, 7007\u20137017 (2020).","journal-title":"Cancer Med."},{"key":"4989_CR37","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1073\/pnas.0408241102","volume":"102","author":"M Afanasyeva","year":"2005","unstructured":"Afanasyeva, M. et al. Impaired up-regulation of CD25 on CD4+ T cells in IFN-\u03b3 knockout mice is associated with progression of myocarditis to heart failure. Proc. Natl Acad. Sci. USA 102, 180\u2013185 (2005).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"4989_CR38","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1093\/cvr\/cvz025","volume":"115","author":"N Grabie","year":"2019","unstructured":"Grabie, N., Lichtman, A. H. & Padera, R. T cell checkpoint regulators in the heart. Cardiovasc. Res. 115, 869\u2013877 (2019).","journal-title":"Cardiovasc. Res."},{"key":"4989_CR39","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1038\/s44161-022-00028-6","volume":"1","author":"AL Koenig","year":"2022","unstructured":"Koenig, A. L. et al. Single-cell transcriptomics reveals cell-type-specific diversification in human heart failure. Nat. Cardiovasc. Res. 1, 263\u2013280 (2022).","journal-title":"Nat. Cardiovasc. Res."},{"key":"4989_CR40","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-64929-x","volume":"10","author":"M Caron","year":"2020","unstructured":"Caron, M. et al. Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity. Sci Rep. 10, 8079 (2020).","journal-title":"Sci Rep."},{"key":"4989_CR41","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14049","volume":"8","author":"GX Zheng","year":"2017","unstructured":"Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).","journal-title":"Nat. Commun."},{"key":"4989_CR42","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1084\/jem.20100223","volume":"207","author":"K Crozat","year":"2010","unstructured":"Crozat, K. et al. The XC chemokine receptor 1 is a conserved selective marker of mammalian cells homologous to mouse CD8\u03b1+ dendritic cells. J. Exp. Med. 207, 1283\u20131292 (2010).","journal-title":"J. Exp. Med."},{"key":"4989_CR43","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24215-4","volume":"12","author":"D Vanhoutte","year":"2021","unstructured":"Vanhoutte, D. et al. Thbs1 induces lethal cardiac atrophy through PERK-ATF4 regulated autophagy. Nat. Commun. 12, 3928 (2021).","journal-title":"Nat. Commun."},{"key":"4989_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21246-9","volume":"12","author":"S Jin","year":"2021","unstructured":"Jin, S. et al. Inference and analysis of cell-cell communication using CellChat. Nat. Commun. 12, 1088 (2021).","journal-title":"Nat. Commun."},{"key":"4989_CR45","first-page":"12","volume":"2","author":"CA Blair","year":"2016","unstructured":"Blair, C. A. et al. A protocol for collecting human cardiac tissue for research. VAD J. 2, 12 (2016).","journal-title":"VAD J."},{"key":"4989_CR46","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1038\/nmeth.4396","volume":"14","author":"MR Corces","year":"2017","unstructured":"Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959\u2013962 (2017).","journal-title":"Nat. Methods"},{"key":"4989_CR47","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1007\/978-1-0716-0668-1_23","volume":"2158","author":"MC Hill","year":"2021","unstructured":"Hill, M. C. & Martin, J. F. Epigenetic assays in purified cardiomyocyte nuclei. Methods Mol. Biol. 2158, 307\u2013321 (2021).","journal-title":"Methods Mol. Biol."},{"key":"4989_CR48","doi-asserted-by":"publisher","first-page":"ra41","DOI":"10.1126\/scisignal.2005781","volume":"8","author":"Y Morikawa","year":"2015","unstructured":"Morikawa, Y. et al. Actin cytoskeletal remodeling with protrusion formation is essential for heart regeneration in Hippo-deficient mice. Sci. Signal. 8, ra41 (2015).","journal-title":"Sci. Signal."},{"key":"4989_CR49","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1016\/j.cels.2018.02.010","volume":"6","author":"S Chevrier","year":"2018","unstructured":"Chevrier, S. et al. Compensation of signal spillover in suspension and imaging mass cytometry. Cell Syst. 6, 612\u2013620.e615 (2018).","journal-title":"Cell Syst."},{"key":"4989_CR50","doi-asserted-by":"publisher","unstructured":"Fleming, S. J., Marioni, J. C. & Babadi, M. CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/791699 (2019).","DOI":"10.1101\/791699"},{"key":"4989_CR51","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289\u20131296 (2019).","journal-title":"Nat. Methods"},{"key":"4989_CR52","doi-asserted-by":"publisher","first-page":"dev168609","DOI":"10.1242\/dev.168609","volume":"145","author":"L Li","year":"2018","unstructured":"Li, L. et al. Pitx2 maintains mitochondrial function during regeneration to prevent myocardial fat deposition. Development 145, dev168609 (2018).","journal-title":"Development"},{"key":"4989_CR53","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284\u2013287 (2012).","journal-title":"OMICS"},{"key":"4989_CR54","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014).","journal-title":"Genome Biol"},{"key":"4989_CR55","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1186\/s12859-019-2879-1","volume":"20","author":"F Marini","year":"2019","unstructured":"Marini, F. & Binder, H. pcaExplorer: an R\/Bioconductor package for interacting with RNA-seq principal components. BMC Bioinf. 20, 331 (2019).","journal-title":"BMC Bioinf."},{"key":"4989_CR56","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms8866","volume":"6","author":"JA Ramilowski","year":"2015","unstructured":"Ramilowski, J. A. et al. A draft network of ligand\u2013receptor-mediated multicellular signalling in human. Nat. Commun. 6, 7866 (2015).","journal-title":"Nat. Commun."},{"key":"4989_CR57","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1126\/science.aad0501","volume":"352","author":"I Tirosh","year":"2016","unstructured":"Tirosh, I. et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352, 189\u2013196 (2016).","journal-title":"Science"},{"key":"4989_CR58","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1016\/j.devcel.2019.01.017","volume":"48","author":"TO Monroe","year":"2019","unstructured":"Monroe, T. O. et al. YAP partially reprograms chromatin accessibility to directly induce adult cardiogenesis in vivo. Dev. Cell 48, 765\u2013779.e767 (2019).","journal-title":"Dev. Cell"},{"key":"4989_CR59","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"4989_CR60","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"4989_CR61","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"4989_CR62","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1093\/biostatistics\/kxr054","volume":"13","author":"KD Hansen","year":"2012","unstructured":"Hansen, K. D., Irizarry, R. A. & Wu, Z. Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics 13, 204\u2013216 (2012).","journal-title":"Biostatistics"},{"key":"4989_CR63","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","volume":"38","author":"S Heinz","year":"2010","unstructured":"Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576\u2013589 (2010).","journal-title":"Mol. Cell"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-022-04989-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-022-04989-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-022-04989-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,4]],"date-time":"2022-08-04T14:27:40Z","timestamp":1659623260000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-022-04989-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,22]]},"references-count":63,"journal-issue":{"issue":"7921","published-print":{"date-parts":[[2022,8,4]]}},"alternative-id":["4989"],"URL":"https:\/\/doi.org\/10.1038\/s41586-022-04989-3","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,22]]},"assertion":[{"value":"25 February 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 June 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 June 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}