{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T00:35:07Z","timestamp":1792802107873,"version":"4.5.0"},"reference-count":70,"publisher":"Springer Science and Business Media LLC","issue":"12","license":[{"start":{"date-parts":[[2019,12,1]],"date-time":"2019-12-01T00:00:00Z","timestamp":1575158400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2019,12,1]],"date-time":"2019-12-01T00:00:00Z","timestamp":1575158400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Cell Biol"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1038\/s41556-019-0428-9","type":"journal-article","created":{"date-parts":[[2019,12,2]],"date-time":"2019-12-02T17:04:55Z","timestamp":1575306295000},"page":"1504-1517","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":64,"title":["Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages"],"prefix":"10.1038","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9215-4829","authenticated-orcid":false,"given":"Irving T. C.","family":"Ling","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9289-0263","authenticated-orcid":false,"given":"Tatjana","family":"Sauka-Spengler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,2]]},"reference":[{"key":"428_CR1","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1053\/j.gastro.2018.01.012","volume":"154","author":"MD Gershon","year":"2018","unstructured":"Gershon, M. D. Development of the enteric nervous system: a genetic guide to the perplexed. Gastroenterology 154, 478\u2013480 (2018).","journal-title":"Gastroenterology"},{"key":"428_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1136\/jmg.2007.053959","volume":"45","author":"J Amiel","year":"2008","unstructured":"Amiel, J. et al. Hirschsprung disease, associated syndromes and genetics: a review. J. Med. Genet. 45, 1\u201314 (2008).","journal-title":"J. Med. Genet."},{"key":"428_CR3","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/j.cell.2016.09.005","volume":"167","author":"S Chatterjee","year":"2016","unstructured":"Chatterjee, S. et al. Enhancer variants synergistically drive dysfunction of a gene regulatory network in Hirschsprung disease. Cell 167, 355\u2013368 (2016).","journal-title":"Cell"},{"key":"428_CR4","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1056\/NEJMoa1706594","volume":"380","author":"JM Tilghman","year":"2019","unstructured":"Tilghman, J. M. et al. Molecular genetic anatomy and risk profile of Hirschsprung\u2019s disease. N. Engl. J. Med. 380, 1421\u20131432 (2019).","journal-title":"N. Engl. J. Med."},{"key":"428_CR5","first-page":"31","volume":"30","author":"NM Le Douarin","year":"1973","unstructured":"Le Douarin, N. M. & Teillet, M. A. The migration of neural crest cells to the wall of the digestive tract in avian embryo. J. Embryol. Exp. Morphol. 30, 31\u201348 (1973).","journal-title":"J. Embryol. Exp. Morphol."},{"key":"428_CR6","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1002\/cne.901010212","volume":"101","author":"CL Yntema","year":"1954","unstructured":"Yntema, C. L. & Hammond, W. S. The origin of intrinsic ganglia of trunk viscera from vagal neural crest in the chick embryo. J. Comp. Neurol. 101, 515\u2013541 (1954).","journal-title":"J. Comp. Neurol."},{"key":"428_CR7","doi-asserted-by":"crossref","first-page":"4335","DOI":"10.1242\/dev.125.21.4335","volume":"125","author":"AJ Burns","year":"1998","unstructured":"Burns, A. J. & Douarin, N. M. The sacral neural crest contributes neurons and glia to the post-umbilical gut: spatiotemporal analysis of the development of the enteric nervous system. Development 125, 4335\u20134347 (1998).","journal-title":"Development"},{"key":"428_CR8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/cne.10448","volume":"456","author":"HM Young","year":"2003","unstructured":"Young, H. M., Bergner, A. J. & Muller, T. Acquisition of neuronal and glial markers by neural crest-derived cells in the mouse intestine. J. Comp. Neurol. 456, 1\u201311 (2003).","journal-title":"J. Comp. Neurol."},{"key":"428_CR9","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/j.ydbio.2006.06.033","volume":"298","author":"BP Vohra","year":"2006","unstructured":"Vohra, B. P. et al. Differential gene expression and functional analysis implicate novel mechanisms in enteric nervous system precursor migration and neuritogenesis. Dev. Biol. 298, 259\u2013271 (2006).","journal-title":"Dev. Biol."},{"key":"428_CR10","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/j.ydbio.2016.06.004","volume":"416","author":"D Schriemer","year":"2016","unstructured":"Schriemer, D. et al. Regulators of gene expression in enteric neural crest cells are putative Hirschsprung disease genes. Dev. Biol. 416, 255\u2013265 (2016).","journal-title":"Dev. Biol."},{"key":"428_CR11","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1053\/j.gastro.2017.10.005","volume":"154","author":"F Memic","year":"2018","unstructured":"Memic, F. et al. Transcription and signaling regulators in developing neuronal subtypes of mouse and human enteric nervous system. Gastroenterology 154, 624\u2013636 (2018).","journal-title":"Gastroenterology"},{"key":"428_CR12","doi-asserted-by":"publisher","first-page":"6919","DOI":"10.1073\/pnas.0602152103","volume":"103","author":"TA Heanue","year":"2006","unstructured":"Heanue, T. A. & Pachnis, V. Expression profiling the developing mammalian enteric nervous system identifies marker and candidate Hirschsprung disease genes. Proc. Natl Acad. Sci. USA 103, 6919\u20136924 (2006).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"428_CR13","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-3653-2","volume":"18","author":"S Roy-Carson","year":"2017","unstructured":"Roy-Carson, S. et al. Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment. BMC Genomics 18, 290 (2017).","journal-title":"BMC Genomics"},{"key":"428_CR14","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1126\/science.aam7511","volume":"356","author":"R Lasrado","year":"2017","unstructured":"Lasrado, R. et al. Lineage-dependent spatial and functional organization of the mammalian enteric nervous system. Science 356, 722\u2013726 (2017).","journal-title":"Science"},{"key":"428_CR15","doi-asserted-by":"publisher","first-page":"eaas9536","DOI":"10.1126\/science.aas9536","volume":"364","author":"R Soldatov","year":"2019","unstructured":"Soldatov, R et al. Spatiotemporal structure of cell fate decisions in murine neural crest. Science 364, eaas9536 (2019).","journal-title":"Science"},{"key":"428_CR16","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1146\/annurev.cellbio.042308.113245","volume":"26","author":"P Betancur","year":"2010","unstructured":"Betancur, P., Bronner-Fraser, M. & Sauka-Spengler, T. Assembling neural crest regulatory circuits into a gene regulatory network. Annu. Rev. Cell Dev. Biol. 26, 581\u2013603 (2010).","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"428_CR17","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1038\/nrm2428","volume":"9","author":"T Sauka-Spengler","year":"2008","unstructured":"Sauka-Spengler, T. & Bronner-Fraser, M. A gene regulatory network orchestrates neural crest formation. Nat. Rev. Mol. Cell Biol. 9, 557\u2013568 (2008).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"428_CR18","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/j.devcel.2019.10.003","volume":"51","author":"RM Williams","year":"2019","unstructured":"Williams, R. M. et al. Reconstruction of the global neural crest gene regulatory network in vivo. Dev. Cell 51, 255\u2013276 (2019).","journal-title":"Dev. Cell"},{"key":"428_CR19","doi-asserted-by":"publisher","first-page":"1570","DOI":"10.1126\/science.aaf2729","volume":"352","author":"M Simoes-Costa","year":"2016","unstructured":"Simoes-Costa, M. & Bronner, M. E. Reprogramming of avian neural crest axial identity and cell fate. Science 352, 1570\u20131573 (2016).","journal-title":"Science"},{"key":"428_CR20","doi-asserted-by":"publisher","first-page":"e1003142","DOI":"10.1371\/journal.pgen.1003142","volume":"8","author":"MS Simoes-Costa","year":"2012","unstructured":"Simoes-Costa, M. S., McKeown, S. J., Tan-Cabugao, J., Sauka-Spengler, T. & Bronner, M. E. Dynamic and differential regulation of stem cell factor FoxD3 in the neural crest is encrypted in the genome. PLoS Genet. 8, e1003142 (2012).","journal-title":"PLoS Genet"},{"key":"428_CR21","doi-asserted-by":"publisher","first-page":"S209","DOI":"10.1016\/j.ydbio.2018.09.015","volume":"444","author":"S Tani-Matsuhana","year":"2018","unstructured":"Tani-Matsuhana, S., Vieceli, F. M., Gandhi, S., Inoue, K. & Bronner, M. E. Transcriptome profiling of the cardiac neural crest reveals a critical role for MafB. Dev. Biol. 444, S209\u2013S218 (2018).","journal-title":"Dev. Biol."},{"key":"428_CR22","doi-asserted-by":"publisher","first-page":"2075","DOI":"10.1242\/dev.02375","volume":"133","author":"N Bondurand","year":"2006","unstructured":"Bondurand, N., Natarajan, D., Barlow, A., Thapar, N. & Pachnis, V. Maintenance of mammalian enteric nervous system progenitors by SOX10 and endothelin 3 signalling. Development 133, 2075\u20132086 (2006).","journal-title":"Development"},{"key":"428_CR23","doi-asserted-by":"publisher","first-page":"dev165753","DOI":"10.1242\/dev.165753","volume":"145","author":"HMT Choi","year":"2018","unstructured":"Choi, H. M. T. et al. Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust. Development 145, dev165753 (2018).","journal-title":"Development"},{"key":"428_CR24","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1016\/j.devcel.2005.01.015","volume":"8","author":"BM Kim","year":"2005","unstructured":"Kim, B. M., Buchner, G., Miletich, I., Sharpe, P. T. & Shivdasani, R. A. The stomach mesenchymal transcription factor Barx1 specifies gastric epithelial identity through inhibition of transient Wnt signaling. Dev. Cell 8, 611\u2013622 (2005).","journal-title":"Dev. Cell"},{"key":"428_CR25","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1016\/j.cell.2018.06.021","volume":"174","author":"A Zeisel","year":"2018","unstructured":"Zeisel, A. et al. Molecular architecture of the mouse nervous system. Cell 174, 999\u20131014 (2018).","journal-title":"Cell"},{"key":"428_CR26","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1016\/j.devcel.2018.11.009","volume":"47","author":"M Lukoseviciute","year":"2018","unstructured":"Lukoseviciute, M. et al. From pioneer to repressor: bimodal FoxD3 activity dynamically remodels neural crest regulatory landscape in vivo. Dev. Cell 47, 608\u2013628 (2018).","journal-title":"Dev. Cell"},{"key":"428_CR27","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"},{"key":"428_CR28","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1002\/gepi.21918","volume":"39","author":"X Zhan","year":"2015","unstructured":"Zhan, X. & Liu, D. J. SEQMINER: an R-package to facilitate the functional interpretation of sequence-based associations. Genet. Epidemiol. 39, 619\u2013623 (2015).","journal-title":"Genet. Epidemiol."},{"key":"428_CR29","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1016\/j.cell.2013.07.007","volume":"154","author":"K Stefflova","year":"2013","unstructured":"Stefflova, K. et al. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell 154, 530\u2013540 (2013).","journal-title":"Cell"},{"key":"428_CR30","doi-asserted-by":"publisher","first-page":"W202","DOI":"10.1093\/nar\/gkp335","volume":"37","author":"TL Bailey","year":"2009","unstructured":"Bailey, T. L. et al. MEME suite: tools for motif discovery and searching. Nucleic Acids Res. 37, W202\u2013W208 (2009).","journal-title":"Nucleic Acids Res"},{"key":"428_CR31","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1174-6","volume":"18","author":"H Gui","year":"2017","unstructured":"Gui, H. et al. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome Biol. 18, 48 (2017).","journal-title":"Genome Biol"},{"key":"428_CR32","doi-asserted-by":"publisher","first-page":"dev160333","DOI":"10.1242\/dev.160333","volume":"145","author":"RM Williams","year":"2018","unstructured":"Williams, R. M. et al. Genome and epigenome engineering CRISPR toolkit for in vivo modulation of cis-regulatory interactions and gene expression in the chicken embryo. Development 145, dev160333 (2018).","journal-title":"Development"},{"key":"428_CR33","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1093\/oxfordjournals.jhered.a109980","volume":"75","author":"PW Lane","year":"1984","unstructured":"Lane, P. W. & Liu, H. M. Association of megacolon with a new dominant spotting gene (Dom) in the mouse. J. Hered. 75, 435\u2013439 (1984).","journal-title":"J. Hered."},{"key":"428_CR34","doi-asserted-by":"publisher","first-page":"e22908","DOI":"10.1371\/journal.pone.0022908","volume":"6","author":"F Zhao","year":"2011","unstructured":"Zhao, F., Bosserhoff, A. K., Buettner, R. & Moser, M. A heart-hand syndrome gene: Tfap2b plays a critical role in the development and remodeling of mouse ductus arteriosus and limb patterning. PLoS One 6, e22908 (2011).","journal-title":"PLoS One"},{"key":"428_CR35","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1038\/nn1131","volume":"6","author":"M Bylund","year":"2003","unstructured":"Bylund, M., Andersson, E., Novitch, B. G. & Muhr, J. Vertebrate neurogenesis is counteracted by Sox1\u20133 activity. Nat. Neurosci. 6, 1162\u20131168 (2003).","journal-title":"Nat. Neurosci."},{"key":"428_CR36","doi-asserted-by":"publisher","first-page":"3156","DOI":"10.1242\/dev.147256","volume":"144","author":"S Bansod","year":"2017","unstructured":"Bansod, S., Kageyama, R. & Ohtsuka, T. Hes5 regulates the transition timing of neurogenesis and gliogenesis in mammalian neocortical development. Development 144, 3156\u20133167 (2017).","journal-title":"Development"},{"key":"428_CR37","first-page":"125","volume":"34","author":"CS Le Lievre","year":"1975","unstructured":"Le Lievre, C. S. & Le Douarin, N. M. Mesenchymal derivatives of the neural crest: analysis of chimaeric quail and chick embryos. J. Embryol. Exp. Morphol. 34, 125\u2013154 (1975).","journal-title":"J. Embryol. Exp. Morphol."},{"key":"428_CR38","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.ydbio.2015.10.026","volume":"409","author":"K Maeda","year":"2016","unstructured":"Maeda, K. et al. Postotic and preotic cranial neural crest cells differently contribute to thyroid development. Dev. Biol. 409, 72\u201383 (2016).","journal-title":"Dev. Biol."},{"key":"428_CR39","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1016\/0012-1606(83)90100-8","volume":"97","author":"ML Kirby","year":"1983","unstructured":"Kirby, M. L. & Stewart, D. E. Neural crest origin of cardiac ganglion cells in the chick embryo: identification and extirpation. Dev. Biol. 97, 433\u2013443 (1983).","journal-title":"Dev. Biol."},{"key":"428_CR40","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/j.ydbio.2004.09.006","volume":"277","author":"AJ Burns","year":"2005","unstructured":"Burns, A. J. & Delalande, J. M. Neural crest cell origin for intrinsic ganglia of the developing chicken lung. Dev. Biol. 277, 63\u201379 (2005).","journal-title":"Dev. Biol."},{"key":"428_CR41","doi-asserted-by":"publisher","first-page":"11980","DOI":"10.1073\/pnas.1710308114","volume":"114","author":"I Espinosa-Medina","year":"2017","unstructured":"Espinosa-Medina, I. et al. Dual origin of enteric neurons in vagal Schwann cell precursors and the sympathetic neural crest. Proc. Natl Acad. Sci. USA 114, 11980\u201311985 (2017).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"428_CR42","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1016\/0016-6480(77)90055-7","volume":"33","author":"J Fontaine","year":"1977","unstructured":"Fontaine, J., Le Lievre, C. & Le Douarin, N. M. What is the developmental fate of the neural crest cells which migrate into the pancreas in the avian embryo? Gen. Comp. Endocrinol. 33, 394\u2013404 (1977).","journal-title":"Gen. Comp. Endocrinol."},{"key":"428_CR43","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1016\/0012-1606(74)90291-7","volume":"41","author":"NM Le Douarin","year":"1974","unstructured":"Le Douarin, N. M. & Teillet, M. A. Experimental analysis of the migration and differentiation of neuroblasts of the autonomic nervous system and of neurectodermal mesenchymal derivatives, using a biological cell marking technique. Dev. Biol. 41, 162\u2013184 (1974).","journal-title":"Dev. Biol."},{"key":"428_CR44","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1242\/dev.118422","volume":"142","author":"S Faure","year":"2015","unstructured":"Faure, S., McKey, J., Sagnol, S. & de Santa Barbara, P. Enteric neural crest cells regulate vertebrate stomach patterning and differentiation. Development 142, 331\u2013342 (2015).","journal-title":"Development"},{"key":"428_CR45","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1126\/science.6606851","volume":"223","author":"DE Bockman","year":"1984","unstructured":"Bockman, D. E. & Kirby, M. L. Dependence of thymus development on derivatives of the neural crest. Science 223, 498\u2013500 (1984).","journal-title":"Science"},{"key":"428_CR46","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.mod.2005.11.004","volume":"123","author":"RM Hakami","year":"2006","unstructured":"Hakami, R. M. et al. Genetic evidence does not support direct regulation of EDNRB by SOX10 in migratory neural crest and the melanocyte lineage. Mech. Dev. 123, 124\u2013134 (2006).","journal-title":"Mech. Dev."},{"key":"428_CR47","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1002\/jmor.1050880104","volume":"88","author":"V Hamburger","year":"1951","unstructured":"Hamburger, V. & Hamilton, H. L. A series of normal stages in the development of the chick embryo. J. Morphol. 88, 49\u201392 (1951).","journal-title":"J. Morphol."},{"key":"428_CR48","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/S0091-679X(08)00212-4","volume":"87","author":"T Sauka-Spengler","year":"2008","unstructured":"Sauka-Spengler, T. & Barembaum, M. Gain- and loss-of-function approaches in the chick embryo. Methods Cell. Biol. 87, 237\u2013256 (2008).","journal-title":"Methods Cell. Biol."},{"key":"428_CR49","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1038\/nmeth.2688","volume":"10","author":"JD Buenrostro","year":"2013","unstructured":"Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213\u20131218 (2013).","journal-title":"Nat. Methods"},{"key":"428_CR50","doi-asserted-by":"publisher","first-page":"W272","DOI":"10.1093\/nar\/gkw398","volume":"44","author":"K Labun","year":"2016","unstructured":"Labun, K., Montague, T. G., Gagnon, J. A., Thyme, S. B. & Valen, E. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res. 44, W272\u2013W276 (2016).","journal-title":"Nucleic Acids Res."},{"key":"428_CR51","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).","journal-title":"Genome Biol"},{"key":"428_CR52","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"428_CR53","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1038\/nmeth.2375","volume":"10","author":"T Daley","year":"2013","unstructured":"Daley, T. & Smith, A. D. Predicting the molecular complexity of sequencing libraries. Nat. Methods 10, 325\u2013327 (2013).","journal-title":"Nat. Methods"},{"key":"428_CR54","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":"428_CR55","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1038\/nature10730","volume":"481","author":"CS Ross-Innes","year":"2012","unstructured":"Ross-Innes, C. S. et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389\u2013393 (2012).","journal-title":"Nature"},{"key":"428_CR56","doi-asserted-by":"publisher","first-page":"2382","DOI":"10.1093\/bioinformatics\/btv145","volume":"31","author":"G Yu","year":"2015","unstructured":"Yu, G., Wang, L. G. & He, Q. Y. ChIPseeker: an R\/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382\u20132383 (2015).","journal-title":"Bioinformatics"},{"key":"428_CR57","doi-asserted-by":"publisher","first-page":"e35","DOI":"10.1093\/nar\/gkq1287","volume":"39","author":"T Ye","year":"2011","unstructured":"Ye, T. et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 39, e35 (2011).","journal-title":"Nucleic Acids Res."},{"key":"428_CR58","doi-asserted-by":"publisher","first-page":"W187","DOI":"10.1093\/nar\/gku365","volume":"42","author":"F Ramirez","year":"2014","unstructured":"Ramirez, F., Dundar, F., Diehl, S., Gruning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187\u2013W191 (2014).","journal-title":"Nucleic Acids Res."},{"key":"428_CR59","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"428_CR60","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923\u2013930 (2014).","journal-title":"Bioinformatics"},{"key":"428_CR61","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","volume":"32","author":"Z Gu","year":"2016","unstructured":"Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847\u20132849 (2016).","journal-title":"Bioinformatics"},{"key":"428_CR62","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":"428_CR63","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2007-8-2-r24","volume":"8","author":"S Gupta","year":"2007","unstructured":"Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L. & Noble, W. S. Quantifying similarity between motifs. Genome Biol. 8, R24 (2007).","journal-title":"Genome Biol"},{"key":"428_CR64","doi-asserted-by":"publisher","first-page":"D252","DOI":"10.1093\/nar\/gkx1106","volume":"46","author":"IV Kulakovskiy","year":"2018","unstructured":"Kulakovskiy, I. V. et al. HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-seq analysis. Nucleic Acids Res. 46, D252\u2013D259 (2018).","journal-title":"Nucleic Acids Res."},{"key":"428_CR65","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ydbio.2005.04.023","volume":"283","author":"WJ Longabaugh","year":"2005","unstructured":"Longabaugh, W. J., Davidson, E. H. & Bolouri, H. Computational representation of developmental genetic regulatory networks. Dev. Biol. 283, 1\u201316 (2005).","journal-title":"Dev. Biol."},{"key":"428_CR66","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":"428_CR67","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/nbt.4096","volume":"36","author":"A Butler","year":"2018","unstructured":"Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies and species. Nat. Biotechnol. 36, 411\u2013420 (2018).","journal-title":"Nat. Biotechnol."},{"key":"428_CR68","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/nbt.2859","volume":"32","author":"C Trapnell","year":"2014","unstructured":"Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381\u2013386 (2014).","journal-title":"Nat. Biotechnol."},{"key":"428_CR69","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1016\/j.cels.2016.08.011","volume":"3","author":"M Baron","year":"2016","unstructured":"Baron, M. et al. A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure. Cell Syst. 3, 346\u2013360 (2016).","journal-title":"Cell Syst."},{"key":"428_CR70","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1038\/nmeth.3337","volume":"12","author":"AM Newman","year":"2015","unstructured":"Newman, A. M. et al. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12, 453\u2013457 (2015).","journal-title":"Nat. Methods"}],"container-title":["Nature Cell Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/s41556-019-0428-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41556-019-0428-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41556-019-0428-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,20]],"date-time":"2023-05-20T21:39:40Z","timestamp":1684618780000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41556-019-0428-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12]]},"references-count":70,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["428"],"URL":"https:\/\/doi.org\/10.1038\/s41556-019-0428-9","relation":{},"ISSN":["1465-7392","1476-4679"],"issn-type":[{"value":"1465-7392","type":"print"},{"value":"1476-4679","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,12]]},"assertion":[{"value":"30 January 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 October 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 December 2019","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"}}]}}