{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:07:58Z","timestamp":1772172478020,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007040","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,9,12]],"date-time":"2019-09-12T00:00:00Z","timestamp":1568246400000}}],"reference-count":39,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2019,8,30]],"date-time":"2019-08-30T00:00:00Z","timestamp":1567123200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007040","type":"journal-article","created":{"date-parts":[[2019,8,30]],"date-time":"2019-08-30T13:32:51Z","timestamp":1567171971000},"page":"e1007040","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["PanoView: An iterative clustering method for single-cell RNA sequencing data"],"prefix":"10.1371","volume":"15","author":[{"given":"Ming-Wen","family":"Hu","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8624-0168","authenticated-orcid":true,"given":"Dong Won","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Sheng","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Donald J.","family":"Zack","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1338-8476","authenticated-orcid":true,"given":"Seth","family":"Blackshaw","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0476-3596","authenticated-orcid":true,"given":"Jiang","family":"Qian","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,8,30]]},"reference":[{"key":"pcbi.1007040.ref001","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/nature13173","article-title":"Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq","volume":"509","author":"B Treutlein","year":"2014","journal-title":"Nature"},{"issue":"6226","key":"pcbi.1007040.ref002","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1126\/science.aaa1934","article-title":"Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq","volume":"347","author":"A Zeisel","year":"2015","journal-title":"Science"},{"issue":"5","key":"pcbi.1007040.ref003","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets","volume":"161","author":"EZ Macosko","year":"2015","journal-title":"Cell"},{"key":"pcbi.1007040.ref004","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/nature14966","article-title":"Single-cell messenger RNA sequencing reveals rare intestinal cell types","author":"D Gr\u00fcn","year":"2015","journal-title":"Nature"},{"key":"pcbi.1007040.ref005","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.cels.2016.08.011","article-title":"A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure","volume":"3","author":"M Baron","year":"2016","journal-title":"Cell Systems"},{"key":"pcbi.1007040.ref006","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1126\/science.1254257","article-title":"Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma","volume":"344","author":"AP Patel","year":"2014","journal-title":"Science"},{"key":"pcbi.1007040.ref007","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s13059-016-0932-1","article-title":"Single-cell analysis of long non-coding RNAs in the developing human neocortex","volume":"17","author":"SJ Liu","year":"2016","journal-title":"Genome Biology"},{"key":"pcbi.1007040.ref008","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.cels.2016.09.002","article-title":"A Single-Cell Transcriptome Atlas of the Human Pancreas","volume":"3","author":"MJ Muraro","year":"2016","journal-title":"Cell Systems Report"},{"key":"pcbi.1007040.ref009","doi-asserted-by":"crossref","first-page":"8557","DOI":"10.1038\/ncomms9557","article-title":"Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear","volume":"6","author":"JC Bruns","year":"2015","journal-title":"Nature Communications"},{"issue":"3","key":"pcbi.1007040.ref010","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.stem.2015.07.013","article-title":"Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis","volume":"17","author":"J Shin","year":"2015","journal-title":"Cell Stem Cell"},{"key":"pcbi.1007040.ref011","doi-asserted-by":"crossref","first-page":"E5643","DOI":"10.1073\/pnas.1408993111","article-title":"Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape","volume":"111","author":"E Marco","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"12","key":"pcbi.1007040.ref012","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1093\/bioinformatics\/btv088","article-title":"Identification of cell types from single-cell transcriptomes using a novel clustering method","volume":"31","author":"C Xu","year":"2015","journal-title":"Bioinformatics"},{"key":"pcbi.1007040.ref013","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/s12859-016-0984-y","article-title":"pcaReduce: hierarchical clustering of single cell transcriptional profiles","volume":"17","author":"J \u017eurauskien\u0117","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1007040.ref014","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nmeth.4236","article-title":"SC3: consensus clustering of single-cell RNA-seq data","volume":"14","author":"VY Kiselev","year":"2017","journal-title":"Nature methods"},{"key":"pcbi.1007040.ref015","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"A Butler","year":"2018","journal-title":"Nature Biotechnology"},{"issue":"15","key":"pcbi.1007040.ref016","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"FA Wolf","year":"2018","journal-title":"BMC Genome Biology"},{"key":"pcbi.1007040.ref017","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1038\/ng.3818","article-title":"Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors","volume":"49","author":"H Li","year":"2017","journal-title":"Nature Genetics"},{"issue":"6","key":"pcbi.1007040.ref018","doi-asserted-by":"crossref","first-page":"e36","DOI":"10.1093\/nar\/gky007","article-title":"dropClust: efficient clustering of ultra-large scRNA-seq data","volume":"46","author":"D Sinha","year":"2018","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"pcbi.1007040.ref019","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.stem.2016.05.010","article-title":"De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data","volume":"19","author":"D Gr\u00fcn","year":"2016","journal-title":"Cell Stem Cell"},{"key":"pcbi.1007040.ref020","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1186\/s13059-016-1010-4","article-title":"Chen, Huidong, Pinello, Luca, Yuan G. GiniClust: detecting rare cell types from single-cell gene expression data with Gini index","volume":"17","author":"LJ Liang","year":"2016","journal-title":"Genome Biology"},{"key":"pcbi.1007040.ref021","unstructured":"A density-based algorithm for discovering clusters in large spatial databases with noise. Proceedings of the Second International Conference on Knowledge Discovery and Data Mining; Augest 2, 1996; 1996."},{"key":"pcbi.1007040.ref022","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1126\/science.aan3351","article-title":"Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex","volume":"357","author":"C Luo","year":"2017","journal-title":"Science"},{"key":"pcbi.1007040.ref023","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1002\/widm.30","article-title":"Density-based clustering. Wiley Interdisciplinary Reviews","volume":"1","author":"H Kriegel","year":"2011","journal-title":"Data Mining and Knowledge Discovery"},{"issue":"1","key":"pcbi.1007040.ref024","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/BF01908075","article-title":"Comparing partitions","volume":"2","author":"L Hubert","year":"1985","journal-title":"Journal of Classification"},{"key":"pcbi.1007040.ref025","volume-title":"Functional Anatomy of the Hypothalamus and Pituitary","author":"RM Lechan","year":"2016"},{"issue":"1","key":"pcbi.1007040.ref026","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1111\/nyas.13263","article-title":"Neuronal systems and circuits involved in the control of food intake and adaptive thermogenesis","volume":"1391","author":"A Caron","year":"2017","journal-title":"ANNALS OF THE NEW YORK ACADEMY OF SCIENCES"},{"issue":"5","key":"pcbi.1007040.ref027","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1002\/wdev.187","article-title":"Patterning, specification, and differentiation in the developing hypothalamus","volume":"4","author":"JL Bedont","year":"2015","journal-title":"Wiley interdisciplinary reviews Developmental biology"},{"issue":"12","key":"pcbi.1007040.ref028","doi-asserted-by":"crossref","first-page":"2991","DOI":"10.1016\/j.celrep.2017.02.069","article-title":"Tissue Myeloid Progenitors Differentiate into Pericytes through TGF-b Signaling in Developing Skin Vasculature","volume":"18","author":"T Yamazaki","year":"2017","journal-title":"Cell Reports"},{"key":"pcbi.1007040.ref029","first-page":"2825","article-title":"Scikit-learn: Machine Learning in Python","volume":"12","author":"F Pedregosa","year":"2011","journal-title":"Journal of Machine Learning Research"},{"issue":"3","key":"pcbi.1007040.ref030","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1109\/MCSE.2007.58","article-title":"Python for Scientific Computing","volume":"9","author":"TE Oliphant","year":"2007","journal-title":"Computing in Science and Engineering"},{"key":"pcbi.1007040.ref031","author":"A Sen","year":"1973"},{"key":"pcbi.1007040.ref032","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1038\/nsmb.2660","article-title":"Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells","volume":"20","author":"L Yan","year":"2013","journal-title":"nature structural and molecular biology"},{"issue":"1","key":"pcbi.1007040.ref033","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.cell.2016.01.047","article-title":"Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos","volume":"165","author":"M Goolam","year":"2016","journal-title":"Cell"},{"issue":"6167","key":"pcbi.1007040.ref034","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1126\/science.1245316","article-title":"Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells","volume":"343","author":"Q Deng","year":"2014","journal-title":"Science"},{"key":"pcbi.1007040.ref035","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1038\/nbt.2967","article-title":"Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex","volume":"32","author":"AA Pollen","year":"2014","journal-title":"Nature Biotechnology"},{"key":"pcbi.1007040.ref036","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/nn.3881","article-title":"Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing","volume":"18","author":"D Usoskin","year":"2015","journal-title":"Nature Neuroscience"},{"issue":"6335","key":"pcbi.1007040.ref037","doi-asserted-by":"crossref","DOI":"10.1126\/science.aah4573","article-title":"Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors","volume":"356","author":"A Villani","year":"2017","journal-title":"Science"},{"key":"pcbi.1007040.ref038","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1126\/science.aad0501","article-title":"Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq","volume":"352","author":"I Tirosh","year":"2016","journal-title":"Science"},{"key":"pcbi.1007040.ref039","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/nn.4495","article-title":"A molecular census of arcuate hypothalamus and median eminence cell types","volume":"20","author":"JN Campbell","year":"2017","journal-title":"Nature Neuroscience"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007040","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,9,12]],"date-time":"2019-09-12T00:00:00Z","timestamp":1568246400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007040","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T23:47:39Z","timestamp":1588981659000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007040"}},"subtitle":[],"editor":[{"given":"Qing","family":"Nie","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,8,30]]},"references-count":39,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2019,8,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007040","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/616862","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,30]]}}}