{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T16:58:59Z","timestamp":1776790739967,"version":"3.51.2"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006053","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,4,19]],"date-time":"2018-04-19T00:00:00Z","timestamp":1524096000000}}],"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2018,4,9]],"date-time":"2018-04-09T00:00:00Z","timestamp":1523232000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Science Foundations","award":["NSF III 1149697"],"award-info":[{"award-number":["NSF III 1149697"]}]},{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["NIH T32GM113846"],"award-info":[{"award-number":["NIH T32GM113846"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AR063070"],"award-info":[{"award-number":["R01 AR063070"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006053","type":"journal-article","created":{"date-parts":[[2018,4,9]],"date-time":"2018-04-09T17:25:23Z","timestamp":1523294723000},"page":"e1006053","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":34,"title":["A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8378-1073","authenticated-orcid":true,"given":"Huanan","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Catherine A. A.","family":"Lee","sequence":"additional","affiliation":[]},{"given":"Zhuliu","family":"Li","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9745-7378","authenticated-orcid":true,"given":"John R.","family":"Garbe","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7314-2550","authenticated-orcid":true,"given":"Cindy R.","family":"Eide","sequence":"additional","affiliation":[]},{"given":"Raphael","family":"Petegrosso","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4916-903X","authenticated-orcid":true,"given":"Rui","family":"Kuang","sequence":"additional","affiliation":[]},{"given":"Jakub","family":"Tolar","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2018,4,9]]},"reference":[{"issue":"6078","key":"ref1","first-page":"183","article-title":"Using gene expression noise to understand gene regulation","volume":"336","author":"B. Munsky","year":"2012"},{"issue":"2","key":"ref2","first-page":"140","article-title":"Single-Cell Genomics: Approaches and Utility in Immunology","volume":"38","author":"Karlynn E. Neu","year":"2017"},{"issue":"3","key":"ref3","first-page":"658","article-title":"Methods, challenges and potentials of single cell RNA-seq","volume":"1","author":"D Hebenstreit","year":"2012"},{"issue":"1","key":"ref4","first-page":"63","article-title":"Design and computational analysis of single-cell RNA-sequencing experiments","volume":"17","author":"R. Bacher","year":"2016"},{"key":"ref5","doi-asserted-by":"crossref","unstructured":"Wang D., Nie F., and Huang H. (2014). Unsupervised feature selection via unified trace ratio formulation and k-means clustering (track). In <italic>Joint European Conference on Machine Learning and Knowledge Discovery in Databases<\/italic>, pages 306\u2013321. Springer.","DOI":"10.1007\/978-3-662-44845-8_20"},{"issue":"7","key":"ref6","first-page":"1160","article-title":"Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq","volume":"21","author":"S. Islam","year":"2011"},{"issue":"7505","key":"ref7","first-page":"363","article-title":"Single-cell RNA-seq reveals dynamic paracrine control of cellular variation","volume":"510","author":"A. K. Shalek","year":"2014"},{"issue":"7453","key":"ref8","first-page":"236","article-title":"Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells","volume":"498","author":"A. K. Shalek","year":"2013"},{"issue":"9","key":"ref9","first-page":"1131","article-title":"Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells","volume":"20","author":"L. Yan","year":"2013"},{"issue":"6226","key":"ref10","first-page":"1138","article-title":"Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq","volume":"347","author":"A. Zeisel","year":"2015"},{"issue":"5","key":"ref11","first-page":"1202","article-title":"Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets","volume":"161","author":"E. Z. Macosko","year":"2015"},{"issue":"5","key":"ref12","first-page":"1187","article-title":"Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells","volume":"161","author":"A. M. Klein","year":"2015"},{"issue":"4","key":"ref13","first-page":"381","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"C. Trapnell","year":"2014"},{"issue":"10","key":"ref14","first-page":"R118","article-title":"Temporal dynamics and transcriptional control using single-cell gene expression analysis","volume":"14","author":"T. Kouno","year":"2013"},{"issue":"12","key":"ref15","first-page":"1974","article-title":"Identification of cell types from single-cell transcriptomes using a novel clustering method","volume":"31","author":"C. Xu","year":"2015"},{"issue":"1","key":"ref16","first-page":"241","article-title":"Zifa: Dimensionality reduction for zero-inflated single-cell gene expression analysis","volume":"16","author":"E. Pierson","year":"2015"},{"issue":"1","key":"ref17","first-page":"363","article-title":"Celltree: an R\/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data","volume":"17","author":"D. duVerle","year":"2016"},{"issue":"5","key":"ref18","first-page":"495","article-title":"Spatial reconstruction of single-cell gene expression data","volume":"33","author":"Rahul Satija","year":"2015"},{"key":"ref19","article-title":"SC3: consensus clustering of single-cell RNA-seq data","author":"Vladimir Yu Kiselev","year":"2017"},{"key":"ref20","unstructured":"Hicks, S. C., Teng, M., and Irizarry, R. A. (2015). On the widespread and critical impact of systematic bias and batch effects in single-cell RNA-seq data. <italic>bioRxiv<\/italic>, page 025528."},{"issue":"4","key":"ref21","first-page":"471","article-title":"Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation","volume":"17","author":"A. A. Kolodziejczyk","year":"2015"},{"issue":"7500","key":"ref22","first-page":"371","article-title":"Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq","volume":"509","author":"B. Treutlein","year":"2014"},{"key":"ref23","first-page":"14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Grace XY Zheng","year":"2017"},{"issue":"D1","key":"ref24","first-page":"D723","article-title":"Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse","volume":"45","author":"JA Blake","year":"2017"},{"issue":"10","key":"ref25","first-page":"1151","article-title":"Desmoplakin Variants Are Associated with Idiopathic Pulmonary Fibrosis","volume":"193","author":"S. K. Mathai","year":"2016"},{"issue":"29","key":"ref26","first-page":"8242","article-title":"Epithelial Notch signaling regulates lung alveolar morphogenesis and airway epithelial integrity","volume":"113","author":"P. N. Tsao","year":"2016"},{"issue":"3","key":"ref27","first-page":"1032","article-title":"Genetic linkage of recessive dystrophic epidermolysis bullosa to the type VII collagen gene","volume":"90","author":"A. Hovnanian","year":"1992"},{"issue":"3","key":"ref28","first-page":"611","article-title":"Type VII collagen forms an extended network of anchoring fibrils","volume":"104","author":"D. R. Keene","year":"1987"},{"issue":"6","key":"ref29","first-page":"987","article-title":"From marrow to matrix: novel gene and cell therapies for epidermolysis bullosa","volume":"23","author":"B. R. Webber","year":"2015"},{"issue":"8","key":"ref30","first-page":"707","article-title":"Quality of life in epidermolysis bullosa","volume":"27","author":"H. M. Horn","year":"2002"},{"issue":"1","key":"ref31","first-page":"107","article-title":"Dystrophic epidermolysis bullosa: pathogenesis and clinical features","volume":"28","author":"L. Bruckner-Tuderman","year":"2010"},{"issue":"1","key":"ref32","first-page":"171","article-title":"Understanding the pathogenesis of recessive dystrophic epidermolysis bullosa squamous cell carcinoma","volume":"28","author":"A. P. South","year":"2010"},{"issue":"7","key":"ref33","first-page":"629","article-title":"Bone marrow transplantation for recessive dystrophic epidermolysis bullosa","volume":"363","author":"J. E. Wagner","year":"2010"},{"issue":"4","key":"ref34","first-page":"1996","article-title":"Transplanted bone marrow\u2013derived circulating PDGFR<italic>\u03b1<\/italic>+ cells restore type VII collagen in recessive dystrophic epidermolysis bullosa mouse skin graft","volume":"194","author":"S. Iinuma","year":"2015"},{"issue":"6","key":"ref35","first-page":"433","article-title":"Serum levels of high mobility group box 1 correlate with disease severity in recessive dystrophic epidermolysis bullosa","volume":"22","author":"G. Petrof","year":"2013"},{"issue":"16","key":"ref36","first-page":"6609","article-title":"PDGFRalpha-positive cells in bone marrow are mobilized by high mobility group box 1 (HMGB1) to regenerate injured epithelia","volume":"108","author":"K. Tamai","year":"2011"},{"issue":"2","key":"ref37","first-page":"203","article-title":"A COL11A1-correlated pan-cancer gene signature of activated fibroblasts for the prioritization of therapeutic targets","volume":"382","author":"D. Jia","year":"2016"},{"issue":"10","key":"ref38","first-page":"1085","article-title":"Gremlin is a key pro-fibrogenic factor in chronic pancreatitis","volume":"93","author":"D. Staloch","year":"2015"},{"key":"ref39","article-title":"Gremlin1 plays a key role in kidney development and renal fibrosis","author":"R. H. Church","year":"2017"},{"key":"ref40","first-page":"13","article-title":"The microfibril-associated glycoproteins (MAGPs) and the microfibrillar niche","volume":"47","author":"R. P. Mecham","year":"2015"},{"issue":"10","key":"ref41","first-page":"1345","article-title":"A survey on transfer learning","volume":"22","author":"S. J. Pan","year":"2010"},{"key":"ref42","unstructured":"Pan S. J., Kwok J. T., and Yang Q. (2008). Transfer learning via dimensionality reduction. In <italic>AAAI<\/italic>, volume 8, pages 677\u2013682."},{"key":"ref43","doi-asserted-by":"crossref","unstructured":"Wang Z., Song Y., and Zhang C. (2008). Transferred dimensionality reduction. In <italic>Joint European Conference on Machine Learning and Knowledge Discovery in Databases<\/italic>, pages 550\u2013565. Springer.","DOI":"10.1007\/978-3-540-87481-2_36"},{"key":"ref44","doi-asserted-by":"crossref","unstructured":"Dai, W., Yang, Q., Xue, G.-R., and Yu, Y. (2008). Self-taught clustering. In <italic>Proceedings of the 25th international conference on Machine learning<\/italic>, pages 200\u2013207. ACM.","DOI":"10.1145\/1390156.1390182"},{"issue":"3","key":"ref45","first-page":"133","article-title":"Computational and analytical challenges in single-cell transcriptomics","volume":"16","author":"O. Stegle","year":"2015"},{"issue":"3","key":"ref46","first-page":"e1006599","article-title":"Visualizing the structure of RNA-seq expression data using grade of membership models","volume":"13","author":"K. Dey","year":"2017"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006053","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,4,19]],"date-time":"2018-04-19T00:00:00Z","timestamp":1524096000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006053","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T09:11:27Z","timestamp":1589015487000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006053"}},"subtitle":[],"editor":[{"given":"Aly","family":"Khan","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,4,9]]},"references-count":46,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2018,4,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006053","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1006053","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,4,9]]}}}