{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T06:05:43Z","timestamp":1777615543686,"version":"3.51.4"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"S7","license":[{"start":{"date-parts":[[2018,12,1]],"date-time":"2018-12-01T00:00:00Z","timestamp":1543622400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12918-018-0638-y","type":"journal-article","created":{"date-parts":[[2018,12,14]],"date-time":"2018-12-14T09:21:43Z","timestamp":1544779303000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["MISC: missing imputation for single-cell RNA sequencing data"],"prefix":"10.1186","volume":"12","author":[{"given":"Mary Qu","family":"Yang","sequence":"first","affiliation":[]},{"given":"Sherman M.","family":"Weissman","sequence":"additional","affiliation":[]},{"given":"William","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Jialing","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Allon","family":"Canaann","sequence":"additional","affiliation":[]},{"given":"Renchu","family":"Guan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,12,14]]},"reference":[{"issue":"11","key":"638_CR1","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1038\/nbt.3711","volume":"34","author":"A Wagner","year":"2016","unstructured":"Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol. 2016;34(11):1145.","journal-title":"Nat Biotechnol"},{"issue":"6","key":"638_CR2","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1038\/nm.4336","volume":"23","author":"A Giustacchini","year":"2017","unstructured":"Giustacchini A, Thongjuea S, Barkas N, Woll PS, Povinelli BJ, Booth CA, Sopp P, Norfo R, Rodriguez-Meira A, Ashley N. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia. Nat Med. 2017;23(6):692\u2013702.","journal-title":"Nat Med"},{"issue":"1","key":"638_CR3","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1186\/s13059-015-0616-2","volume":"16","author":"ML Leung","year":"2015","unstructured":"Leung ML, Wang Y, Waters J, Navin NE. SNES: single nucleus exome sequencing. Genome Biol. 2015;16(1):55.","journal-title":"Genome Biol"},{"issue":"11","key":"638_CR4","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1038\/nmeth.2639","volume":"10","author":"S Picelli","year":"2013","unstructured":"Picelli S, Bj\u00f6rklund \u00c5K, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods. 2013;10(11):1096.","journal-title":"Nat Methods"},{"issue":"6030","key":"638_CR5","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1126\/science.1198704","volume":"332","author":"SC Bendall","year":"2011","unstructured":"Bendall SC, Simonds EF, Qiu P, El-ad DA, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science (New York, NY). 2011;332(6030):687\u201396.","journal-title":"Science (New York, NY)"},{"issue":"7511","key":"638_CR6","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1038\/nature13544","volume":"511","author":"H Guo","year":"2014","unstructured":"Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y, Yan J, Ren X, Lin S, Li J. The DNA methylation landscape of human early embryos. Nature. 2014;511(7511):606.","journal-title":"Nature"},{"issue":"6237","key":"638_CR7","doi-asserted-by":"publisher","first-page":"910","DOI":"10.1126\/science.aab1601","volume":"348","author":"DA Cusanovich","year":"2015","unstructured":"Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science (New York, NY). 2015;348(6237):910\u20134.","journal-title":"Science (New York, NY)"},{"issue":"7469","key":"638_CR8","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nature12593","volume":"502","author":"T Nagano","year":"2013","unstructured":"Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P. Single-cell hi-C reveals cell-to-cell variability in chromosome structure. Nature. 2013;502(7469):59.","journal-title":"Nature"},{"issue":"5","key":"638_CR9","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","volume":"161","author":"EZ Macosko","year":"2015","unstructured":"Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161(5):1202\u201314.","journal-title":"Cell"},{"issue":"1","key":"638_CR10","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1016\/j.cell.2015.05.047","volume":"162","author":"JH Levine","year":"2015","unstructured":"Levine JH, Simonds EF, Bendall SC, Davis KL, El-ad DA, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell. 2015;162(1):184\u201397.","journal-title":"Cell"},{"issue":"3","key":"638_CR11","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1038\/nrg3833","volume":"16","author":"O Stegle","year":"2015","unstructured":"Stegle O, Teichmann SA, Marioni JC. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet. 2015;16(3):133.","journal-title":"Nat Rev Genet"},{"issue":"13","key":"638_CR12","doi-asserted-by":"publisher","first-page":"1867","DOI":"10.1093\/bioinformatics\/btu134","volume":"30","author":"F Buettner","year":"2014","unstructured":"Buettner F, Moignard V, G\u00f6ttgens B, Theis FJ. Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data. Bioinformatics. 2014;30(13):1867\u201375.","journal-title":"Bioinformatics"},{"issue":"4","key":"638_CR13","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1016\/j.molcel.2015.05.005","volume":"58","author":"Y Wang","year":"2015","unstructured":"Wang Y, Navin NE. Advances and applications of single-cell sequencing technologies. Mol Cell. 2015;58(4):598\u2013609.","journal-title":"Mol Cell"},{"issue":"7","key":"638_CR14","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1038\/nmeth.2967","volume":"11","author":"PV Kharchenko","year":"2014","unstructured":"Kharchenko PV, Silberstein L, Scadden DT. Bayesian approach to single-cell differential expression analysis. Nat Methods. 2014;11(7):740.","journal-title":"Nat Methods"},{"issue":"1","key":"638_CR15","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1186\/s12859-016-1176-5","volume":"17","author":"D DeTomaso","year":"2016","unstructured":"DeTomaso D, Yosef N. FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data. BMC bioinformatics. 2016;17(1):315.","journal-title":"BMC bioinformatics"},{"key":"638_CR16","doi-asserted-by":"crossref","unstructured":"Ma H, King I, Lyu MR. Effective missing data prediction for collaborative filtering. In: Proceedings of the 30th annual international ACM SIGIR conference on research and development in information retrieval. Amsterdam, The Netherlands: ACM; 2007. p. 39\u201346.","DOI":"10.1145\/1277741.1277751"},{"issue":"6226","key":"638_CR17","doi-asserted-by":"publisher","first-page":"1138","DOI":"10.1126\/science.aaa1934","volume":"347","author":"A Zeisel","year":"2015","unstructured":"Zeisel A, Mu\u00f1oz-Manchado AB, Codeluppi S, L\u00f6nnerberg P, La Manno G, Jur\u00e9us A, Marques S, Munguba H, He L, Betsholtz C. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science (New York, NY). 2015;347(6226):1138\u201342.","journal-title":"Science (New York, NY)"},{"key":"638_CR18","doi-asserted-by":"crossref","unstructured":"Lin C-J, Weng RC, Keerthi SS. Trust region newton methods for large-scale logistic regression. In: Proceedings of the 24th international conference on machine learning. Corvalis, Oregon, USA: ACM; 2007. p. 561\u20138.","DOI":"10.1145\/1273496.1273567"},{"issue":"1\u20132","key":"638_CR19","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1007\/s10994-010-5221-8","volume":"85","author":"H-F Yu","year":"2011","unstructured":"Yu H-F, Huang F-L, Lin C-J. Dual coordinate descent methods for logistic regression and maximum entropy models. Mach Learn. 2011;85(1\u20132):41\u201375.","journal-title":"Mach Learn"},{"issue":"Aug","key":"638_CR20","first-page":"1871","volume":"9","author":"R-E Fan","year":"2008","unstructured":"Fan R-E, Chang K-W, Hsieh C-J, Wang X-R, Lin C-J. LIBLINEAR: a library for large linear classification. J Mach Learn Res. 2008;9(Aug):1871\u20134.","journal-title":"J Mach Learn Res"},{"issue":"7","key":"638_CR21","doi-asserted-by":"publisher","first-page":"362","DOI":"10.1016\/S0168-9525(03)00140-9","volume":"19","author":"E Eisenberg","year":"2003","unstructured":"Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends in genetics : TIG. 2003;19(7):362\u20135.","journal-title":"Trends in genetics : TIG"},{"issue":"4","key":"638_CR22","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1016\/j.cell.2015.10.039","volume":"163","author":"D Gr\u00fcn","year":"2015","unstructured":"Gr\u00fcn D, van Oudenaarden A. Design and analysis of single-cell sequencing experiments. Cell. 2015;163(4):799\u2013810.","journal-title":"Cell"}],"updated-by":[{"DOI":"10.1186\/s12918-019-0681-3","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T00:00:00Z","timestamp":1548115200000}}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-018-0638-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12918-018-0638-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-018-0638-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,12,14]],"date-time":"2019-12-14T00:08:33Z","timestamp":1576282113000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-018-0638-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12]]},"references-count":22,"journal-issue":{"issue":"S7","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["638"],"URL":"https:\/\/doi.org\/10.1186\/s12918-018-0638-y","relation":{"correction":[{"id-type":"doi","id":"10.1186\/s12918-019-0681-3","asserted-by":"object"}]},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12]]},"assertion":[{"value":"14 December 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 January 2019","order":2,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Correction","order":3,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"It was highlighted that the original article [1] contained a typesetting error in the last name of Allon Canaan. This was incorrectly captured as Allon Canaann in the original article which has since been updated.","order":4,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"114"}}