{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:29Z","timestamp":1772138009617,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,8,24]],"date-time":"2020-08-24T00:00:00Z","timestamp":1598227200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000163","name":"ARC","doi-asserted-by":"publisher","award":["200100200"],"award-info":[{"award-number":["200100200"]}],"id":[{"id":"10.13039\/100000163","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["DP170101306"],"award-info":[{"award-number":["DP170101306"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Australian Government Research Training Program"},{"DOI":"10.13039\/501100001787","name":"University of South Australia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001787","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,20]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Predicting cell locations is important since with the understanding of cell locations, we may estimate the function of cells and their integration with the spatial environment. Thus, the DREAM challenge on single-cell transcriptomics required participants to predict the locations of single cells in the Drosophila embryo using single-cell transcriptomic data.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We have developed over 50 pipelines by combining different ways of preprocessing the RNA-seq data, selecting the genes, predicting the cell locations and validating predicted cell locations, resulting in the winning methods which were ranked second in sub-challenge 1, first in sub-challenge 2 and third in sub-challenge 3. In this paper, we present an R package, SCTCwhatateam, which includes all the methods we developed and the Shiny web application to facilitate the research on single-cell spatial reconstruction. All the data and the example use cases are available in the Supplementary data.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bib\/bbaa181","type":"journal-article","created":{"date-parts":[[2020,7,15]],"date-time":"2020-07-15T07:14:14Z","timestamp":1594797254000},"source":"Crossref","is-referenced-by-count":0,"title":["The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8884-3584","authenticated-orcid":false,"given":"Vu V H","family":"Pham","sequence":"first","affiliation":[{"name":"University of South Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaomei","family":"Li","sequence":"additional","affiliation":[{"name":"University of South Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Buu","family":"Truong","sequence":"additional","affiliation":[{"name":"University of South Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thin","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Applied Artificial Intelligence Institute (A2I2) at Deakin University"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lin","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Information Technology and Mathematical Sciences, University of South Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiuyong","family":"Li","sequence":"additional","affiliation":[{"name":"School of Information Technology and Mathematical Sciences, University of South Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thuc D","family":"Le","sequence":"additional","affiliation":[{"name":"University of South Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,8,25]]},"reference":[{"key":"2021082500110006700_ref1","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/nbt.3209","article-title":"High-throughput spatial mapping of single-cell rna-seq data to tissue of origin","volume":"33","author":"Achim","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2021082500110006700_ref2","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1038\/nature21065","article-title":"Single-cell spatial reconstruction reveals global division of labour in the mammalian liver","volume":"542","author":"Halpern","year":"2017","journal-title":"Nature"},{"key":"2021082500110006700_ref3","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.3192","article-title":"Spatial reconstruction of single-cell gene expression data","volume":"33","author":"Satija","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2021082500110006700_ref4","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1126\/science.aan3235","article-title":"The drosophila embryo at single-cell transcriptome resolution","volume":"358","author":"Karaiskos","year":"2017","journal-title":"Science"},{"key":"2021082500110006700_ref5","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/0005-2795(75)90109-9","article-title":"Comparison of the predicted and observed secondary structure of t4 phage lysozyme","volume":"405","author":"Matthews","year":"1975","journal-title":"Biochimica et Biophysica Acta (BBA)-Protein Structure"},{"key":"2021082500110006700_ref6","first-page":"93","volume-title":"ACM Sigmod Record","author":"Breunig","year":"2000"},{"key":"2021082500110006700_ref7","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1016\/j.cell.2018.05.061","article-title":"Recovering gene interactions from single-cell data using data diffusion","volume":"174","author":"Dijk","year":"2018","journal-title":"Cell"},{"key":"2021082500110006700_ref8","doi-asserted-by":"crossref","first-page":"1250689","DOI":"10.1126\/science.1250689","article-title":"Systems biology. Conditional density-based analysis of t cell signaling in single-cell data","volume":"346","author":"Krishnaswamy","year":"2014","journal-title":"Science (New York, NY)"},{"key":"2021082500110006700_ref9","article-title":"Predicting cellular position in the drosophila embryo from single-cell transcriptomics data","volume":"796029","author":"Tanevski","year":"2019","journal-title":"bioRxiv"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/3\/bbaa181\/37965309\/bbaa181.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/3\/bbaa181\/37965309\/bbaa181.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,24]],"date-time":"2021-08-24T20:11:15Z","timestamp":1629835875000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaa181\/5896572"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8,25]]},"references-count":9,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,5,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaa181","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.05.09.086397","asserted-by":"object"}]},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,5]]},"published":{"date-parts":[[2020,8,25]]},"article-number":"bbaa181"}}