{"id":"https://openalex.org/W3081239913","doi":"https://doi.org/10.1093/bib/bbaa181","title":"The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge","display_name":"The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge","publication_year":2020,"publication_date":"2020-07-15","ids":{"openalex":"https://openalex.org/W3081239913","doi":"https://doi.org/10.1093/bib/bbaa181","mag":"3081239913","pmid":"https://pubmed.ncbi.nlm.nih.gov/34020545"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa181","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaa181","pdf_url":"https://academic.oup.com/bib/article-pdf/22/3/bbaa181/37965309/bbaa181.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/22/3/bbaa181/37965309/bbaa181.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062956281","display_name":"Vu Pham","orcid":"https://orcid.org/0000-0002-8884-3584"},"institutions":[{"id":"https://openalex.org/I170239107","display_name":"University of South Australia","ror":"https://ror.org/01p93h210","country_code":"AU","type":"education","lineage":["https://openalex.org/I170239107"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Vu V H Pham","raw_affiliation_strings":["University of South Australia"],"raw_orcid":"https://orcid.org/0000-0002-8884-3584","affiliations":[{"raw_affiliation_string":"University of South Australia","institution_ids":["https://openalex.org/I170239107"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100413473","display_name":"Xiaomei Li","orcid":"https://orcid.org/0000-0002-8870-3186"},"institutions":[{"id":"https://openalex.org/I170239107","display_name":"University of South Australia","ror":"https://ror.org/01p93h210","country_code":"AU","type":"education","lineage":["https://openalex.org/I170239107"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Xiaomei Li","raw_affiliation_strings":["University of South Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of South Australia","institution_ids":["https://openalex.org/I170239107"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066650734","display_name":"Buu Truong","orcid":"https://orcid.org/0000-0003-0043-0812"},"institutions":[{"id":"https://openalex.org/I170239107","display_name":"University of South Australia","ror":"https://ror.org/01p93h210","country_code":"AU","type":"education","lineage":["https://openalex.org/I170239107"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Buu Truong","raw_affiliation_strings":["University of South Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of South Australia","institution_ids":["https://openalex.org/I170239107"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100705489","display_name":"Thin Nguyen","orcid":"https://orcid.org/0000-0003-3467-8963"},"institutions":[{"id":"https://openalex.org/I149704539","display_name":"Deakin University","ror":"https://ror.org/02czsnj07","country_code":"AU","type":"education","lineage":["https://openalex.org/I149704539"]},{"id":"https://openalex.org/I4210156221","display_name":"Allen Institute for Artificial Intelligence","ror":"https://ror.org/05w520734","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210156221"]}],"countries":["AU","US"],"is_corresponding":false,"raw_author_name":"Thin Nguyen","raw_affiliation_strings":["Applied Artificial Intelligence Institute (A2I2) at Deakin University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Applied Artificial Intelligence Institute (A2I2) at Deakin University","institution_ids":["https://openalex.org/I4210156221","https://openalex.org/I149704539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100383342","display_name":"Lin Liu","orcid":"https://orcid.org/0000-0003-2843-5738"},"institutions":[{"id":"https://openalex.org/I170239107","display_name":"University of South Australia","ror":"https://ror.org/01p93h210","country_code":"AU","type":"education","lineage":["https://openalex.org/I170239107"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Lin Liu","raw_affiliation_strings":["School of Information Technology and Mathematical Sciences, University of South Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Technology and Mathematical Sciences, University of South Australia","institution_ids":["https://openalex.org/I170239107"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012177739","display_name":"Jiuyong Li","orcid":"https://orcid.org/0000-0002-9023-1878"},"institutions":[{"id":"https://openalex.org/I170239107","display_name":"University of South Australia","ror":"https://ror.org/01p93h210","country_code":"AU","type":"education","lineage":["https://openalex.org/I170239107"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jiuyong Li","raw_affiliation_strings":["School of Information Technology and Mathematical Sciences, University of South Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Technology and Mathematical Sciences, University of South Australia","institution_ids":["https://openalex.org/I170239107"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035846381","display_name":"Thuc Duy Le","orcid":"https://orcid.org/0000-0002-9732-4313"},"institutions":[{"id":"https://openalex.org/I170239107","display_name":"University of South Australia","ror":"https://ror.org/01p93h210","country_code":"AU","type":"education","lineage":["https://openalex.org/I170239107"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Thuc D Le","raw_affiliation_strings":["University of South Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of South Australia","institution_ids":["https://openalex.org/I170239107"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5035846381"],"corresponding_institution_ids":["https://openalex.org/I170239107"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.8335,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.71672539,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11020","display_name":"Immune Cell Function and Interaction","score":0.9790999889373779,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.964900016784668,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/position","display_name":"Position (finance)","score":0.5812661647796631},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.574646532535553},{"id":"https://openalex.org/keywords/dream","display_name":"Dream","score":0.42525625228881836},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3739698529243469},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3447553515434265},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22351229190826416},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.10778805613517761},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.07864567637443542}],"concepts":[{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.5812661647796631},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.574646532535553},{"id":"https://openalex.org/C2781095916","wikidata":"https://www.wikidata.org/wiki/Q36348","display_name":"Dream","level":2,"score":0.42525625228881836},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3739698529243469},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3447553515434265},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22351229190826416},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.10778805613517761},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.07864567637443542},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa181","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaa181","pdf_url":"https://academic.oup.com/bib/article-pdf/22/3/bbaa181/37965309/bbaa181.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34020545","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34020545","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbaa181","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaa181","pdf_url":"https://academic.oup.com/bib/article-pdf/22/3/bbaa181/37965309/bbaa181.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G462952484","display_name":null,"funder_award_id":"DP170101306","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G8703593047","display_name":null,"funder_award_id":"200100200","funder_id":"https://openalex.org/F4320338275","funder_display_name":"Division of Arctic Sciences"}],"funders":[{"id":"https://openalex.org/F4320320979","display_name":"University of South Australia","ror":"https://ror.org/01p93h210"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320338275","display_name":"Division of Arctic Sciences","ror":"https://ror.org/02trddg58"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1977544680","https://openalex.org/W2069089843","https://openalex.org/W2079296583","https://openalex.org/W2109553965","https://openalex.org/W2585175142","https://openalex.org/W2605624585","https://openalex.org/W2805619986","https://openalex.org/W2979951699","https://openalex.org/W7014708188"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W1762480892","https://openalex.org/W597599663","https://openalex.org/W3194824274","https://openalex.org/W4205387075","https://openalex.org/W1537165133","https://openalex.org/W2390579330","https://openalex.org/W1578892932","https://openalex.org/W2387132837"],"abstract_inverted_index":{"MOTIVATION:":[0],"Predicting":[1],"cell":[2,11,72,77],"locations":[3,39,73],"is":[4],"important":[5],"since":[6],"with":[7,23],"the":[8,16,24,28,38,44,64,68,71,81,112,117,123,130,133,140],"understanding":[9],"of":[10,18,40,62],"locations,":[12,78],"we":[13,103,114],"may":[14],"estimate":[15],"function":[17],"cells":[19,42],"and":[20,74,95,116,132],"their":[21],"integration":[22],"spatial":[25,127],"environment.":[26],"Thus,":[27],"DREAM":[29],"challenge":[30],"on":[31,125],"single-cell":[32,48,126],"transcriptomics":[33],"required":[34],"participants":[35],"to":[36,121],"predict":[37],"single":[41],"in":[43,80,88,92,97,139],"Drosophila":[45],"embryo":[46],"using":[47],"transcriptomic":[49],"data.":[50,142],"RESULTS:":[51],"We":[52],"have":[53],"developed":[54,115],"over":[55],"50":[56],"pipelines":[57],"by":[58],"combining":[59],"different":[60],"ways":[61],"preprocessing":[63],"RNA-seq":[65],"data,":[66],"selecting":[67],"genes,":[69],"predicting":[70],"validating":[75],"predicted":[76],"resulting":[79],"winning":[82],"methods":[83,113],"which":[84,109],"were":[85],"ranked":[86],"second":[87],"sub-challenge":[89,93,98],"1,":[90],"first":[91],"2":[94],"third":[96],"3.":[99],"In":[100],"this":[101],"paper,":[102],"present":[104],"an":[105],"R":[106],"package,":[107],"SCTCwhatateam,":[108],"includes":[110],"all":[111],"Shiny":[118],"web":[119],"application":[120],"facilitate":[122],"research":[124],"reconstruction.":[128],"All":[129],"data":[131],"example":[134],"use":[135],"cases":[136],"are":[137],"available":[138],"Supplementary":[141]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}