{"id":"https://openalex.org/W2995326310","doi":"https://doi.org/10.1093/bioinformatics/btz936","title":"scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization","display_name":"scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization","publication_year":2019,"publication_date":"2019-12-13","ids":{"openalex":"https://openalex.org/W2995326310","doi":"https://doi.org/10.1093/bioinformatics/btz936","mag":"2995326310","pmid":"https://pubmed.ncbi.nlm.nih.gov/31845960"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz936","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz936","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2474/33116663/btz936.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/36/8/2474/33116663/btz936.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066984337","display_name":"Zhanying Feng","orcid":"https://orcid.org/0000-0002-5727-3929"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhanying Feng","raw_affiliation_strings":["CEMS, NCMIS, MDIS, Academy of Mathematics and System Science, Chinese Academy of Sciences , Beijing 100190, China","School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"],"affiliations":[{"raw_affiliation_string":"CEMS, NCMIS, MDIS, Academy of Mathematics and System Science, Chinese Academy of Sciences , Beijing 100190, China","institution_ids":["https://openalex.org/I4210120485","https://openalex.org/I4210095018","https://openalex.org/I19820366"]},{"raw_affiliation_string":"School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057252937","display_name":"Xianwen Ren","orcid":"https://orcid.org/0000-0002-8558-5401"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xianwen Ren","raw_affiliation_strings":["School of Life Sciences , Peking University, Beijing 100871, China"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences , Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022121149","display_name":"Yuan Fang","orcid":"https://orcid.org/0000-0003-0483-2237"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuan Fang","raw_affiliation_strings":["School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011214780","display_name":"Yining Yin","orcid":"https://orcid.org/0000-0001-9156-321X"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yining Yin","raw_affiliation_strings":["School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108700028","display_name":"Chongqing Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chutian Huang","raw_affiliation_strings":["School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000557849","display_name":"Zhao Yimin","orcid":null},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yimin Zhao","raw_affiliation_strings":["School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan University , Wuhan 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5115599758","display_name":"Yong Wang","orcid":"https://orcid.org/0000-0003-0695-5273"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yong Wang","raw_affiliation_strings":["CEMS, NCMIS, MDIS, Academy of Mathematics and System Science, Chinese Academy of Sciences , Beijing 100190, China","Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223, China","School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049, China"],"affiliations":[{"raw_affiliation_string":"CEMS, NCMIS, MDIS, Academy of Mathematics and System Science, Chinese Academy of Sciences , Beijing 100190, China","institution_ids":["https://openalex.org/I4210120485","https://openalex.org/I4210095018","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223, China","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5115599758"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485","https://openalex.org/I4210165038"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8524,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.73301655,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"8","first_page":"2474","last_page":"2485"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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/T10773","display_name":"Extracellular vesicles in disease","score":0.9905999898910522,"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/T11313","display_name":"Immune cells in cancer","score":0.9889000058174133,"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/rna-seq","display_name":"RNA-Seq","score":0.5859495997428894},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.470276415348053},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43302056193351746},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.43166911602020264},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42172741889953613},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3051806092262268},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2197664976119995},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14049476385116577},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1365983784198761},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.1357266902923584}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5859495997428894},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.470276415348053},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43302056193351746},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.43166911602020264},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42172741889953613},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3051806092262268},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2197664976119995},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14049476385116577},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1365983784198761},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.1357266902923584}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz936","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz936","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2474/33116663/btz936.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31845960","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31845960","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz936","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz936","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/8/2474/33116663/btz936.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/1","display_name":"No poverty","score":0.6000000238418579}],"awards":[{"id":"https://openalex.org/G1037933201","display_name":null,"funder_award_id":"61671444","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1723593689","display_name":null,"funder_award_id":"11871463","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3523307272","display_name":null,"funder_award_id":"61621003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8126262038","display_name":null,"funder_award_id":"91730301","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8325739885","display_name":null,"funder_award_id":"11661141019","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2995326310.pdf","grobid_xml":"https://content.openalex.org/works/W2995326310.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W839653734","https://openalex.org/W1943713353","https://openalex.org/W2023887100","https://openalex.org/W2025828346","https://openalex.org/W2040912608","https://openalex.org/W2068881679","https://openalex.org/W2081870862","https://openalex.org/W2102212449","https://openalex.org/W2116403037","https://openalex.org/W2121639473","https://openalex.org/W2140258573","https://openalex.org/W2146512944","https://openalex.org/W2187089797","https://openalex.org/W2191641478","https://openalex.org/W2302476265","https://openalex.org/W2306630387","https://openalex.org/W2416402039","https://openalex.org/W2511262512","https://openalex.org/W2788348358","https://openalex.org/W2798887274","https://openalex.org/W2799273685","https://openalex.org/W2804460316","https://openalex.org/W2807881681","https://openalex.org/W2902059429","https://openalex.org/W2906625258","https://openalex.org/W2912993019","https://openalex.org/W2952016241","https://openalex.org/W2952303649","https://openalex.org/W2952943331","https://openalex.org/W6752347511","https://openalex.org/W6764857659"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933","https://openalex.org/W1971332228"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
