{"id":"https://openalex.org/W4200514377","doi":"https://doi.org/10.1093/bioinformatics/btab831","title":"scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data","display_name":"scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data","publication_year":2021,"publication_date":"2021-12-03","ids":{"openalex":"https://openalex.org/W4200514377","doi":"https://doi.org/10.1093/bioinformatics/btab831","pmid":"https://pubmed.ncbi.nlm.nih.gov/34888622"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab831","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab831","pdf_url":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btab831","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075215786","display_name":"Johannes Smolander","orcid":"https://orcid.org/0000-0003-3872-9668"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Johannes Smolander","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, 20520 Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, 20520 Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073153242","display_name":"Sini Junttila","orcid":"https://orcid.org/0000-0003-3754-5584"},"institutions":[{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Sini Junttila","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, 20520 Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, 20520 Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005848551","display_name":"Mikko S. Ven\u00e4l\u00e4inen","orcid":"https://orcid.org/0000-0003-1777-4259"},"institutions":[{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Mikko S Ven\u00e4l\u00e4inen","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, 20520 Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, 20520 Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062339398","display_name":"Laura L. Elo","orcid":"https://orcid.org/0000-0001-5648-4532"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Laura L Elo","raw_affiliation_strings":["Institute of Biomedicine, University of Turku , 20520 Turku, Finland","Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, 20520 Turku, Finland"],"affiliations":[{"raw_affiliation_string":"Institute of Biomedicine, University of Turku , 20520 Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, 20520 Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5075215786"],"corresponding_institution_ids":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8927,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.73559131,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"38","issue":"5","first_page":"1328","last_page":"1335"},"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/T10773","display_name":"Extracellular vesicles in disease","score":0.9923999905586243,"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":0.9688000082969666,"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":0.7614558935165405},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6503095626831055},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.6256788969039917},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6034499406814575},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.45236486196517944},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3480601906776428},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31848931312561035},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.14216765761375427},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1262369453907013},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.12350675463676453},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11063915491104126},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0931098461151123}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7614558935165405},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6503095626831055},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.6256788969039917},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6034499406814575},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.45236486196517944},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3480601906776428},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31848931312561035},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.14216765761375427},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1262369453907013},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12350675463676453},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11063915491104126},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0931098461151123},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab831","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab831","pdf_url":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34888622","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34888622","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},{"id":"pmh:oai:pubmedcentral.nih.gov:8825760","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8825760","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.utupub.fi:10024/167977","is_oa":false,"landing_page_url":"https://www.utupub.fi/handle/10024/167977","pdf_url":null,"source":{"id":"https://openalex.org/S4306402470","display_name":"UTUPub (University of Turku)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I155660961","host_organization_name":"University of Turku","host_organization_lineage":["https://openalex.org/I155660961"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab831","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab831","pdf_url":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1310452693","display_name":null,"funder_award_id":"296801","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G3060148298","display_name":null,"funder_award_id":"310561","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G4240401644","display_name":null,"funder_award_id":"335611","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G4428230132","display_name":"Tools to translate proteomes to human health and diagnostics","funder_award_id":"310561","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G5084329356","display_name":null,"funder_award_id":"314443","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G509809563","display_name":"Immunoregulation and Therapeutic Precision in Rheumatoid Arthritis","funder_award_id":"335434","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G788331715","display_name":null,"funder_award_id":"335434","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G900722120","display_name":null,"funder_award_id":"329278","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W2138754805","https://openalex.org/W2187089797","https://openalex.org/W2572662684","https://openalex.org/W2598326928","https://openalex.org/W2766437506","https://openalex.org/W2897346235","https://openalex.org/W2916020270","https://openalex.org/W2925075625","https://openalex.org/W2927507212","https://openalex.org/W2949067670","https://openalex.org/W2951084686","https://openalex.org/W2951799803","https://openalex.org/W3009684066","https://openalex.org/W3042928139","https://openalex.org/W3047141442","https://openalex.org/W3100742177","https://openalex.org/W3127539648","https://openalex.org/W3165360138","https://openalex.org/W3197405088","https://openalex.org/W3200372303","https://openalex.org/W4251002338","https://openalex.org/W6674723449","https://openalex.org/W6680294583","https://openalex.org/W6801237206"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W4323768008","https://openalex.org/W1941703695","https://openalex.org/W3131574667","https://openalex.org/W4394426846","https://openalex.org/W4360995134","https://openalex.org/W4248382324","https://openalex.org/W3023605104","https://openalex.org/W2039473718"],"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":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":4}],"updated_date":"2026-03-03T08:47:05.690250","created_date":"2025-10-10T00:00:00"}
