{"id":"https://openalex.org/W4220850758","doi":"https://doi.org/10.1093/bioinformatics/btac171","title":"BSDE: barycenter single-cell differential expression for case\u2013control studies","display_name":"BSDE: barycenter single-cell differential expression for case\u2013control studies","publication_year":2022,"publication_date":"2022-03-23","ids":{"openalex":"https://openalex.org/W4220850758","doi":"https://doi.org/10.1093/bioinformatics/btac171"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac171","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac171","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2765/43704896/btac171.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":"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","datacite","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2765/43704896/btac171.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016695484","display_name":"Mengqi Zhang","orcid":"https://orcid.org/0000-0002-1091-1014"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mengqi Zhang","raw_affiliation_strings":["Department of Surgery, Perelman Medical School, University of Pennsylvania , Philadelphia, PA 19104, USA"],"affiliations":[{"raw_affiliation_string":"Department of Surgery, Perelman Medical School, University of Pennsylvania , Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082423400","display_name":"F Richard Guo","orcid":"https://orcid.org/0000-0002-2081-7398"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"F Richard Guo","raw_affiliation_strings":["Statistical Laboratory, University of Cambridge , Cambridge CB3 0WB, UK"],"affiliations":[{"raw_affiliation_string":"Statistical Laboratory, University of Cambridge , Cambridge CB3 0WB, UK","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5016695484"],"corresponding_institution_ids":["https://openalex.org/I79576946"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9547,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.72485704,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"38","issue":"10","first_page":"2765","last_page":"2772"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994000196456909,"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":0.9994000196456909,"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/T12528","display_name":"IL-33, ST2, and ILC Pathways","score":0.9628000259399414,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9577999711036682,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6824323534965515},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.523087739944458},{"id":"https://openalex.org/keywords/nonparametric-statistics","display_name":"Nonparametric statistics","score":0.4847104549407959},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.48146429657936096},{"id":"https://openalex.org/keywords/parametric-statistics","display_name":"Parametric statistics","score":0.46655505895614624},{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.46426156163215637},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41650205850601196},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35159581899642944},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.2615135908126831},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1985766887664795},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19014444947242737},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11418122053146362},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.10144773125648499}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6824323534965515},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.523087739944458},{"id":"https://openalex.org/C102366305","wikidata":"https://www.wikidata.org/wiki/Q1097688","display_name":"Nonparametric statistics","level":2,"score":0.4847104549407959},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.48146429657936096},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.46655505895614624},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.46426156163215637},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41650205850601196},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35159581899642944},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.2615135908126831},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1985766887664795},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19014444947242737},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11418122053146362},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.10144773125648499},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btac171","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac171","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2765/43704896/btac171.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":"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":"pmh:oai:www.repository.cam.ac.uk:1810/338053","is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/338053","pdf_url":"https://www.repository.cam.ac.uk/bitstreams/f2c895d8-f322-47e7-8a61-167279b9d02c/download","source":{"id":"https://openalex.org/S4306401776","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"essn: 1367-4811","raw_type":"Article"},{"id":"pmh:doi:10.17863/cam.85462","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9113363","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9113363","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/335319","is_oa":false,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/335319","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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":"Article"},{"id":"doi:10.17863/cam.82751","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.82751","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.17863/cam.85462","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.85462","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac171","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac171","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2765/43704896/btac171.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":"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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4220850758.pdf","grobid_xml":"https://content.openalex.org/works/W4220850758.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1837170756","https://openalex.org/W1896921323","https://openalex.org/W1967327758","https://openalex.org/W1968333723","https://openalex.org/W1984883254","https://openalex.org/W1985846684","https://openalex.org/W2002433576","https://openalex.org/W2031123734","https://openalex.org/W2036996178","https://openalex.org/W2040085463","https://openalex.org/W2059218087","https://openalex.org/W2078482008","https://openalex.org/W2111725927","https://openalex.org/W2114104545","https://openalex.org/W2162978315","https://openalex.org/W2179438025","https://openalex.org/W2190545194","https://openalex.org/W2193667971","https://openalex.org/W2264062397","https://openalex.org/W2292417525","https://openalex.org/W2599075603","https://openalex.org/W2604272474","https://openalex.org/W2607325898","https://openalex.org/W2747877289","https://openalex.org/W2772962389","https://openalex.org/W2783406084","https://openalex.org/W2793453767","https://openalex.org/W2799273685","https://openalex.org/W2799922543","https://openalex.org/W2911279170","https://openalex.org/W2946016273","https://openalex.org/W2949275240","https://openalex.org/W2950541340","https://openalex.org/W2950583356","https://openalex.org/W2951560273","https://openalex.org/W2981477552","https://openalex.org/W2988699331","https://openalex.org/W3013888740","https://openalex.org/W3040876684","https://openalex.org/W3043849620","https://openalex.org/W3087159033","https://openalex.org/W3108941787","https://openalex.org/W3162888433","https://openalex.org/W4207056242","https://openalex.org/W4233762729","https://openalex.org/W4287245321","https://openalex.org/W6795007937"],"related_works":["https://openalex.org/W2096947471","https://openalex.org/W2011903341","https://openalex.org/W2013882407","https://openalex.org/W2992516105","https://openalex.org/W1981436518","https://openalex.org/W2897428363","https://openalex.org/W1485223389","https://openalex.org/W2401523190","https://openalex.org/W1979697693","https://openalex.org/W2529605301"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Single-cell":[2],"sequencing":[3,42,210],"brings":[4],"about":[5],"a":[6,86,129,140],"revolutionarily":[7],"high":[8],"resolution":[9],"for":[10,62,65,89,92,101],"finding":[11,90],"differentially":[12],"expressed":[13],"genes":[14],"(DEGs)":[15],"by":[16,116,152,169],"disentangling":[17],"highly":[18],"heterogeneous":[19],"cell":[20,34,147,217],"tissues.":[21],"Yet,":[22],"such":[23],"analysis":[24,189],"is":[25,181],"so":[26],"far":[27],"mostly":[28],"focused":[29],"on":[30,156],"comparing":[31],"between":[32,69],"different":[33],"types":[35],"from":[36,54,154,172,184,219],"the":[37,96,111,136,164,173,191],"same":[38],"individual.":[39],"As":[40],"single-cell":[41,82,209],"becomes":[43],"cheaper":[44],"and":[45,71,104,145,159,176,205,221],"easier":[46],"to":[47],"use,":[48],"an":[49],"increasing":[50],"number":[51],"of":[52,98,131],"datasets":[53,155,211],"case\u2013control":[55,93],"studies":[56],"are":[57,150,167,227],"becoming":[58],"available,":[59],"which":[60,163],"call":[61],"new":[63],"methods":[64],"identifying":[66],"differential":[67,83,132],"expressions":[68,133],"case":[70],"control":[72],"individuals.":[73],"Results":[74],"To":[75],"bridge":[76],"this":[77],"gap,":[78],"we":[79,122],"propose":[80],"barycenter":[81],"expression":[84],"(BSDE),":[85],"nonparametric":[87],"method":[88,109],"DEGs":[91,149],"studies.":[94],"Through":[95,120],"use":[97],"optimal":[99],"transportation":[100],"aggregating":[102],"distributions":[103],"computing":[105],"their":[106],"distances,":[107],"our":[108],"overcomes":[110],"restrictive":[112],"parametric":[113],"assumptions":[114],"imposed":[115],"standard":[117],"mixed-effect-modeling":[118],"approaches.":[119],"simulations,":[121],"show":[123],"that":[124],"BSDE":[125,153,180],"can":[126,197,212],"accurately":[127],"detect":[128],"variety":[130],"while":[134],"maintaining":[135],"type-I":[137],"error":[138],"at":[139,203,229],"prescribed":[141],"level.":[142],"Further,":[143],"1345":[144],"1568":[146],"type-specific":[148],"identified":[151],"pulmonary":[157],"fibrosis":[158],"multiple":[160],"sclerosis,":[161],"among":[162],"top":[165],"findings":[166],"supported":[168],"previous":[170],"results":[171],"literature.":[174],"Availability":[175],"implementation":[177],"R":[178,192],"package":[179],"freely":[182],"available":[183,228],"doi.org/10.5281/zenodo.6332254.":[185],"For":[186],"real":[187],"data":[188,226],"with":[190,215],"package,":[193],"see":[194],"doi.org/10.5281/zenodo.6332566.":[195],"These":[196],"also":[198],"be":[199,213],"accessed":[200],"thorough":[201],"GitHub":[202],"github.com/mqzhanglab/BSDE":[204],"github.com/mqzhanglab/BSDE_pipeline.":[206],"The":[207],"two":[208],"download":[214],"UCSC":[216],"browser":[218],"cells.ucsc.edu/?ds=ms":[220],"cells.ucsc.edu/?ds=lung-pf-control.":[222],"Supplementary":[223,225],"information":[224],"Bioinformatics":[230],"online.":[231]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2022-04-03T00:00:00"}
