{"id":"https://openalex.org/W2989628906","doi":"https://doi.org/10.1093/bioinformatics/btz877","title":"Cerebro: interactive visualization of scRNA-seq data","display_name":"Cerebro: interactive visualization of scRNA-seq data","publication_year":2019,"publication_date":"2019-11-22","ids":{"openalex":"https://openalex.org/W2989628906","doi":"https://doi.org/10.1093/bioinformatics/btz877","mag":"2989628906"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz877","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz877","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/7/2311/33027672/btz877.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/7/2311/33027672/btz877.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061353572","display_name":"Roman Hillje","orcid":"https://orcid.org/0000-0002-3528-9276"},"institutions":[{"id":"https://openalex.org/I6141010","display_name":"European Institute of Oncology","ror":"https://ror.org/02vr0ne26","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I6141010"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Roman Hillje","raw_affiliation_strings":["Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , 20139 Milan"],"affiliations":[{"raw_affiliation_string":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , 20139 Milan","institution_ids":["https://openalex.org/I6141010"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057101865","display_name":"Pier Giuseppe Pelicci","orcid":"https://orcid.org/0000-0002-5076-2316"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]},{"id":"https://openalex.org/I6141010","display_name":"European Institute of Oncology","ror":"https://ror.org/02vr0ne26","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I6141010"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Pier Giuseppe Pelicci","raw_affiliation_strings":["Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , 20139 Milan","Department of Oncology and Hemato-Oncology, Universit\u00e0 Degli Studi di Milano , Milan 20122, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , 20139 Milan","institution_ids":["https://openalex.org/I6141010"]},{"raw_affiliation_string":"Department of Oncology and Hemato-Oncology, Universit\u00e0 Degli Studi di Milano , Milan 20122, Italy","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023655228","display_name":"Lucilla Luzi","orcid":"https://orcid.org/0000-0002-8746-4179"},"institutions":[{"id":"https://openalex.org/I6141010","display_name":"European Institute of Oncology","ror":"https://ror.org/02vr0ne26","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I6141010"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Lucilla Luzi","raw_affiliation_strings":["Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , 20139 Milan"],"affiliations":[{"raw_affiliation_string":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , 20139 Milan","institution_ids":["https://openalex.org/I6141010"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5057101865","https://openalex.org/A5061353572"],"corresponding_institution_ids":["https://openalex.org/I189158943","https://openalex.org/I6141010"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.4094,"has_fulltext":false,"cited_by_count":101,"citation_normalized_percentile":{"value":0.93592273,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"36","issue":"7","first_page":"2311","last_page":"2313"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9843999743461609,"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":0.7932597398757935},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6480810046195984},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.6221654415130615},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5958005785942078},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.508394181728363},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4699447453022003},{"id":"https://openalex.org/keywords/interactive-visualization","display_name":"Interactive visualization","score":0.45962774753570557},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4562160074710846},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4179404377937317},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1286330223083496}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7932597398757935},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6480810046195984},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.6221654415130615},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5958005785942078},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.508394181728363},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4699447453022003},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.45962774753570557},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4562160074710846},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4179404377937317},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1286330223083496},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","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},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz877","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz877","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/7/2311/33027672/btz877.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:air.unimi.it:2434/930386","is_oa":true,"landing_page_url":"https://hdl.handle.net/2434/930386","pdf_url":null,"source":{"id":"https://openalex.org/S4306400516","display_name":"Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189158943","host_organization_name":"University of Milan","host_organization_lineage":["https://openalex.org/I189158943"],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7141853","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7141853","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz877","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz877","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/7/2311/33027672/btz877.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4000000059604645,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G6516794423","display_name":null,"funder_award_id":"341131","funder_id":"https://openalex.org/F4320338335","funder_display_name":"H2020 European Research Council"},{"id":"https://openalex.org/G8547984245","display_name":null,"funder_award_id":"IG-2017-20162","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"}],"funders":[{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2989628906.pdf","grobid_xml":"https://content.openalex.org/works/W2989628906.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W2010457001","https://openalex.org/W2070050178","https://openalex.org/W2130410032","https://openalex.org/W2159707944","https://openalex.org/W2236952019","https://openalex.org/W2345356016","https://openalex.org/W2747877289","https://openalex.org/W2753908609","https://openalex.org/W2759082725","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2807856729","https://openalex.org/W2924067995","https://openalex.org/W2952520709","https://openalex.org/W2970372573","https://openalex.org/W2971398276","https://openalex.org/W2973034691"],"related_works":["https://openalex.org/W2013728941","https://openalex.org/W4225274103","https://openalex.org/W2006240110","https://openalex.org/W2751110224","https://openalex.org/W2147036980","https://openalex.org/W1510524001","https://openalex.org/W1973315673","https://openalex.org/W2520625499","https://openalex.org/W2996372188","https://openalex.org/W2131473689"],"abstract_inverted_index":{"Abstract":[0],"Despite":[1],"the":[2,10,70,103,188,195,213,226],"growing":[3],"availability":[4],"of":[5,12,60,69,106,112,117,194],"sophisticated":[6],"bioinformatic":[7,24,67],"methods":[8],"for":[9,51,124,177],"analysis":[11,191],"single-cell":[13,62],"RNA-seq":[14],"data,":[15],"few":[16],"tools":[17],"exist":[18],"that":[19,182],"allow":[20],"biologists":[21,181],"without":[22,65],"extensive":[23],"expertise":[25],"to":[26,146,166,186],"directly":[27],"visualize":[28],"and":[29,35,46,53,58,75,84,88,121,127,129,153,163,168,179,192,198,205],"interact":[30],"with":[31,134],"their":[32],"own":[33],"data":[34,64,167,232],"results.":[36],"Here,":[37],"we":[38,170],"present":[39],"Cerebro":[40,149,172,201],"(cell":[41],"report":[42],"browser),":[43],"a":[44,159,174],"Shiny-":[45],"Electron-based":[47],"standalone":[48],"desktop":[49],"application":[50],"macOS":[52],"Windows":[54],"which":[55,154],"allows":[56],"investigation":[57],"inspection":[59],"pre-processed":[61],"transcriptomics":[63],"requiring":[66],"experience":[68],"user.":[71],"Through":[72,158],"an":[73],"interactive":[74],"intuitive":[76],"graphical":[77],"interface,":[78],"users":[79],"can":[80,150],"(i)":[81],"explore":[82],"similarities":[83],"heterogeneity":[85],"between":[86,190],"samples":[87],"cell":[89],"clusters":[90],"in":[91],"two-dimensional":[92],"or":[93,99,109],"three-dimensional":[94],"projections":[95],"such":[96],"as":[97],"t-SNE":[98],"UMAP,":[100],"(ii)":[101],"display":[102,131],"expression":[104],"level":[105],"single":[107],"genes":[108,120,123],"gene":[110],"sets":[111],"interest,":[113],"(iii)":[114],"browse":[115],"tables":[116],"most":[118],"expressed":[119],"marker":[122],"each":[125],"sample":[126],"cluster":[128],"(iv)":[130],"trajectories":[132],"calculated":[133],"Monocle":[135],"2.":[136],"We":[137],"provide":[138],"three":[139],"examples":[140],"prepared":[141],"from":[142],"publicly":[143],"available":[144,209,218,234],"datasets":[145,207],"show":[147],"how":[148],"be":[151],"used":[152],"are":[155,208,223,233],"its":[156],"capabilities.":[157],"focus":[160],"on":[161],"flexibility":[162],"direct":[164],"access":[165],"results,":[169],"think":[171],"offers":[173],"collaborative":[175],"framework":[176],"bioinformaticians":[178],"experimental":[180],"facilitates":[183],"effective":[184],"interaction":[185],"shorten":[187],"gap":[189],"interpretation":[193],"data.":[196],"Availability":[197],"implementation":[199],"The":[200],"application,":[202],"additional":[203],"documentation,":[204],"example":[206],"at":[210,219,235],"https://github.com/romanhaa/Cerebro.":[211],"Similarly,":[212],"cerebroApp":[214],"R":[215],"package":[216],"is":[217],"https://github.com/romanhaa/cerebroApp.":[220],"All":[221],"components":[222],"released":[224],"under":[225],"MIT":[227],"License.":[228],"Supplementary":[229,231],"information":[230],"Bioinformatics":[236],"online.":[237]},"counts_by_year":[{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":32},{"year":2023,"cited_by_count":19},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":11}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2019-12-05T00:00:00"}
