{"id":"https://openalex.org/W4353017199","doi":"https://doi.org/10.1093/bib/bbad103","title":"Poincar\u00e9 maps for visualization of large protein families","display_name":"Poincar\u00e9 maps for visualization of large protein families","publication_year":2023,"publication_date":"2023-03-22","ids":{"openalex":"https://openalex.org/W4353017199","doi":"https://doi.org/10.1093/bib/bbad103","pmid":"https://pubmed.ncbi.nlm.nih.gov/36946414"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad103","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad103","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081472810","display_name":"Anna Klimovskaia Susmelj","orcid":"https://orcid.org/0000-0002-1057-6690"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210122261","display_name":"Swiss Data Science Center","ror":"https://ror.org/02hdt9m26","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I2799323385","https://openalex.org/I35440088","https://openalex.org/I4210122261","https://openalex.org/I5124864"]},{"id":"https://openalex.org/I4210131658","display_name":"Biognosys (Switzerland)","ror":"https://ror.org/03dr7j353","country_code":"CH","type":"company","lineage":["https://openalex.org/I4210131658"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Anna Klimovskaia Susmelj","raw_affiliation_strings":["Biognosys AG , Wagistrasse 21, 8952 Schlieren , Switzerland","Swiss Data Science Center, ETH Zurich and EPFL , Zurich , Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-1057-6690","affiliations":[{"raw_affiliation_string":"Biognosys AG , Wagistrasse 21, 8952 Schlieren , Switzerland","institution_ids":["https://openalex.org/I4210131658"]},{"raw_affiliation_string":"Swiss Data Science Center, ETH Zurich and EPFL , Zurich , Switzerland","institution_ids":["https://openalex.org/I4210122261","https://openalex.org/I35440088","https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091765296","display_name":"Yani Ren","orcid":"https://orcid.org/0009-0009-3426-2897"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Yani Ren","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union, INSERM, BIGR , F-75014 Paris , France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union, INSERM, BIGR , F-75014 Paris , France","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066727566","display_name":"Yann Vander Meersche","orcid":"https://orcid.org/0000-0002-6680-8104"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Yann Vander Meersche","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union, INSERM, BIGR , F-75014 Paris , France"],"raw_orcid":"https://orcid.org/0000-0002-6680-8104","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union, INSERM, BIGR , F-75014 Paris , France","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I154526488"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060243916","display_name":"Jean\u2010Christophe Gelly","orcid":"https://orcid.org/0000-0001-5138-361X"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Jean-Christophe Gelly","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union, INSERM, BIGR , F-75014 Paris , France"],"raw_orcid":"https://orcid.org/0000-0001-5138-361X","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union, INSERM, BIGR , F-75014 Paris , France","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I154526488"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081577635","display_name":"Tatiana Galochkina","orcid":"https://orcid.org/0000-0002-3608-5208"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Tatiana Galochkina","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union, INSERM, BIGR , F-75014 Paris , France"],"raw_orcid":"https://orcid.org/0000-0002-3608-5208","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union, INSERM, BIGR , F-75014 Paris , France","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I154526488"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5060243916","https://openalex.org/A5081577635"],"corresponding_institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.8722,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.73793772,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"24","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9819999933242798,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.970300018787384,"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/visualization","display_name":"Visualization","score":0.8767253160476685},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8589762449264526},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.663649320602417},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6166259050369263},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5775268077850342},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4561852514743805},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4375312924385071},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3588404655456543},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34278637170791626},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2543814182281494},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24940010905265808},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23607772588729858}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.8767253160476685},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8589762449264526},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.663649320602417},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6166259050369263},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5775268077850342},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4561852514743805},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4375312924385071},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3588404655456543},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34278637170791626},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2543814182281494},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24940010905265808},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23607772588729858},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad103","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad103","pdf_url":null,"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:36946414","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36946414","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":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1608086581","display_name":null,"funder_award_id":"ANR-18-IDEX-0001","funder_id":"https://openalex.org/F4320319990","funder_display_name":"National Institute for Health and Care Research"},{"id":"https://openalex.org/G4032633170","display_name":null,"funder_award_id":"ANR-21-CE45-0019","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1483679902","https://openalex.org/W1798483425","https://openalex.org/W1970999032","https://openalex.org/W1974050623","https://openalex.org/W2030205108","https://openalex.org/W2051210555","https://openalex.org/W2100659202","https://openalex.org/W2104343831","https://openalex.org/W2112727175","https://openalex.org/W2122940069","https://openalex.org/W2128668364","https://openalex.org/W2156628505","https://openalex.org/W2187089797","https://openalex.org/W2889326414","https://openalex.org/W2950954328","https://openalex.org/W2951149542","https://openalex.org/W2972411752","https://openalex.org/W2995361046","https://openalex.org/W2997958114","https://openalex.org/W3035622618","https://openalex.org/W3049229588","https://openalex.org/W3136918052","https://openalex.org/W3137047737","https://openalex.org/W3142481250","https://openalex.org/W4213112325","https://openalex.org/W4223644783","https://openalex.org/W4234797890"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2341492732","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W4287027380","https://openalex.org/W1699080303"],"abstract_inverted_index":{"In":[0],"the":[1,8],"era":[2],"of":[3,7,36,54,73,84],"constantly":[4],"increasing":[5],"amounts":[6],"available":[9,96],"protein":[10,58,74],"data,":[11],"a":[12,47],"relevant":[13],"and":[14,69,81],"interpretable":[15],"visualization":[16,35,72],"becomes":[17],"crucial,":[18],"especially":[19],"for":[20,34,51,71],"tasks":[21],"requiring":[22],"human":[23],"expertise.":[24],"Poincar\u00e9":[25,62],"disk":[26],"projection":[27],"has":[28],"previously":[29],"demonstrated":[30],"its":[31,67],"important":[32],"efficiency":[33,68],"biological":[37],"data":[38],"such":[39],"as":[40,77,79,101],"single-cell":[41],"RNAseq":[42],"data.":[43],"Here,":[44],"we":[45],"develop":[46],"new":[48],"method":[49],"Poincar\u00e9MSA":[50,87],"visual":[52],"representation":[53],"complex":[55],"relationships":[56],"between":[57],"sequences":[59],"based":[60],"on":[61],"maps":[63],"embedding.":[64],"We":[65],"demonstrate":[66],"potential":[70],"family":[75],"topology":[76],"well":[78],"evolutionary":[80],"functional":[82],"annotation":[83],"uncharacterized":[85],"sequences.":[86],"is":[88],"implemented":[89],"in":[90],"open":[91],"source":[92],"Python":[93],"code":[94],"with":[95],"interactive":[97],"Google":[98],"Colab":[99],"notebooks":[100],"described":[102],"at":[103],"https://www.dsimb.inserm.fr/POINCARE_MSA.":[104]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
