{"id":"https://openalex.org/W4282946267","doi":"https://doi.org/10.1093/nar/gkac396","title":"3DGenBench: a web-server to benchmark computational models for 3D Genomics","display_name":"3DGenBench: a web-server to benchmark computational models for 3D Genomics","publication_year":2022,"publication_date":"2022-05-25","ids":{"openalex":"https://openalex.org/W4282946267","doi":"https://doi.org/10.1093/nar/gkac396","pmid":"https://pubmed.ncbi.nlm.nih.gov/35639501"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkac396","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac396","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gkac396","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041310299","display_name":"Polina Belokopytova","orcid":"https://orcid.org/0000-0003-1390-7341"},"institutions":[{"id":"https://openalex.org/I188973947","display_name":"Novosibirsk State University","ror":"https://ror.org/04t2ss102","country_code":"RU","type":"education","lineage":["https://openalex.org/I188973947"]},{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210118499","display_name":"Tomsk National Research Medical Center","ror":"https://ror.org/01z0w8p93","country_code":"RU","type":"healthcare","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210118499"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Polina Belokopytova","raw_affiliation_strings":["Institute of Cytology and Genetics (Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences RUSSIAN FEDERATION 630090 Novosibirsk Prospekt Lavrentyeva 10 For telegrams: Novosibirsk 90 TSITOLOGIYA - Russia)","Tomsk National Research Medical Center (Tomsk - Russia)","NSU - Novosibirsk State University (Pirogova str. 2, 630090 Novosibirsk - Russia)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Cytology and Genetics (Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences RUSSIAN FEDERATION 630090 Novosibirsk Prospekt Lavrentyeva 10 For telegrams: Novosibirsk 90 TSITOLOGIYA - Russia)","institution_ids":["https://openalex.org/I4210116466"]},{"raw_affiliation_string":"Tomsk National Research Medical Center (Tomsk - Russia)","institution_ids":["https://openalex.org/I4210118499"]},{"raw_affiliation_string":"NSU - Novosibirsk State University (Pirogova str. 2, 630090 Novosibirsk - Russia)","institution_ids":["https://openalex.org/I188973947"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110955091","display_name":"Emil Viesn\u00e1","orcid":null},"institutions":[{"id":"https://openalex.org/I188973947","display_name":"Novosibirsk State University","ror":"https://ror.org/04t2ss102","country_code":"RU","type":"education","lineage":["https://openalex.org/I188973947"]},{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Emil Viesn\u00e1","raw_affiliation_strings":["NSU - Novosibirsk State University (Pirogova str. 2, 630090 Novosibirsk - Russia)","Institute of Cytology and Genetics (Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences RUSSIAN FEDERATION 630090 Novosibirsk Prospekt Lavrentyeva 10 For telegrams: Novosibirsk 90 TSITOLOGIYA - Russia)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NSU - Novosibirsk State University (Pirogova str. 2, 630090 Novosibirsk - Russia)","institution_ids":["https://openalex.org/I188973947"]},{"raw_affiliation_string":"Institute of Cytology and Genetics (Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences RUSSIAN FEDERATION 630090 Novosibirsk Prospekt Lavrentyeva 10 For telegrams: Novosibirsk 90 TSITOLOGIYA - Russia)","institution_ids":["https://openalex.org/I4210116466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021716093","display_name":"Mateusz Chili\u0144ski","orcid":"https://orcid.org/0000-0001-6641-8504"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Mateusz Chili\u0144ski","raw_affiliation_strings":["UW - University of Warsaw (Krakowskie Przedmie\u015bcie 26/28 00-927 Warsaw - Poland)","Warsaw University of Technology [Warsaw] (Pl. Politechniki 1 00-661 Warsaw - Poland)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UW - University of Warsaw (Krakowskie Przedmie\u015bcie 26/28 00-927 Warsaw - Poland)","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Warsaw University of Technology [Warsaw] (Pl. Politechniki 1 00-661 Warsaw - Poland)","institution_ids":["https://openalex.org/I108403487"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065001210","display_name":"Yifeng Qi","orcid":"https://orcid.org/0000-0002-1511-5818"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yifeng Qi","raw_affiliation_strings":["MIT - Massachusetts Institute of Technology (77 Massachusetts Ave, Cambridge, MA 02139 - United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MIT - Massachusetts Institute of Technology (77 Massachusetts Ave, Cambridge, MA 02139 - United States)","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025374487","display_name":"Hossein Salari","orcid":null},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Hossein Salari","raw_affiliation_strings":["LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I113428412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090755680","display_name":"Marco Di Stefano","orcid":"https://orcid.org/0000-0001-6195-4754"},"institutions":[{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Marco Di Stefano","raw_affiliation_strings":["UM - Universit\u00e9 de Montpellier (163 rue Auguste Broussonnet - 34090 Montpellier - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UM - Universit\u00e9 de Montpellier (163 rue Auguste Broussonnet - 34090 Montpellier - France)","institution_ids":["https://openalex.org/I19894307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090553213","display_name":"Andrea Esposito","orcid":"https://orcid.org/0000-0002-5903-8439"},"institutions":[{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Esposito","raw_affiliation_strings":["University of Naples Federico II = Universit\u00e0 degli studi di Napoli Federico II (Via Cintia Monte S. Angelo, 80126 Napoli, Italy - Italy)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Naples Federico II = Universit\u00e0 degli studi di Napoli Federico II (Via Cintia Monte S. Angelo, 80126 Napoli, Italy - Italy)","institution_ids":["https://openalex.org/I71267560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047594490","display_name":"Mattia Conte","orcid":"https://orcid.org/0000-0002-6670-9800"},"institutions":[{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mattia Conte","raw_affiliation_strings":["University of Naples Federico II = Universit\u00e0 degli studi di Napoli Federico II (Via Cintia Monte S. Angelo, 80126 Napoli, Italy - Italy)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Naples Federico II = Universit\u00e0 degli studi di Napoli Federico II (Via Cintia Monte S. Angelo, 80126 Napoli, Italy - Italy)","institution_ids":["https://openalex.org/I71267560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058085500","display_name":"Andrea M. Chiariello","orcid":"https://orcid.org/0000-0002-6112-0167"},"institutions":[{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea M Chiariello","raw_affiliation_strings":["University of Naples Federico II = Universit\u00e0 degli studi di Napoli Federico II (Via Cintia Monte S. Angelo, 80126 Napoli, Italy - Italy)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Naples Federico II = Universit\u00e0 degli studi di Napoli Federico II (Via Cintia Monte S. Angelo, 80126 Napoli, Italy - Italy)","institution_ids":["https://openalex.org/I71267560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048504577","display_name":"Vladimir B. Teif","orcid":"https://orcid.org/0000-0002-5931-7534"},"institutions":[{"id":"https://openalex.org/I110002522","display_name":"University of Essex","ror":"https://ror.org/02nkf1q06","country_code":"GB","type":"education","lineage":["https://openalex.org/I110002522"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Vladimir B Teif","raw_affiliation_strings":["University of Essex (Wivenhoe Park Colchester CO4 3SQ - United Kingdom)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Essex (Wivenhoe Park Colchester CO4 3SQ - United Kingdom)","institution_ids":["https://openalex.org/I110002522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021916927","display_name":"Dariusz Plewczy\u0144ski","orcid":"https://orcid.org/0000-0002-3840-7610"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Dariusz Plewczynski","raw_affiliation_strings":["Warsaw University of Technology [Warsaw] (Pl. Politechniki 1 00-661 Warsaw - Poland)","UW - University of Warsaw (Krakowskie Przedmie\u015bcie 26/28 00-927 Warsaw - Poland)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Warsaw University of Technology [Warsaw] (Pl. Politechniki 1 00-661 Warsaw - Poland)","institution_ids":["https://openalex.org/I108403487"]},{"raw_affiliation_string":"UW - University of Warsaw (Krakowskie Przedmie\u015bcie 26/28 00-927 Warsaw - Poland)","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023560103","display_name":"Bin Zhang","orcid":"https://orcid.org/0000-0002-3685-7503"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bin Zhang","raw_affiliation_strings":["MIT - Massachusetts Institute of Technology (77 Massachusetts Ave, Cambridge, MA 02139 - United States)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MIT - Massachusetts Institute of Technology (77 Massachusetts Ave, Cambridge, MA 02139 - United States)","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090174880","display_name":"Daniel Jost","orcid":"https://orcid.org/0000-0002-9877-6864"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I113428412","display_name":"\u00c9cole Normale Sup\u00e9rieure de Lyon","ror":"https://ror.org/04zmssz18","country_code":"FR","type":"education","lineage":["https://openalex.org/I113428412","https://openalex.org/I203339264"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Daniel Jost","raw_affiliation_strings":["LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LBMC UMR 5239 - Laboratoire de biologie et mod\u00e9lisation de la cellule (Ecole Normale Sup\u00e9rieure\r\n46 All\u00e9e d'Italie\r\n69364 Lyon Cedex 07 - France)","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I113428412"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031476631","display_name":"Veniamin Fishman","orcid":"https://orcid.org/0000-0002-5573-3100"},"institutions":[{"id":"https://openalex.org/I188973947","display_name":"Novosibirsk State University","ror":"https://ror.org/04t2ss102","country_code":"RU","type":"education","lineage":["https://openalex.org/I188973947"]},{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]},{"id":"https://openalex.org/I4210118499","display_name":"Tomsk National Research Medical Center","ror":"https://ror.org/01z0w8p93","country_code":"RU","type":"healthcare","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210118499"]},{"id":"https://openalex.org/I4392021246","display_name":"AIRI - Artificial Intelligence Research Institute","ror":"https://ror.org/014a87f14","country_code":"RU","type":"nonprofit","lineage":["https://openalex.org/I4392021246"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Veniamin Fishman","raw_affiliation_strings":["Tomsk National Research Medical Center (Tomsk - Russia)","Institute of Cytology and Genetics (Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences RUSSIAN FEDERATION 630090 Novosibirsk Prospekt Lavrentyeva 10 For telegrams: Novosibirsk 90 TSITOLOGIYA - Russia)","NSU - Novosibirsk State University (Pirogova str. 2, 630090 Novosibirsk - Russia)","AIRI - Artificial Intelligence  Research Institute (Russia)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tomsk National Research Medical Center (Tomsk - Russia)","institution_ids":["https://openalex.org/I4210118499"]},{"raw_affiliation_string":"Institute of Cytology and Genetics (Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences RUSSIAN FEDERATION 630090 Novosibirsk Prospekt Lavrentyeva 10 For telegrams: Novosibirsk 90 TSITOLOGIYA - Russia)","institution_ids":["https://openalex.org/I4210116466"]},{"raw_affiliation_string":"NSU - Novosibirsk State University (Pirogova str. 2, 630090 Novosibirsk - Russia)","institution_ids":["https://openalex.org/I188973947"]},{"raw_affiliation_string":"AIRI - Artificial Intelligence  Research Institute (Russia)","institution_ids":["https://openalex.org/I4392021246"]}]}],"institutions":[],"countries_distinct_count":6,"institutions_distinct_count":12,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3264,"currency":"EUR","value_usd":3520},"fwci":1.4102,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.80914238,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"50","issue":"W1","first_page":"W4","last_page":"W12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9983000159263611,"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/T11482","display_name":"RNA modifications and cancer","score":0.9976000189781189,"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/benchmarking","display_name":"Benchmarking","score":0.9006678462028503},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.8448489308357239},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6834337115287781},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5862103700637817},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5624288320541382},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5489535331726074},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.548603355884552},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48859864473342896},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.48663219809532166},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.45183974504470825},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4281757175922394},{"id":"https://openalex.org/keywords/functional-genomics","display_name":"Functional genomics","score":0.4181327521800995},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.411138117313385},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.4106062650680542},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.25602155923843384},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15833187103271484},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15768542885780334},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.1570436954498291}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.9006678462028503},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.8448489308357239},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6834337115287781},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5862103700637817},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5624288320541382},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5489535331726074},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.548603355884552},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48859864473342896},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.48663219809532166},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.45183974504470825},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4281757175922394},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.4181327521800995},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.411138117313385},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.4106062650680542},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.25602155923843384},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15833187103271484},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15768542885780334},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.1570436954498291},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkac396","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac396","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:35639501","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35639501","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:repository.essex.ac.uk:37524","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401236","display_name":"Open Access at Essex (University of Essex)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I110002522","host_organization_name":"University of Essex","host_organization_lineage":["https://openalex.org/I110002522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9252746","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9252746","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9252746/pdf/gkac396.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:HAL:hal-04190582v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04190582","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 2022, 50 (W1), pp.W4-W12. &#x27E8;10.1093/nar/gkac396&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkac396","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac396","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5099999904632568,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G1263946287","display_name":null,"funder_award_id":"FSUS-2020-0040","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"},{"id":"https://openalex.org/G1793489493","display_name":null,"funder_award_id":"21-65-00017","funder_id":"https://openalex.org/F4320306201","funder_display_name":"Russell Sage Foundation"},{"id":"https://openalex.org/G1815115329","display_name":null,"funder_award_id":"2019/35/O/ST6/02484","funder_id":"https://openalex.org/F4320322650","funder_display_name":"Narodowym Centrum Nauki"},{"id":"https://openalex.org/G1897187657","display_name":null,"funder_award_id":"121031800061-7","funder_id":"https://openalex.org/F8308531777","funder_display_name":"Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences"},{"id":"https://openalex.org/G246426947","display_name":null,"funder_award_id":"ANR-18-CE45-0022-01","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G3131612253","display_name":null,"funder_award_id":"21-65-00017","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"},{"id":"https://openalex.org/G3488688524","display_name":null,"funder_award_id":"R35 GM133580","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6876561401","display_name":null,"funder_award_id":"ANR-18","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7091979907","display_name":"Quantitative modeling of the 3D dynamical organization of chromosomes","funder_award_id":"ANR-18-CE45-0022","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7721710951","display_name":null,"funder_award_id":"R35GM133580","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G885068622","display_name":null,"funder_award_id":"CA18127","funder_id":"https://openalex.org/F4320320366","funder_display_name":"European Cooperation in Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320306201","display_name":"Russell Sage Foundation","ror":"https://ror.org/02yh9se80"},{"id":"https://openalex.org/F4320320366","display_name":"European Cooperation in Science and Technology","ror":"https://ror.org/01bstzn19"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320322650","display_name":"Narodowym Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F8308531777","display_name":"Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1973062929","https://openalex.org/W2074915491","https://openalex.org/W2195190137","https://openalex.org/W2481029670","https://openalex.org/W2528263447","https://openalex.org/W2558061074","https://openalex.org/W2584394140","https://openalex.org/W2736857446","https://openalex.org/W2756584474","https://openalex.org/W2765567136","https://openalex.org/W2792493536","https://openalex.org/W2797313452","https://openalex.org/W2797715364","https://openalex.org/W2888425844","https://openalex.org/W2890753820","https://openalex.org/W2898514070","https://openalex.org/W2914685295","https://openalex.org/W2945135442","https://openalex.org/W2948487481","https://openalex.org/W2950463539","https://openalex.org/W2952699651","https://openalex.org/W2952940726","https://openalex.org/W2953105755","https://openalex.org/W2953543256","https://openalex.org/W2993022331","https://openalex.org/W3005268570","https://openalex.org/W3027193015","https://openalex.org/W3038841557","https://openalex.org/W3089167850","https://openalex.org/W3107536938","https://openalex.org/W3124946892","https://openalex.org/W3125103290","https://openalex.org/W4220950749"],"related_works":["https://openalex.org/W189065216","https://openalex.org/W2116734196","https://openalex.org/W2353729507","https://openalex.org/W2092829297","https://openalex.org/W2119426880","https://openalex.org/W2129833142","https://openalex.org/W2364340602","https://openalex.org/W1485242531","https://openalex.org/W4385370162","https://openalex.org/W179557453"],"abstract_inverted_index":{"Modeling":[0],"3D":[1,53,139],"genome":[2],"organisation":[3],"has":[4],"been":[5],"booming":[6],"in":[7,69,81,157],"the":[8,13,22,27,115,158],"last":[9],"years":[10],"thanks":[11],"to":[12,33,107,130,136],"availability":[14],"of":[15,18,29,52,64,91,103,152],"experimental":[16,108],"datasets":[17],"genomic":[19],"contacts.":[20],"However,":[21],"field":[23],"is":[24,57,143],"currently":[25],"missing":[26],"standardisation":[28],"methods":[30],"and":[31,36,72,76,84,142],"metrics":[32],"compare":[34],"predictions":[35,102],"experiments.":[37],"We":[38],"present":[39],"3DGenBench,":[40,114],"a":[41,60,96,104,132],"web":[42,134],"server":[43,135],"available":[44],"at":[45],"https://inc-cost.eu/benchmarking/,":[46],"that":[47,100],"allows":[48],"benchmarking":[49],"computational":[50,105],"models":[51,141],"Genomics.":[54],"The":[55],"benchmark":[56],"performed":[58],"using":[59,110],"manually":[61],"curated":[62],"dataset":[63],"39":[65],"capture":[66],"Hi-C":[67,79],"profiles":[68,80],"wild":[70],"type":[71],"genome-edited":[73],"mouse":[74],"cells,":[75],"five":[77],"genome-wide":[78],"human,":[82],"mouse,":[83],"Drosophila":[85],"cells.":[86],"3DGenBench":[87,128],"performs":[88],"two":[89],"kinds":[90],"analysis,":[92],"each":[93],"supplied":[94],"with":[95,125],"specific":[97],"scoring":[98],"module":[99],"compares":[101],"method":[106],"data":[109],"several":[111],"metrics.":[112],"With":[113],"user":[116],"obtains":[117],"model":[118],"performance":[119],"scores,":[120],"allowing":[121],"an":[122,146],"unbiased":[123],"comparison":[124],"other":[126],"models.":[127],"aims":[129],"become":[131],"reference":[133],"test":[137],"new":[138,150],"genomics":[140],"conceived":[144],"as":[145],"evolving":[147],"platform":[148],"where":[149],"types":[151],"analysis":[153],"will":[154],"be":[155],"implemented":[156],"future.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2022-06-16T00:00:00"}
