{"id":"https://openalex.org/W2914768668","doi":"https://doi.org/10.1109/bibm.2018.8621097","title":"Clustering and Comparison of Hierarchies in the Spatial Organization of Chromatin","display_name":"Clustering and Comparison of Hierarchies in the Spatial Organization of Chromatin","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2914768668","doi":"https://doi.org/10.1109/bibm.2018.8621097","mag":"2914768668"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621097","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621097","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5039781558","display_name":"Olga Pushkareva","orcid":null},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Olga Pushkareva","raw_affiliation_strings":["Department of Computer Science, National Research University Higher School of Economics, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National Research University Higher School of Economics, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063451139","display_name":"Alexander Kurashenko","orcid":null},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexander Kurashenko","raw_affiliation_strings":["Department of Molecular Biology, Moscow State University, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061648119","display_name":"Uliana Moskvina","orcid":null},"institutions":[{"id":"https://openalex.org/I125989756","display_name":"Skolkovo Institute of Science and Technology","ror":"https://ror.org/03f9nc143","country_code":"RU","type":"education","lineage":["https://openalex.org/I125989756"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Uliana Moskvina","raw_affiliation_strings":["Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia","institution_ids":["https://openalex.org/I125989756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042012232","display_name":"Anatoly R. Rubinov","orcid":null},"institutions":[{"id":"https://openalex.org/I4210107660","display_name":"Institute for Information Transmission Problems","ror":"https://ror.org/013w2d378","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210107660"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Anatoly R. Rubinov","raw_affiliation_strings":["Institute for Information Transmission Problems RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Information Transmission Problems RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210107660"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016957787","display_name":"Mikhail S. Gelfand","orcid":"https://orcid.org/0000-0003-4181-0846"},"institutions":[{"id":"https://openalex.org/I4210107660","display_name":"Institute for Information Transmission Problems","ror":"https://ror.org/013w2d378","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210107660"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Mikhail S. Gelfand","raw_affiliation_strings":["Institute for Information Transmission Problems RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Information Transmission Problems RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210107660"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"58","issue":null,"first_page":"2482","last_page":"2487"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9914000034332275,"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/chromatin","display_name":"Chromatin","score":0.7847431898117065},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.6548332571983337},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6475152969360352},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6463451385498047},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5910738110542297},{"id":"https://openalex.org/keywords/spatial-organization","display_name":"Spatial organization","score":0.5855344533920288},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.56635981798172},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5339291095733643},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44915950298309326},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42622247338294983},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26517242193222046},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.21700161695480347},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1904153823852539},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15542331337928772},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12037155032157898},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.11145108938217163}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7847431898117065},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.6548332571983337},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6475152969360352},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6463451385498047},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5910738110542297},{"id":"https://openalex.org/C175779824","wikidata":"https://www.wikidata.org/wiki/Q7574078","display_name":"Spatial organization","level":2,"score":0.5855344533920288},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.56635981798172},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5339291095733643},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44915950298309326},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42622247338294983},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26517242193222046},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.21700161695480347},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1904153823852539},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15542331337928772},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12037155032157898},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.11145108938217163},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2018.8621097","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621097","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2073026107","https://openalex.org/W2097798909","https://openalex.org/W2152605077","https://openalex.org/W2169389191","https://openalex.org/W2310342073","https://openalex.org/W2625231465"],"related_works":["https://openalex.org/W2152861454","https://openalex.org/W3004891660","https://openalex.org/W4286930115","https://openalex.org/W2969540308","https://openalex.org/W1842891956","https://openalex.org/W2299066600","https://openalex.org/W3200375535","https://openalex.org/W2911265521","https://openalex.org/W4308632684","https://openalex.org/W2374108210"],"abstract_inverted_index":{"Recent":[0],"development":[1],"of":[2,13,22,34,72,79,84],"high-throughput":[3],"3C-based":[4],"technologies":[5],"made":[6],"it":[7],"possible":[8],"to":[9,111,141],"study":[10,109],"spatial":[11],"organization":[12],"chromatin":[14,23],"in":[15],"the":[16,47,67,70,82,85,98,105,143],"nucleus":[17],"and":[18,55,75,88,115,126,139],"revealed":[19],"new":[20],"units":[21],"organization-":[24],"Topologically":[25],"Associating":[26],"Domains":[27],"(TADs).":[28],"Each":[29],"such":[30,146],"domain":[31],"is":[32,96],"comprized":[33],"DNA":[35],"regions":[36],"actively":[37],"contacting":[38],"with":[39],"each":[40],"other":[41],"while":[42],"having":[43],"fewer":[44],"contact":[45,137],"outside":[46],"domain.":[48],"TADs":[49,68,87],"are":[50],"conserved":[51],"between":[52,57,104,145],"cell":[53],"lines":[54],"even":[56],"related":[58],"species.":[59],"While":[60],"there":[61],"exist":[62],"numerous":[63],"bioinformatics":[64],"tools":[65],"for":[66],"identification,":[69],"choice":[71],"a":[73,113,132],"method":[74],"its":[76],"adjustable":[77],"set":[78],"parameters":[80],"influences":[81],"number":[83],"identified":[86,106],"their":[89],"characteristics.":[90],"Besides,":[91],"one":[92],"more":[93],"common":[94],"disadvantage":[95],"that":[97,130],"most":[99],"methods":[100,140],"may":[101],"leave":[102],"gaps":[103],"TADs.":[107],"This":[108],"aimed":[110],"develop":[112],"robust":[114],"universal":[116],"tool":[117],"which":[118],"would":[119],"overcome":[120],"these":[121],"limitations.":[122],"We":[123],"have":[124],"developed":[125],"implemented":[127],"an":[128],"algorithm,":[129],"builds":[131],"hierarchical":[133],"tree":[134],"on":[135],"Hi-C":[136],"matrices":[138],"calculate":[142],"differences":[144],"trees.":[147]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}