{"id":"https://openalex.org/W2912178255","doi":"https://doi.org/10.1109/bibm.2018.8621157","title":"Optimal Modularity Method (OMM) for unbiased TADs detection in chromatin contact maps of single cells","display_name":"Optimal Modularity Method (OMM) for unbiased TADs detection in chromatin contact maps of single cells","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2912178255","doi":"https://doi.org/10.1109/bibm.2018.8621157","mag":"2912178255"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621157","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621157","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":"article","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/A5041646890","display_name":"Kirill Polovnikov","orcid":"https://orcid.org/0000-0001-9903-9623"},"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"]},{"id":"https://openalex.org/I4210150146","display_name":"Moscow State University","ror":"https://ror.org/050a13t43","country_code":"TJ","type":"education","lineage":["https://openalex.org/I4210150146"]}],"countries":["RU","TJ"],"is_corresponding":true,"raw_author_name":"K. Polovnikov","raw_affiliation_strings":["Physics Department, Moscow State University, Moscow"],"affiliations":[{"raw_affiliation_string":"Physics Department, Moscow State University, Moscow","institution_ids":["https://openalex.org/I4210150146","https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061217069","display_name":"A. Gorsky","orcid":"https://orcid.org/0000-0002-1619-3148"},"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/I1313323035","https://openalex.org/I4210097085","https://openalex.org/I4210107660"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"A. Gorsky","raw_affiliation_strings":["Institute of Information Transmission Problems RAS, Moscow"],"affiliations":[{"raw_affiliation_string":"Institute of Information Transmission Problems RAS, Moscow","institution_ids":["https://openalex.org/I4210107660"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000367020","display_name":"Sergei Nechaev","orcid":"https://orcid.org/0000-0002-3268-9039"},"institutions":[{"id":"https://openalex.org/I118517470","display_name":"P.N. Lebedev Physical Institute of the Russian Academy of Sciences","ror":"https://ror.org/01jkd3546","country_code":"RU","type":"facility","lineage":["https://openalex.org/I118517470","https://openalex.org/I1313323035","https://openalex.org/I2800498218","https://openalex.org/I4210096333"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"S. Nechaev","raw_affiliation_strings":["P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow"],"affiliations":[{"raw_affiliation_string":"P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Moscow","institution_ids":["https://openalex.org/I118517470"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041646890"],"corresponding_institution_ids":["https://openalex.org/I19880235","https://openalex.org/I4210150146"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13360812,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"485","issue":null,"first_page":"2480","last_page":"2481"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.998199999332428,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9972000122070312,"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/chromosome","display_name":"Chromosome","score":0.6356830596923828},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6237844824790955},{"id":"https://openalex.org/keywords/modularity","display_name":"Modularity (biology)","score":0.5982927083969116},{"id":"https://openalex.org/keywords/interphase","display_name":"Interphase","score":0.5865790247917175},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5756327509880066},{"id":"https://openalex.org/keywords/chromosome-conformation-capture","display_name":"Chromosome conformation capture","score":0.5513904094696045},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5184152126312256},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5155872702598572},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4554242491722107},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.4454692304134369},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4363473653793335},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4329657554626465},{"id":"https://openalex.org/keywords/margin","display_name":"Margin (machine learning)","score":0.4170430898666382},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4061213731765747},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3760398030281067},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3453728258609772},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32506299018859863},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3036438822746277},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.16361647844314575},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.13335105776786804},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12212014198303223}],"concepts":[{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.6356830596923828},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6237844824790955},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.5982927083969116},{"id":"https://openalex.org/C29452124","wikidata":"https://www.wikidata.org/wiki/Q835950","display_name":"Interphase","level":2,"score":0.5865790247917175},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5756327509880066},{"id":"https://openalex.org/C93946551","wikidata":"https://www.wikidata.org/wiki/Q5113914","display_name":"Chromosome conformation capture","level":5,"score":0.5513904094696045},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5184152126312256},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5155872702598572},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4554242491722107},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4454692304134369},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4363473653793335},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4329657554626465},{"id":"https://openalex.org/C774472","wikidata":"https://www.wikidata.org/wiki/Q6760393","display_name":"Margin (machine learning)","level":2,"score":0.4170430898666382},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4061213731765747},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3760398030281067},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3453728258609772},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32506299018859863},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3036438822746277},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.16361647844314575},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.13335105776786804},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12212014198303223},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2018.8621157","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621157","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":5,"referenced_works":["https://openalex.org/W2070021921","https://openalex.org/W2151936673","https://openalex.org/W2416738288","https://openalex.org/W2914735613","https://openalex.org/W6758994941"],"related_works":["https://openalex.org/W1992830050","https://openalex.org/W1994525023","https://openalex.org/W1980054129","https://openalex.org/W1968813707","https://openalex.org/W2077871972","https://openalex.org/W3195254751","https://openalex.org/W3116849561","https://openalex.org/W2136004413","https://openalex.org/W2111997778","https://openalex.org/W3180808842"],"abstract_inverted_index":{"It":[0],"becomes":[1],"clear":[2],"that":[3],"chromosome":[4,10,101],"contact":[5],"maps,":[6,39],"constructed":[7],"via":[8],"genome-wide":[9],"capture":[11],"technique":[12],"Hi-C,":[13],"in":[14,54,65,81,103,110],"principle,":[15],"might":[16],"provide":[17],"the":[18,34,37,40,56,62,66,72,91,100,111],"full":[19],"information":[20],"on":[21],"spatial":[22,41],"structure":[23],"of":[24,29,36,43,58,74,96,113],"chromosomes":[25,45],"at":[26],"different":[27],"stages":[28],"cellular":[30],"cycle.":[31],"According":[32],"to":[33],"analyses":[35],"population-averaged":[38,114],"conformation":[42],"interphase":[44],"features":[46],"a":[47,75],"set":[48],"of,":[49],"so-called,":[50],"topologically-associated":[51],"domains":[52],"(TADs),":[53],"which":[55],"density":[57],"contacts":[59],"well":[60],"exceeds":[61],"one":[63],"calculated":[64],"adjacent":[67],"regions":[68],"[1].":[69],"Even":[70],"though":[71],"definition":[73],"TAD":[76],"is":[77],"not":[78],"precise":[79],"and":[80],"practice":[82],"often":[83],"includes":[84],"some":[85],"phenomenological":[86],"cutoff":[87],"parameters":[88],"for":[89],"density,":[90],"crucial":[92],"issue":[93],"concerning":[94],"stability":[95],"TADs":[97],"boundaries":[98],"along":[99],"sequence":[102],"each":[104],"individual":[105],"cell":[106],"cannot":[107],"be":[108],"addressed":[109],"framework":[112],"Hi-C":[115],"maps.":[116]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
