{"id":"https://openalex.org/W4411028907","doi":"https://doi.org/10.1145/3715020.3715050","title":"Gene Expression Variability Linked to Chromatin Clique Configurations and cis-Regulatory Elements","display_name":"Gene Expression Variability Linked to Chromatin Clique Configurations and cis-Regulatory Elements","publication_year":2024,"publication_date":"2024-11-28","ids":{"openalex":"https://openalex.org/W4411028907","doi":"https://doi.org/10.1145/3715020.3715050"},"language":"en","primary_location":{"id":"doi:10.1145/3715020.3715050","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3715020.3715050","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3715020.3715050","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2024 8th International Conference on Computational Biology and Bioinformatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3715020.3715050","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039669097","display_name":"Gatis Melkus","orcid":"https://orcid.org/0000-0002-3077-6809"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Gatis Melkus","raw_affiliation_strings":["Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia"],"raw_orcid":"https://orcid.org/0000-0002-3077-6809","affiliations":[{"raw_affiliation_string":"Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093021639","display_name":"Andrejs Sizovs","orcid":"https://orcid.org/0009-0004-6958-9965"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Andrejs Sizovs","raw_affiliation_strings":["Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia"],"raw_orcid":"https://orcid.org/0009-0004-6958-9965","affiliations":[{"raw_affiliation_string":"Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093021638","display_name":"Sandra Silina","orcid":null},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Sandra Silina","raw_affiliation_strings":["Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia"],"raw_orcid":"https://orcid.org/0009-0000-3917-9026","affiliations":[{"raw_affiliation_string":"Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039679271","display_name":"P\u0113teris Ru\u010devskis","orcid":null},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Peteris Rucevskis","raw_affiliation_strings":["Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia"],"raw_orcid":"https://orcid.org/0009-0006-6189-2008","affiliations":[{"raw_affiliation_string":"Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064697845","display_name":"Lelde L\u0101ce","orcid":"https://orcid.org/0000-0001-7650-2355"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Lelde Lace","raw_affiliation_strings":["Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia"],"raw_orcid":"https://orcid.org/0000-0001-7650-2355","affiliations":[{"raw_affiliation_string":"Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032271647","display_name":"Edgars Celms","orcid":"https://orcid.org/0000-0001-9608-3792"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Edgars Celms","raw_affiliation_strings":["Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia"],"raw_orcid":"https://orcid.org/0000-0001-9608-3792","affiliations":[{"raw_affiliation_string":"Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035792920","display_name":"Juris V\u012bksna","orcid":"https://orcid.org/0000-0003-2283-2978"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Juris Viksna","raw_affiliation_strings":["Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia"],"raw_orcid":"https://orcid.org/0000-0003-2283-2978","affiliations":[{"raw_affiliation_string":"Research Laboratory of System Modeling and Software Technologies, Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia","institution_ids":["https://openalex.org/I91123046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I91123046"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.3830165,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"84","last_page":"90"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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/T10604","display_name":"RNA Research and Splicing","score":0.9879999756813049,"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":0.9675999879837036,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.802251935005188},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5485131144523621},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5450298190116882},{"id":"https://openalex.org/keywords/clique","display_name":"Clique","score":0.537196934223175},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5178454518318176},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.47520527243614197},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4673595428466797},{"id":"https://openalex.org/keywords/chia-pet","display_name":"ChIA-PET","score":0.4566445052623749},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4462142586708069},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41449400782585144},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41254910826683044},{"id":"https://openalex.org/keywords/chromatin-remodeling","display_name":"Chromatin remodeling","score":0.17066696286201477},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16768068075180054},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11909961700439453}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.802251935005188},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5485131144523621},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5450298190116882},{"id":"https://openalex.org/C2777035058","wikidata":"https://www.wikidata.org/wiki/Q1662634","display_name":"Clique","level":2,"score":0.537196934223175},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5178454518318176},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.47520527243614197},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4673595428466797},{"id":"https://openalex.org/C67258246","wikidata":"https://www.wikidata.org/wiki/Q5065897","display_name":"ChIA-PET","level":5,"score":0.4566445052623749},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4462142586708069},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41449400782585144},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41254910826683044},{"id":"https://openalex.org/C167227067","wikidata":"https://www.wikidata.org/wiki/Q5113739","display_name":"Chromatin remodeling","level":4,"score":0.17066696286201477},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16768068075180054},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11909961700439453},{"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:10.1145/3715020.3715050","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3715020.3715050","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3715020.3715050","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2024 8th International Conference on Computational Biology and Bioinformatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3715020.3715050","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3715020.3715050","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3715020.3715050","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2024 8th International Conference on Computational Biology and Bioinformatics","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G3339825221","display_name":null,"funder_award_id":"lzp-2021/1-0236","funder_id":"https://openalex.org/F4320323269","funder_display_name":"Latvijas Zin\u0101tnes Padome"}],"funders":[{"id":"https://openalex.org/F4320323269","display_name":"Latvijas Zin\u0101tnes Padome","ror":"https://ror.org/02ar66p97"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411028907.pdf","grobid_xml":"https://content.openalex.org/works/W4411028907.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W175516305","https://openalex.org/W1965425724","https://openalex.org/W1986223165","https://openalex.org/W2018838463","https://openalex.org/W2082532751","https://openalex.org/W2108797218","https://openalex.org/W2209883607","https://openalex.org/W2461061549","https://openalex.org/W2766116317","https://openalex.org/W2887694579","https://openalex.org/W2955994579","https://openalex.org/W3011893069","https://openalex.org/W3015684736","https://openalex.org/W3045910546","https://openalex.org/W3109279595","https://openalex.org/W3109356327","https://openalex.org/W3127140457","https://openalex.org/W3161540023","https://openalex.org/W3166654832","https://openalex.org/W3208534634","https://openalex.org/W4224249716","https://openalex.org/W4283821449","https://openalex.org/W4285490847","https://openalex.org/W4378470165","https://openalex.org/W4388615740","https://openalex.org/W4398133250"],"related_works":["https://openalex.org/W2008077261","https://openalex.org/W3191994734","https://openalex.org/W2037920273","https://openalex.org/W4214521951","https://openalex.org/W4241694212","https://openalex.org/W4234876096","https://openalex.org/W4243928696","https://openalex.org/W3040477867","https://openalex.org/W3145419749","https://openalex.org/W3038565614"],"abstract_inverted_index":{"This":[0],"study":[1],"explores":[2],"the":[3,27,35],"relationship":[4],"between":[5],"combinations":[6],"of":[7,15,29,41,85],"EN-CODE":[8],"cis-Regulatory":[9],"Elements":[10],"(cCREs)":[11],"within":[12],"topological":[13,37],"elements":[14,68,87],"chromatin":[16,30],"interaction":[17,31],"networks":[18,32],"and":[19,33,88],"gene":[20,55],"expression":[21,56,74,94],"patterns.We":[22],"assign":[23],"cCRE":[24,47],"annotations":[25],"to":[26,54,72],"nodes":[28],"categorize":[34],"network's":[36],"elements,":[38],"particularly":[39],"cliques":[40,61],"size":[42],"3,":[43],"based":[44],"on":[45],"their":[46],"composition,":[48],"studying":[49],"how":[50],"these":[51],"compositions":[52],"relate":[53],"profiles.Our":[57],"findings":[58],"show":[59],"that":[60],"enriched":[62],"with":[63,76],"multiple":[64],"enhancer-like":[65],"or":[66],"promoter-like":[67],"are":[69],"generally":[70,92],"linked":[71],"higher":[73],"levels":[75],"some":[77],"notable":[78],"exceptions,":[79],"while":[80],"those":[81],"containing":[82],"a":[83,99],"mix":[84],"CTCF":[86],"DNase-only":[89],"sites":[90],"display":[91],"lower":[93],"levels.In":[95],"addition,":[96],"we":[97],"identify":[98],"specific":[100]},"counts_by_year":[],"updated_date":"2026-08-23T07:36:19.812096","created_date":"2025-10-10T00:00:00"}
