{"id":"https://openalex.org/W4396965897","doi":"https://doi.org/10.1007/978-1-0716-3989-4_3","title":"Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts","display_name":"Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4396965897","doi":"https://doi.org/10.1007/978-1-0716-3989-4_3","pmid":"https://pubmed.ncbi.nlm.nih.gov/38045397","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/10690252"},"language":"en","primary_location":{"id":"doi:10.1007/978-1-0716-3989-4_3","doi":"https://doi.org/10.1007/978-1-0716-3989-4_3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-0716-3989-4_3","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","norway-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"volume":{"id":"https://openalex.org/W4396966282","display_name":"Research in Computational Molecular Biology"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2023/11/22/2023.11.22.568259.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000329336","display_name":"Askar Gafurov","orcid":"https://orcid.org/0009-0006-5270-831X","observed_orcids":["https://orcid.org/0009-0006-5270-831X"]},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Askar Gafurov","raw_affiliation_strings":["Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia","institution_ids":["https://openalex.org/I74788687"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053772564","display_name":"Tom\u00e1\u0161 Vina\u0159","orcid":"https://orcid.org/0000-0003-3898-3447","observed_orcids":["https://orcid.org/0000-0003-3898-3447"]},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Tom\u00e1\u0161 Vina\u0159","raw_affiliation_strings":["Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia","institution_ids":["https://openalex.org/I74788687"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066909672","display_name":"Paul Medvedev","orcid":"https://orcid.org/0000-0003-3143-594X","observed_orcids":["https://orcid.org/0000-0003-3143-594X"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Medvedev","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, USA","Department of Computer Science and Engineering, The Pennsylvania State University, State College, USA","Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, The Pennsylvania State University, State College, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058053699","display_name":"Bro\u0148a Brejov\u00e1","orcid":"https://orcid.org/0000-0002-9483-1766","observed_orcids":["https://orcid.org/0000-0002-9483-1766"]},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":true,"raw_author_name":"Bro\u0148a Brejov\u00e1","raw_affiliation_strings":["Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia","institution_ids":["https://openalex.org/I74788687"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5058053699"],"corresponding_institution_ids":["https://openalex.org/I74788687"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06176593,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"14758","issue":null,"first_page":"38","last_page":"53"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6503999829292297,"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":0.6503999829292297,"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":0.14669999480247498,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.08330000191926956,"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/genomic-intervals","display_name":"genomic intervals","score":0.5099999904632568},{"id":"https://openalex.org/keywords/null-models","display_name":"null models","score":0.7509999871253967},{"id":"https://openalex.org/keywords/p-value-calculation","display_name":"p-value estimation","score":0.7860000133514404},{"id":"https://openalex.org/keywords/normal-approximation","display_name":"Gaussian approximation","score":0.6909999847412109},{"id":"https://openalex.org/keywords/gc-content-bias","display_name":"GC content bias","score":0.7749999761581421},{"id":"https://openalex.org/keywords/genomic-context","display_name":"genomic context","score":0.6480000019073486},{"id":"https://openalex.org/keywords/enrichment-analysis","display_name":"enrichment analysis","score":0.5189999938011169},{"id":"https://openalex.org/keywords/parallel-algorithms","display_name":"parallel algorithms","score":0.43299999833106995}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6836527585983276},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.49630671739578247},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4769093990325928},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4626759886741638},{"id":"https://openalex.org/C169857963","wikidata":"https://www.wikidata.org/wiki/Q1461038","display_name":"Test statistic","level":3,"score":0.4342747926712036},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.3987239897251129},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3652057349681854},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3279913067817688},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22240135073661804},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2147214710712433},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.18972334265708923},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13107356429100037},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1007/978-1-0716-3989-4_3","doi":"https://doi.org/10.1007/978-1-0716-3989-4_3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-0716-3989-4_3","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","norway-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"doi:10.1101/2023.11.22.568259","doi":"https://doi.org/10.1101/2023.11.22.568259","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2023.11.22.568259","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/11/22/2023.11.22.568259.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:38045397","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38045397","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,"listed_in":[],"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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmid:40297196","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40297196","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,"listed_in":[],"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":"Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- )","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12037170","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12037170","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12037170/pdf/nihms-2069669.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,"listed_in":[],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Res Comput Mol Biol","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:10690252","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10690252","pdf_url":null,"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,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1101/2023.11.22.568259","doi":"https://doi.org/10.1101/2023.11.22.568259","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2023.11.22.568259","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/11/22/2023.11.22.568259.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1532411095","display_name":"Bioinformatika patog\u00e9nov a pangen\u00f3mov","funder_award_id":"1/0538/22","funder_id":"https://openalex.org/F4320323641","funder_display_name":"Vedeck\u00e1 Grantov\u00e1 Agent\u00fara M\u0160VVa\u0160 SR a SAV"},{"id":"https://openalex.org/G185880553","display_name":null,"funder_award_id":"1/0463/","funder_id":"https://openalex.org/F4320323641","funder_display_name":"Vedeck\u00e1 Grantov\u00e1 Agent\u00fara M\u0160VVa\u0160 SR a SAV"},{"id":"https://openalex.org/G434337789","display_name":null,"funder_award_id":"HORIZON2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G47515928","display_name":"Komparat\u00edvna transkriptomika ako okno do sveta z\u00e1kladn\u00fdch biologick\u00fdch procesov","funder_award_id":"APVV-22-0144","funder_id":"https://openalex.org/F4320323251","funder_display_name":"Agent\u00fara na Podporu V\u00fdskumu a V\u00fdvoja"},{"id":"https://openalex.org/G6114000545","display_name":null,"funder_award_id":"22-0144","funder_id":"https://openalex.org/F4320323251","funder_display_name":"Agent\u00fara na Podporu V\u00fdskumu a V\u00fdvoja"},{"id":"https://openalex.org/G6636646442","display_name":"A k-mer-based search engine for sequencing databases","funder_award_id":"2138585","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6697205189","display_name":"Pan-genome Graph Algorithms and Data Integration","funder_award_id":"872539","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6948331134","display_name":null,"funder_award_id":"APVV-22-","funder_id":"https://openalex.org/F4320323251","funder_display_name":"Agent\u00fara na Podporu V\u00fdskumu a V\u00fdvoja"},{"id":"https://openalex.org/G7571258075","display_name":"Alternat\u00edvne reprezent\u00e1cie ve\u013ek\u00fdch genomick\u00fdch d\u00e1t","funder_award_id":"1/0463/20","funder_id":"https://openalex.org/F4320323641","funder_display_name":"Vedeck\u00e1 Grantov\u00e1 Agent\u00fara M\u0160VVa\u0160 SR a SAV"},{"id":"https://openalex.org/G8013789063","display_name":null,"funder_award_id":"872539","funder_id":"https://openalex.org/F4320323251","funder_display_name":"Agent\u00fara na Podporu V\u00fdskumu a V\u00fdvoja"},{"id":"https://openalex.org/G9000871591","display_name":"Leveraging k-mer sketching statistics to enhance metagenomic methods and alignment algorithms","funder_award_id":"R01GM146462","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323251","display_name":"Agent\u00fara na Podporu V\u00fdskumu a V\u00fdvoja","ror":"https://ror.org/037nx0e70"},{"id":"https://openalex.org/F4320323641","display_name":"Vedeck\u00e1 Grantov\u00e1 Agent\u00fara M\u0160VVa\u0160 SR a SAV","ror":"https://ror.org/044gwpv05"},{"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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4396965897.pdf","grobid_xml":"https://content.openalex.org/works/W4396965897.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W114565888","https://openalex.org/W2034197594","https://openalex.org/W2054940035","https://openalex.org/W2092885708","https://openalex.org/W2095720871","https://openalex.org/W2102619694","https://openalex.org/W2107026277","https://openalex.org/W2108744961","https://openalex.org/W2133938268","https://openalex.org/W2135407780","https://openalex.org/W2166187656","https://openalex.org/W2167595480","https://openalex.org/W2180834397","https://openalex.org/W2184563578","https://openalex.org/W2325380770","https://openalex.org/W2905471889","https://openalex.org/W2943766116","https://openalex.org/W2952285719","https://openalex.org/W4220886647","https://openalex.org/W4220999759","https://openalex.org/W4226341779","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W4403280437","https://openalex.org/W4226341779","https://openalex.org/W2952285719","https://openalex.org/W2108744961","https://openalex.org/W2163180646","https://openalex.org/W6939776992","https://openalex.org/W2247637961","https://openalex.org/W6902316027","https://openalex.org/W2806402073","https://openalex.org/W6902391606"],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2024-05-17T00:00:00"}