{"id":"https://openalex.org/W2979304081","doi":"https://doi.org/10.1109/tcbb.2018.2864564","title":"Exploring Frequented Regions in Pan-Genomic Graphs","display_name":"Exploring Frequented Regions in Pan-Genomic Graphs","publication_year":2018,"publication_date":"2018-08-09","ids":{"openalex":"https://openalex.org/W2979304081","doi":"https://doi.org/10.1109/tcbb.2018.2864564","mag":"2979304081","pmid":"https://pubmed.ncbi.nlm.nih.gov/30106690"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2018.2864564","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2864564","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5012589523","display_name":"Alan Cleary","orcid":"https://orcid.org/0000-0002-6567-5346"},"institutions":[{"id":"https://openalex.org/I1310183320","display_name":"National Center for Genome Resources","ror":"https://ror.org/01p4cne93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1310183320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan Cleary","raw_affiliation_strings":["National Center for Genome Resources, Santa Fe, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Genome Resources, Santa Fe, NM, USA","institution_ids":["https://openalex.org/I1310183320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083833340","display_name":"Thiruvarangan Ramaraj","orcid":"https://orcid.org/0000-0002-7333-1041"},"institutions":[{"id":"https://openalex.org/I1310183320","display_name":"National Center for Genome Resources","ror":"https://ror.org/01p4cne93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1310183320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thiruvarangan Ramaraj","raw_affiliation_strings":["National Center for Genome Resources, Santa Fe, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Genome Resources, Santa Fe, NM, USA","institution_ids":["https://openalex.org/I1310183320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010719226","display_name":"Indika Kahanda","orcid":"https://orcid.org/0000-0002-4536-6917"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Indika Kahanda","raw_affiliation_strings":["Gianforte School of Computing, Montana State University, Bozeman, MT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gianforte School of Computing, Montana State University, Bozeman, MT, USA","institution_ids":["https://openalex.org/I23732399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071538924","display_name":"Joann Mudge","orcid":"https://orcid.org/0000-0002-2972-1640"},"institutions":[{"id":"https://openalex.org/I1310183320","display_name":"National Center for Genome Resources","ror":"https://ror.org/01p4cne93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1310183320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joann Mudge","raw_affiliation_strings":["National Center for Genome Resources, Santa Fe, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Genome Resources, Santa Fe, NM, USA","institution_ids":["https://openalex.org/I1310183320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084888509","display_name":"Brendan Mumey","orcid":"https://orcid.org/0000-0001-7151-2124"},"institutions":[{"id":"https://openalex.org/I23732399","display_name":"Montana State University","ror":"https://ror.org/02w0trx84","country_code":"US","type":"education","lineage":["https://openalex.org/I23732399","https://openalex.org/I4210126032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brendan Mumey","raw_affiliation_strings":["Gianforte School of Computing, Montana State University, Bozeman, MT, USA"],"raw_orcid":"https://orcid.org/0000-0001-7151-2124","affiliations":[{"raw_affiliation_string":"Gianforte School of Computing, Montana State University, Bozeman, MT, USA","institution_ids":["https://openalex.org/I23732399"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5413,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.66253946,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"16","issue":"5","first_page":"1424","last_page":"1435"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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":0.9987000226974487,"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":0.9952999949455261,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9940000176429749,"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/genome","display_name":"Genome","score":0.5296347737312317},{"id":"https://openalex.org/keywords/traverse","display_name":"Traverse","score":0.5168300271034241},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4832794964313507},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.4606139659881592},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4430520534515381},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37822091579437256},{"id":"https://openalex.org/keywords/yeast","display_name":"Yeast","score":0.3698294758796692},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2977299094200134},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19785431027412415},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.19317159056663513},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.08542785048484802}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5296347737312317},{"id":"https://openalex.org/C176809094","wikidata":"https://www.wikidata.org/wiki/Q15401496","display_name":"Traverse","level":2,"score":0.5168300271034241},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4832794964313507},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.4606139659881592},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4430520534515381},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37822091579437256},{"id":"https://openalex.org/C2779222958","wikidata":"https://www.wikidata.org/wiki/Q45422","display_name":"Yeast","level":2,"score":0.3698294758796692},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2977299094200134},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19785431027412415},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.19317159056663513},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.08542785048484802}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013211","descriptor_name":"Staphylococcus aureus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2018.2864564","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2864564","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30106690","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30106690","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4661963578","display_name":null,"funder_award_id":"DBI-1542262","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320311310","display_name":"Montana State University","ror":"https://ror.org/02w0trx84"},{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W134498522","https://openalex.org/W820014006","https://openalex.org/W1484413656","https://openalex.org/W1485041102","https://openalex.org/W1499138327","https://openalex.org/W1522477135","https://openalex.org/W1641749581","https://openalex.org/W1868469711","https://openalex.org/W1921457844","https://openalex.org/W1964940342","https://openalex.org/W1967974152","https://openalex.org/W1973208002","https://openalex.org/W1985341534","https://openalex.org/W1985644065","https://openalex.org/W1991427331","https://openalex.org/W2010361633","https://openalex.org/W2026413985","https://openalex.org/W2034400748","https://openalex.org/W2035847787","https://openalex.org/W2059608229","https://openalex.org/W2091328482","https://openalex.org/W2093931624","https://openalex.org/W2098296210","https://openalex.org/W2104846587","https://openalex.org/W2106387257","https://openalex.org/W2119821739","https://openalex.org/W2126969584","https://openalex.org/W2127901812","https://openalex.org/W2131180151","https://openalex.org/W2131374321","https://openalex.org/W2142057428","https://openalex.org/W2150550043","https://openalex.org/W2157546065","https://openalex.org/W2158262405","https://openalex.org/W2225892715","https://openalex.org/W2403828158","https://openalex.org/W2547528004","https://openalex.org/W2952366981","https://openalex.org/W2963158913","https://openalex.org/W4212839863","https://openalex.org/W4233756358","https://openalex.org/W4239510810","https://openalex.org/W6605560838","https://openalex.org/W6628750762","https://openalex.org/W6629740768","https://openalex.org/W6675716505","https://openalex.org/W7055789414"],"related_works":["https://openalex.org/W2377402383","https://openalex.org/W2380835401","https://openalex.org/W2381912691","https://openalex.org/W2350381577","https://openalex.org/W2353618196","https://openalex.org/W2348074676","https://openalex.org/W1982584572","https://openalex.org/W1963983419","https://openalex.org/W4232406862","https://openalex.org/W2397070560"],"abstract_inverted_index":{"We":[0,20,64,84],"consider":[1],"the":[2,25,39,66,75,86],"problem":[3,41],"of":[4,55,68,89,110],"identifying":[5,93],"regions":[6,23,32],"within":[7],"a":[8],"pan-genome":[9,61],"De":[10],"Bruijn":[11],"graph":[12,62],"that":[13,27,97,104],"are":[14,106],"traversed":[15],"by":[16,113],"many":[17],"sequence":[18],"paths.":[19],"define":[21],"such":[22,91],"and":[24,42,60,80,102,116],"subpaths":[26],"traverse":[28],"them":[29],"as":[30,92],"frequented":[31],"(FRs).":[33],"In":[34],"this":[35],"work,":[36],"we":[37,51],"formalize":[38],"FR":[40],"describe":[43],"an":[44],"efficient":[45],"algorithm":[46],"for":[47,74,108],"finding":[48],"FRs.":[49],"Subsequently,":[50],"propose":[52],"some":[53],"applications":[54,70],"FRs":[56,90,105],"based":[57],"on":[58],"machine-learning":[59],"simplification.":[63],"demonstrate":[65],"effectiveness":[67],"these":[69],"using":[71],"data":[72],"sets":[73],"organisms":[76],"Staphylococcus":[77],"aureus":[78],"(bacterium)":[79],"Saccharomyces":[81],"cerevisiae":[82],"(yeast).":[83],"corroborate":[85],"biological":[87],"relevance":[88],"introgressions":[94],"in":[95,99],"yeast":[96,111],"aid":[98],"alcohol":[100],"tolerance,":[101],"show":[103],"useful":[107],"classification":[109],"strains":[112],"industrial":[114],"use":[115],"visualizing":[117],"pan-genomic":[118],"space.":[119]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
