{"id":"https://openalex.org/W2302110566","doi":"https://doi.org/10.1093/bioinformatics/btv673","title":"<i>CHRONOS</i>: a time-varying method for microRNA-mediated subpathway enrichment analysis","display_name":"<i>CHRONOS</i>: a time-varying method for microRNA-mediated subpathway enrichment analysis","publication_year":2015,"publication_date":"2015-11-14","ids":{"openalex":"https://openalex.org/W2302110566","doi":"https://doi.org/10.1093/bioinformatics/btv673","mag":"2302110566"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv673","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv673","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/6/884/49018296/bioinformatics_32_6_884.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/6/884/49018296/bioinformatics_32_6_884.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082119404","display_name":"Aristidis G. Vrahatis","orcid":"https://orcid.org/0000-0003-1892-0000"},"institutions":[{"id":"https://openalex.org/I174878644","display_name":"University of Patras","ror":"https://ror.org/017wvtq80","country_code":"GR","type":"education","lineage":["https://openalex.org/I174878644"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Aristidis G. Vrahatis","raw_affiliation_strings":["1 Department of Computer Engineering and Informatics,","2 Department of Medical Physics, School of Medicine, University of Patras, Patras 26500, Greece,"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Engineering and Informatics,","institution_ids":[]},{"raw_affiliation_string":"2 Department of Medical Physics, School of Medicine, University of Patras, Patras 26500, Greece,","institution_ids":["https://openalex.org/I174878644"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089495557","display_name":"Konstantina Dimitrakopoulou","orcid":"https://orcid.org/0000-0001-7159-0093"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Konstantina Dimitrakopoulou","raw_affiliation_strings":["3 Centre for Cancer Biomarkers CCBIO and Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway and"],"affiliations":[{"raw_affiliation_string":"3 Centre for Cancer Biomarkers CCBIO and Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway and","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001694584","display_name":"Panos Balomenos","orcid":"https://orcid.org/0000-0002-1074-5933"},"institutions":[{"id":"https://openalex.org/I174878644","display_name":"University of Patras","ror":"https://ror.org/017wvtq80","country_code":"GR","type":"education","lineage":["https://openalex.org/I174878644"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Panos Balomenos","raw_affiliation_strings":["1 Department of Computer Engineering and Informatics,","2 Department of Medical Physics, School of Medicine, University of Patras, Patras 26500, Greece,"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Engineering and Informatics,","institution_ids":[]},{"raw_affiliation_string":"2 Department of Medical Physics, School of Medicine, University of Patras, Patras 26500, Greece,","institution_ids":["https://openalex.org/I174878644"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104359657","display_name":"Athanasios K. Tsakalidis","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Athanasios K. Tsakalidis","raw_affiliation_strings":["1 Department of Computer Engineering and Informatics,"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Engineering and Informatics,","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080347335","display_name":"Anastasios Bezerianos","orcid":"https://orcid.org/0000-0002-8199-6000"},"institutions":[{"id":"https://openalex.org/I174878644","display_name":"University of Patras","ror":"https://ror.org/017wvtq80","country_code":"GR","type":"education","lineage":["https://openalex.org/I174878644"]},{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["GR","SG"],"is_corresponding":false,"raw_author_name":"Anastasios Bezerianos","raw_affiliation_strings":["2 Department of Medical Physics, School of Medicine, University of Patras, Patras 26500, Greece,","4 SINAPSE Institute, Center of Life Sciences, National University of Singapore, Singapore 117456"],"affiliations":[{"raw_affiliation_string":"2 Department of Medical Physics, School of Medicine, University of Patras, Patras 26500, Greece,","institution_ids":["https://openalex.org/I174878644"]},{"raw_affiliation_string":"4 SINAPSE Institute, Center of Life Sciences, National University of Singapore, Singapore 117456","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5082119404"],"corresponding_institution_ids":["https://openalex.org/I174878644"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2636,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.88539409,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"32","issue":"6","first_page":"884","last_page":"892"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9998000264167786,"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/T10604","display_name":"RNA Research and Splicing","score":0.9998000264167786,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9983000159263611,"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/computer-science","display_name":"Computer science","score":0.4914361238479614},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3234047293663025}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4914361238479614},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3234047293663025}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btv673","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv673","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/6/884/49018296/bioinformatics_32_6_884.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/6/884","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/6/884","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv673","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv673","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/6/884/49018296/bioinformatics_32_6_884.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3998201246","display_name":null,"funder_award_id":"Social","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G5374134968","display_name":null,"funder_award_id":"European Social Fund","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2302110566.pdf","grobid_xml":"https://content.openalex.org/works/W2302110566.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1122340077","https://openalex.org/W1546952499","https://openalex.org/W1618390401","https://openalex.org/W1990678336","https://openalex.org/W1992310781","https://openalex.org/W1992334380","https://openalex.org/W1994195407","https://openalex.org/W1999086631","https://openalex.org/W2010371279","https://openalex.org/W2015291385","https://openalex.org/W2018389019","https://openalex.org/W2019801716","https://openalex.org/W2037231299","https://openalex.org/W2037299986","https://openalex.org/W2059184968","https://openalex.org/W2062533676","https://openalex.org/W2063080163","https://openalex.org/W2069009920","https://openalex.org/W2080218141","https://openalex.org/W2087464689","https://openalex.org/W2088201796","https://openalex.org/W2098223033","https://openalex.org/W2100628034","https://openalex.org/W2100768460","https://openalex.org/W2100980426","https://openalex.org/W2106248311","https://openalex.org/W2107940314","https://openalex.org/W2110687686","https://openalex.org/W2112677798","https://openalex.org/W2113484804","https://openalex.org/W2119261703","https://openalex.org/W2119454933","https://openalex.org/W2126086567","https://openalex.org/W2127536416","https://openalex.org/W2130410032","https://openalex.org/W2133658633","https://openalex.org/W2134118500","https://openalex.org/W2140000393","https://openalex.org/W2145825942","https://openalex.org/W2153034056","https://openalex.org/W2159444728","https://openalex.org/W2163379431","https://openalex.org/W2165040702","https://openalex.org/W2165696776","https://openalex.org/W2597289420","https://openalex.org/W2963190765","https://openalex.org/W6681383220"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3031052312","https://openalex.org/W4389568370","https://openalex.org/W3032375762","https://openalex.org/W1995515455","https://openalex.org/W2080531066","https://openalex.org/W2586801360","https://openalex.org/W3108674512","https://openalex.org/W1506200166","https://openalex.org/W1489783725"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"In":[2],"the":[3,9,32,39,45,51,55,64,109,113,118,127,137,158],"era":[4],"of":[5,12,38,57,66,117,132,162],"network":[6],"medicine":[7],"and":[8,34,96,105,112,129,146,165],"rapid":[10],"growth":[11],"paired":[13],"time":[14,87],"series":[15,88],"mRNA/microRNA":[16,89],"expression":[17,90],"experiments,":[18],"there":[19],"is":[20,168],"an":[21],"urgent":[22],"need":[23],"for":[24],"pathway":[25,94,140],"enrichment":[26],"analysis":[27],"methods":[28,49,155],"able":[29],"to":[30,136,144],"capture":[31,126],"time-":[33],"condition-specific":[35],"\u2018active":[36],"parts\u2019":[37],"biological":[40],"circuitry":[41],"as":[42,44],"well":[43],"microRNA":[46],"impact.":[47],"Current":[48],"ignore":[50],"multiple":[52],"dynamical":[53],"\u2018themes\u2019\u2014in":[54],"form":[56],"enriched":[58],"biologically":[59],"relevant":[60],"microRNA-mediated":[61,100],"subpathways\u2014that":[62],"determine":[63],"functionality":[65],"signaling":[67],"networks":[68],"across":[69],"time.":[70],"Results:":[71],"To":[72],"address":[73],"these":[74],"challenges,":[75],"we":[76,122],"developed":[77],"time-vaRying":[78],"enriCHment":[79],"integrOmics":[80],"Subpathway":[81],"aNalysis":[82],"tOol":[83],"(CHRONOS)":[84],"by":[85],"integrating":[86],"data":[91,148,178],"with":[92],"KEGG":[93],"maps":[95],"microRNA-target":[97],"interactions.":[98],"Specifically,":[99],"subpathway":[101],"topologies":[102],"are":[103,179],"extracted":[104],"evaluated":[106],"based":[107],"on":[108],"temporal":[110],"transition":[111],"fold":[114],"change":[115],"activity":[116],"linked":[119],"genes/microRNAs.":[120],"Further,":[121],"provide":[123],"measures":[124],"that":[125,150],"structural":[128],"functional":[130],"features":[131],"subpathways":[133],"in":[134],"relation":[135],"complete":[138],"organism":[139],"atlas.":[141],"Our":[142],"application":[143],"synthetic":[145],"real":[147],"shows":[149],"CHRONOS":[151,167],"outperforms":[152],"current":[153],"subpathway-based":[154],"into":[156],"unraveling":[157],"inherent":[159],"dynamic":[160],"properties":[161],"pathways.":[163],"Availability":[164],"implementation:":[166],"freely":[169],"available":[170,180],"at":[171,181],"http://biosignal.med.upatras.gr/chronos/.":[172],"Contact:":[173],"tassos.bezerianos@nus.edu.sg.":[174],"Supplementary":[175,177],"information:":[176],"Bioinformatics":[182],"online.":[183]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}
