{"id":"https://openalex.org/W2937563420","doi":"https://doi.org/10.1177/1094342019840792","title":"<i>HPG-HMapper</i>: A DNA hydroxymethylation analysis tool","display_name":"<i>HPG-HMapper</i>: A DNA hydroxymethylation analysis tool","publication_year":2019,"publication_date":"2019-04-15","ids":{"openalex":"https://openalex.org/W2937563420","doi":"https://doi.org/10.1177/1094342019840792","mag":"2937563420"},"language":"en","primary_location":{"id":"doi:10.1177/1094342019840792","is_oa":true,"landing_page_url":"https://doi.org/10.1177/1094342019840792","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1177/1094342019840792","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023898091","display_name":"C\u00e9sar Gonz\u00e1lez","orcid":null},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"C\u00e9sar Gonz\u00e1lez","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Universidad de Valencia, Valencia, Spain"],"affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Universidad de Valencia, Valencia, Spain","institution_ids":["https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057445351","display_name":"Mariano P\u00e9rez","orcid":"https://orcid.org/0000-0002-0380-451X"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Mariano P\u00e9rez","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Universidad de Valencia, Valencia, Spain"],"affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Universidad de Valencia, Valencia, Spain","institution_ids":["https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032238726","display_name":"Juan M. Ordu\u00f1a","orcid":"https://orcid.org/0000-0002-2932-0214"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Juan M Ordu\u00f1a","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Universidad de Valencia, Valencia, Spain"],"affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Universidad de Valencia, Valencia, Spain","institution_ids":["https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032748495","display_name":"Felipe Javier Chaves","orcid":"https://orcid.org/0000-0001-8009-3689"},"institutions":[{"id":"https://openalex.org/I4210092133","display_name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red Diabetes y Enfermedades Metab\u00f3licas Asociadas","ror":"https://ror.org/00dwgct76","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4210092133","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210158373","display_name":"INCLIVA Health Research Institute","ror":"https://ror.org/059wbyv33","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210158373"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Javier Chaves","raw_affiliation_strings":["INCLIVA Health Research Institute, CIBERDEM, Valencia, Spain"],"affiliations":[{"raw_affiliation_string":"INCLIVA Health Research Institute, CIBERDEM, Valencia, Spain","institution_ids":["https://openalex.org/I4210158373","https://openalex.org/I4210092133"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024001086","display_name":"Ana-B\u00e1rbara Garc\u00eda","orcid":null},"institutions":[{"id":"https://openalex.org/I4210158373","display_name":"INCLIVA Health Research Institute","ror":"https://ror.org/059wbyv33","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210158373"]},{"id":"https://openalex.org/I4210092133","display_name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red Diabetes y Enfermedades Metab\u00f3licas Asociadas","ror":"https://ror.org/00dwgct76","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4210092133","https://openalex.org/I4387152914"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Ana-B\u00e1rbara Garc\u00eda","raw_affiliation_strings":["INCLIVA Health Research Institute, CIBERDEM, Valencia, Spain"],"affiliations":[{"raw_affiliation_string":"INCLIVA Health Research Institute, CIBERDEM, Valencia, Spain","institution_ids":["https://openalex.org/I4210158373","https://openalex.org/I4210092133"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5032238726"],"corresponding_institution_ids":["https://openalex.org/I16097986"],"apc_list":null,"apc_paid":null,"fwci":0.3409,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.58088778,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"34","issue":"1","first_page":"57","last_page":"65"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9997000098228455,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","score":0.9509999752044678,"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/T11478","display_name":"Caching and Content Delivery","score":0.9503999948501587,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6377896666526794},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.628165066242218},{"id":"https://openalex.org/keywords/bisulfite","display_name":"Bisulfite","score":0.5023324489593506},{"id":"https://openalex.org/keywords/memory-footprint","display_name":"Memory footprint","score":0.45762452483177185},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.4148407578468323},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.4137651324272156},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1958107054233551},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.17137977480888367},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13459810614585876}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6377896666526794},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.628165066242218},{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.5023324489593506},{"id":"https://openalex.org/C74912251","wikidata":"https://www.wikidata.org/wiki/Q6815727","display_name":"Memory footprint","level":2,"score":0.45762452483177185},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.4148407578468323},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.4137651324272156},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1958107054233551},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.17137977480888367},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13459810614585876},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1177/1094342019840792","is_oa":true,"landing_page_url":"https://doi.org/10.1177/1094342019840792","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1177/1094342019840792","is_oa":true,"landing_page_url":"https://doi.org/10.1177/1094342019840792","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2865403304","display_name":null,"funder_award_id":"TIN2015-66972-C5-5-R","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"}],"funders":[{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W2043472013","https://openalex.org/W2065186500","https://openalex.org/W2067897366","https://openalex.org/W2069895399","https://openalex.org/W2073358648","https://openalex.org/W2074746593","https://openalex.org/W2103810926","https://openalex.org/W2111538587","https://openalex.org/W2131374955","https://openalex.org/W2158231606","https://openalex.org/W2159433569","https://openalex.org/W2199847904","https://openalex.org/W2200334237","https://openalex.org/W2516502549","https://openalex.org/W2591635079","https://openalex.org/W2743895667"],"related_works":["https://openalex.org/W2805216920","https://openalex.org/W2619376220","https://openalex.org/W2064302386","https://openalex.org/W2134949149","https://openalex.org/W2035236309","https://openalex.org/W2895945844","https://openalex.org/W2033196363","https://openalex.org/W1964177829","https://openalex.org/W2075918583","https://openalex.org/W2039097638"],"abstract_inverted_index":{"DNA":[0,45,61],"methylation":[1],"(mC)":[2],"and":[3,17,83,88,93,117,142],"hydroxymethylation":[4],"(hmC)":[5],"can":[6],"significantly":[7],"affect":[8],"the":[9,60,76,89,105,118,135],"normal":[10],"human":[11],"development,":[12],"as":[13,15,73],"well":[14],"health":[16],"disease":[18],"status.":[19],"hmC":[20,46,62],"studies":[21],"require":[22],"not":[23],"only":[24],"specific":[25],"treatment":[26],"of":[27,43,79,91,101,107,111],"DNA,":[28],"but":[29],"also":[30],"software":[31,40,56],"tools":[32,41],"for":[33,58],"their":[34],"analysis.":[35],"However,":[36],"there":[37],"are":[38],"no":[39],"capable":[42],"analyzing":[44,59],"currently.":[47],"In":[48],"this":[49,102],"article,":[50],"we":[51],"propose":[52],"HPG-HMapper,":[53],"a":[54,131,147],"parallel":[55],"tool":[57,71,103],"data":[63,75],"obtained":[64],"by":[65],"ten-eleven":[66],"translocation\u2013assisted":[67],"bisulfite":[68],"sequencing.":[69],"This":[70],"takes":[72],"input":[74],"output":[77],"files":[78],"mC":[80,86],"aligner":[81],"tools,":[82],"it":[84],"yields":[85],"maps":[87],"accounting":[90],"methylated":[92],"hydroxymethylated":[94],"bases":[95],"on":[96,114,122],"each":[97],"chromosome.":[98],"The":[99,125],"design":[100],"includes":[104],"consideration":[106],"different":[108],"approaches,":[109],"one":[110,120],"them":[112],"based":[113,121],"binary":[115],"trees":[116],"other":[119],"bit":[123],"arrays.":[124],"performance":[126],"evaluation":[127],"results":[128],"show":[129],"that":[130],"hybrid":[132],"implementation":[133],"is":[134],"most":[136],"efficient":[137],"option,":[138],"allowing":[139],"fast":[140],"read":[141],"update":[143],"operations":[144],"while":[145],"keeping":[146],"small":[148],"memory":[149],"footprint.":[150]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
