{"id":"https://openalex.org/W2922853552","doi":"https://doi.org/10.1109/empdp.2019.8671567","title":"MethylFASTQ: A Tool Simulating Bisulfite Sequencing Data","display_name":"MethylFASTQ: A Tool Simulating Bisulfite Sequencing Data","publication_year":2019,"publication_date":"2019-02-01","ids":{"openalex":"https://openalex.org/W2922853552","doi":"https://doi.org/10.1109/empdp.2019.8671567","mag":"2922853552"},"language":"en","primary_location":{"id":"doi:10.1109/empdp.2019.8671567","is_oa":false,"landing_page_url":"https://doi.org/10.1109/empdp.2019.8671567","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2318/1695383","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045242635","display_name":"Giulia Piaggeschi","orcid":"https://orcid.org/0000-0002-4882-635X"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Giulia Piaggeschi","raw_affiliation_strings":["Dept. of Computer Science, University of Turin, Turin, Italy"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of Turin, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000359857","display_name":"Nicola Licheri","orcid":"https://orcid.org/0000-0003-1075-7333"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Nicola Licheri","raw_affiliation_strings":["Dept. of Computer Science, University of Turin, Turin, Italy"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of Turin, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089112383","display_name":"Greta Romano","orcid":"https://orcid.org/0000-0002-9076-8501"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Greta Romano","raw_affiliation_strings":["Dept. of Computer Science, University of Turin, Turin, Italy"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of Turin, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082219669","display_name":"Simone Pernice","orcid":"https://orcid.org/0000-0001-7124-4676"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simone Pernice","raw_affiliation_strings":["Dept. of Computer Science, University of Turin, Turin, Italy"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of Turin, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023290184","display_name":"Laura Follia","orcid":"https://orcid.org/0000-0003-1580-0505"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Laura Follia","raw_affiliation_strings":["Dept. of Computer Science, University of Turin, Turin, Italy"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of Turin, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087228664","display_name":"Giulio Ferrero","orcid":"https://orcid.org/0000-0002-4580-0680"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giulio Ferrero","raw_affiliation_strings":["Dept. of Computer Science, University of Turin, Turin, Italy"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, University of Turin, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5045242635"],"corresponding_institution_ids":["https://openalex.org/I55143463"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02021323,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"28","issue":null,"first_page":"334","last_page":"339"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","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/T10269","display_name":"Epigenetics and DNA Methylation","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/T11482","display_name":"RNA modifications and cancer","score":0.9789000153541565,"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/T13157","display_name":"Cancer-related gene regulation","score":0.9200000166893005,"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/bisulfite","display_name":"Bisulfite","score":0.8770577907562256},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.7704588770866394},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7677280902862549},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.6535895466804504},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.4719775319099426},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4606836140155792},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.44420263171195984},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3625067472457886},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2634391188621521},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17719310522079468},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11185988783836365},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08696863055229187}],"concepts":[{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.8770577907562256},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.7704588770866394},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7677280902862549},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6535895466804504},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4719775319099426},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4606836140155792},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.44420263171195984},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3625067472457886},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2634391188621521},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17719310522079468},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11185988783836365},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08696863055229187},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/empdp.2019.8671567","is_oa":false,"landing_page_url":"https://doi.org/10.1109/empdp.2019.8671567","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)","raw_type":"proceedings-article"},{"id":"pmh:oai:iris.unito.it:2318/1695383","is_oa":true,"landing_page_url":"http://hdl.handle.net/2318/1695383","pdf_url":null,"source":{"id":"https://openalex.org/S4306400637","display_name":"Institutional Research Information System University of Turin (University of Turin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I55143463","host_organization_name":"University of Turin","host_organization_lineage":["https://openalex.org/I55143463"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:iris.unito.it:2318/1695383","is_oa":true,"landing_page_url":"http://hdl.handle.net/2318/1695383","pdf_url":null,"source":{"id":"https://openalex.org/S4306400637","display_name":"Institutional Research Information System University of Turin (University of Turin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I55143463","host_organization_name":"University of Turin","host_organization_lineage":["https://openalex.org/I55143463"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1963590871","https://openalex.org/W2106889224","https://openalex.org/W2114850508","https://openalex.org/W2131374955","https://openalex.org/W2150612144","https://openalex.org/W2157539385","https://openalex.org/W2161488606","https://openalex.org/W2467325308","https://openalex.org/W2950096631"],"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/W1964177829","https://openalex.org/W2075918583","https://openalex.org/W2911544435","https://openalex.org/W1991992597"],"abstract_inverted_index":{"DNA":[0,4,20,34],"methylation":[1,21,168,224],"is":[2,22,58,92],"a":[3,146,156,160,232],"modification":[5],"playing":[6],"an":[7,86,123,182,204],"important":[8],"role":[9],"in":[10,117,132,137,149],"several":[11],"diseases,":[12],"including":[13],"cancer.":[14],"The":[15,26],"gold-standard":[16],"technique":[17],"for":[18,47,219],"measuring":[19],"Bisulfite":[23],"Sequencing":[24],"(BS).":[25],"treatment":[27],"with":[28,181,195,210],"bisulfite":[29,130,221,237],"alters":[30],"the":[31,36,52,62,69,80,93,111,153,164,167,171,191],"sequence":[32],"of":[33,38,54,68,155,170,185,193,206],"making":[35],"analysis":[37],"BS":[39,49,99,157],"data":[40,50,88],"computationally":[41],"difficult.":[42],"There":[43],"are":[44],"many":[45],"tools":[46],"analysing":[48],"but":[51],"choice":[53],"which":[55],"to":[56,61,78,84,97,197,234],"use":[57,215],"difficult":[59],"due":[60],"extensive":[63],"biological":[64],"and":[65,72,83,188,213,223],"technical":[66],"variability":[67],"data.":[70,239],"Synthetic":[71],"real":[73],"datasets":[74,131,208],"can":[75],"be":[76],"exploited":[77],"evaluate":[79],"tool":[81,96,104,126,212,233],"performance":[82],"obtain":[85],"accurate":[87],"analysis.":[89],"Today,":[90],"Sherman":[91,198],"only":[94],"available":[95],"generate":[98,235],"synthetic":[100,129,207,236],"datasets.":[101],"However,":[102],"this":[103,115,118],"does":[105],"not":[106],"report":[107,161,190],"any":[108],"information":[109,165],"about":[110,166],"methylated":[112,174],"cytosines.":[113],"For":[114],"purpose,":[116],"paper":[119],"we":[120,177,189,201,214,228],"present":[121],"MethyIFASTQ,":[122],"easy-to-use":[124],"bioinformatics":[125],"that":[127],"generates":[128],"FASTQ":[133,150],"format.":[134],"MethylFASTQ":[135,179,194,230],"works":[136],"parallel":[138],"manner":[139],"using":[140],"producer-consumer":[141],"approach.":[142],"It":[143],"returns:":[144],"i)":[145],"complete":[147],"dataset":[148,172],"format":[151],"simulating":[152],"results":[154],"experiment":[158],"ii)":[159],"file":[162],"storing":[163],"level":[169],"(i.e.":[173],"cytosines).":[175],"First,":[176],"test":[178],"performances":[180],"increasing":[183],"number":[184],"concurrent":[186],"processes":[187],"comparison":[192],"respect":[196],"tool.":[199],"Then,":[200],"also":[202],"describe":[203],"application":[205],"generated":[209],"our":[211],"them":[216],"as":[217,231],"input":[218],"two":[220],"mapping":[222],"calling":[225],"tools.":[226],"Finally,":[227],"propose":[229],"sequencing":[238]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
