{"id":"https://openalex.org/W2128653886","doi":"https://doi.org/10.1155/2014/472045","title":"Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools","display_name":"Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools","publication_year":2014,"publication_date":"2014-04-15","ids":{"openalex":"https://openalex.org/W2128653886","doi":"https://doi.org/10.1155/2014/472045","mag":"2128653886","pmid":"https://pubmed.ncbi.nlm.nih.gov/24839440"},"language":"en","primary_location":{"id":"doi:10.1155/2014/472045","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2014/472045","pdf_url":"https://downloads.hindawi.com/archive/2014/472045.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://downloads.hindawi.com/archive/2014/472045.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068069408","display_name":"Hong Tran","orcid":"https://orcid.org/0000-0002-5625-2018"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong Tran","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA"],"raw_orcid":"https://orcid.org/0000-0002-5625-2018","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010719216","display_name":"Jacob Porter","orcid":"https://orcid.org/0000-0001-7322-2390"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob Porter","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA"],"raw_orcid":"https://orcid.org/0000-0001-7322-2390","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Ming-an Sun","orcid":"https://orcid.org/0000-0001-7921-1086"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ming-an Sun","raw_affiliation_strings":["Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"],"raw_orcid":"https://orcid.org/0000-0001-7921-1086","affiliations":[{"raw_affiliation_string":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070711045","display_name":"Hehuang Xie","orcid":"https://orcid.org/0000-0001-5739-1653"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hehuang Xie","raw_affiliation_strings":["Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100741571","display_name":"Liqing Zhang","orcid":"https://orcid.org/0000-0002-3936-4376"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Liqing Zhang","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100741571"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":1.8928,"has_fulltext":true,"cited_by_count":49,"citation_normalized_percentile":{"value":0.85844898,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2014","issue":null,"first_page":"1","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10096","display_name":"Metal-Organic Frameworks: Synthesis and Applications","score":0.9563999772071838,"subfield":{"id":"https://openalex.org/subfields/1604","display_name":"Inorganic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10096","display_name":"Metal-Organic Frameworks: Synthesis and Applications","score":0.9563999772071838,"subfield":{"id":"https://openalex.org/subfields/1604","display_name":"Inorganic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9553999900817871,"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/T10995","display_name":"Methane Hydrates and Related Phenomena","score":0.9424999952316284,"subfield":{"id":"https://openalex.org/subfields/2304","display_name":"Environmental Chemistry"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bisulfite","display_name":"Bisulfite","score":0.7632668614387512},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.726725161075592},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4426901340484619},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41777151823043823},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.125468909740448},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0987558662891388},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.09842795133590698}],"concepts":[{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.7632668614387512},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.726725161075592},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4426901340484619},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41777151823043823},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.125468909740448},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0987558662891388},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.09842795133590698},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1155/2014/472045","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2014/472045","pdf_url":"https://downloads.hindawi.com/archive/2014/472045.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24839440","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24839440","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":"Advances in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3000500","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4009243","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/78972","is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/78972","pdf_url":null,"source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article - Refereed"}],"best_oa_location":{"id":"doi:10.1155/2014/472045","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2014/472045","pdf_url":"https://downloads.hindawi.com/archive/2014/472045.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128653886.pdf","grobid_xml":"https://content.openalex.org/works/W2128653886.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1989568035","https://openalex.org/W1990937720","https://openalex.org/W1995078504","https://openalex.org/W2030380828","https://openalex.org/W2037113830","https://openalex.org/W2046387526","https://openalex.org/W2051273886","https://openalex.org/W2051465150","https://openalex.org/W2064730301","https://openalex.org/W2067130606","https://openalex.org/W2072249518","https://openalex.org/W2078028724","https://openalex.org/W2091193685","https://openalex.org/W2093931624","https://openalex.org/W2096441981","https://openalex.org/W2103441770","https://openalex.org/W2106889224","https://openalex.org/W2112113834","https://openalex.org/W2123750815","https://openalex.org/W2124985265","https://openalex.org/W2128793361","https://openalex.org/W2131232216","https://openalex.org/W2131374955","https://openalex.org/W2133229506","https://openalex.org/W2136145671","https://openalex.org/W2139760555","https://openalex.org/W2149118757","https://openalex.org/W2149784730","https://openalex.org/W2152642144","https://openalex.org/W2158322625","https://openalex.org/W2165293958","https://openalex.org/W2166694026","https://openalex.org/W2170551349","https://openalex.org/W2184782031"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2054484492","https://openalex.org/W2905022623","https://openalex.org/W1990950482","https://openalex.org/W2811448415","https://openalex.org/W2619376220","https://openalex.org/W3008042233","https://openalex.org/W2953262169"],"abstract_inverted_index":{"Background.":[0],"Large-scale":[1],"bisulfite":[2,48,63,176],"treatment":[3],"and":[4,25,41,45,72,82,105,115,151,154],"short":[5,49,64,178],"reads":[6,50,94],"sequencing":[7,231],"technology":[8],"allow":[9],"comprehensive":[10],"estimation":[11],"of":[12,15,20,30,77,93,107,136,172,192,212,229],"methylation":[13,32],"states":[14],"Cs":[16],"in":[17,134],"the":[18,91,100,130,141,144,190,205,210,222,227],"genomes":[19],"different":[21],"tissues,":[22],"cell":[23],"types,":[24],"developmental":[26],"stages.":[27],"Accurate":[28],"characterization":[29],"DNA":[31],"is":[33,163,168],"essential":[34],"for":[35,174],"understanding":[36],"genotype":[37],"phenotype":[38],"association,":[39],"gene":[40],"environment":[42],"interaction,":[43],"diseases,":[44],"cancer.":[46],"Aligning":[47],"to":[51,99],"a":[52,57,165,169,183],"reference":[53],"genome":[54],"has":[55],"been":[56],"challenging":[58],"task.":[59],"We":[60,85,118],"compared":[61],"five":[62,131],"read":[65],"mapping":[66,78,88,126,137,175,186,197],"tools,":[67],"BSMAP,":[68,150],"Bismark,":[69],"BS-Seeker,":[70],"BiSS,":[71,149],"BRAT-BW,":[73],"representing":[74],"two":[75],"classes":[76],"algorithms":[79],"(hash":[80],"table":[81],"suffix/prefix":[83],"tries).":[84],"examined":[86],"their":[87,230],"efficiency":[89],"(i.e.,":[90],"percentage":[92],"that":[95],"can":[96,195],"be":[97],"mapped":[98],"genomes),":[101],"usability,":[102],"running":[103],"time,":[104],"effects":[106],"changing":[108],"default":[109],"parameter":[110],"settings":[111],"using":[112],"both":[113],"real":[114,145],"simulated":[116],"reads.":[117,179],"also":[119,208],"investigated":[120],"how":[121],"preprocessing":[122],"data":[123],"might":[124],"affect":[125],"efficiency.":[127,187],"Conclusion.":[128],"Among":[129],"programs":[132],"compared,":[133],"terms":[135],"efficiency,":[138,198],"Bismark":[139,167],"performs":[140],"best":[142],"on":[143,226],"data,":[146],"followed":[147],"by":[148],"finally":[152],"BRAT-BW":[153],"BS-Seeker":[155],"with":[156],"very":[157],"similar":[158],"performance.":[159],"If":[160],"CPU":[161],"time":[162],"not":[164,200],"constraint,":[166],"good":[170],"choice":[171],"program":[173],"treated":[177],"Data":[180],"quality":[181,228],"impacts":[182],"great":[184],"deal":[185],"Although":[188],"increasing":[189],"number":[191],"mismatches":[193],"allowed":[194],"increase":[196],"it":[199],"only":[201],"significantly":[202],"slows":[203],"down":[204],"program,":[206],"but":[207],"runs":[209],"risk":[211],"having":[213],"increased":[214],"false":[215],"positives.":[216],"Therefore,":[217],"users":[218],"should":[219],"carefully":[220],"set":[221],"related":[223],"parameters":[224],"depending":[225],"data.":[232]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
