{"id":"https://openalex.org/W2011101362","doi":"https://doi.org/10.1109/iccabs.2014.6863920","title":"Improving bisulfite short-read mapping efficiency with hairpin-bisulfite data","display_name":"Improving bisulfite short-read mapping efficiency with hairpin-bisulfite data","publication_year":2014,"publication_date":"2014-06-01","ids":{"openalex":"https://openalex.org/W2011101362","doi":"https://doi.org/10.1109/iccabs.2014.6863920","mag":"2011101362"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2014.6863920","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2014.6863920","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/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":["Computer Science, Virginia Tech, Blacksburg, VA, USA","Computer Science, Virginia Tech Blacksburg, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science, Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Computer Science, Virginia Tech Blacksburg, USA#TAB#","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115604209","display_name":"Ming-an Sun","orcid":"https://orcid.org/0000-0002-4661-3027"},"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, USA","Virginia Bioinformatics Institute, Virginia Tech., Blacksburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Virginia Bioinformatics Institute, Virginia Tech., Blacksburg, 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, USA","Virginia Bioinformatics Institute, Virginia Tech., Blacksburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Virginia Bioinformatics Institute, Virginia Tech., Blacksburg, 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":false,"raw_author_name":"Liqing Zhang","raw_affiliation_strings":["Computer Science, Virginia Tech, Blacksburg, VA, USA","Computer Science, Virginia Tech Blacksburg, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science, Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Computer Science, Virginia Tech Blacksburg, USA#TAB#","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":0.2846,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.59053205,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9886999726295471,"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":0.9865000247955322,"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":0.9612730741500854},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.8212823867797852},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.626977264881134},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5584619641304016},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.5095767974853516},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.492710143327713},{"id":"https://openalex.org/keywords/sodium-bisulfite","display_name":"Sodium bisulfite","score":0.48115503787994385},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.46236446499824524},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.43838998675346375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42134231328964233},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.35013121366500854},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.23165801167488098},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17980125546455383}],"concepts":[{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.9612730741500854},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.8212823867797852},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.626977264881134},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5584619641304016},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5095767974853516},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.492710143327713},{"id":"https://openalex.org/C2775959488","wikidata":"https://www.wikidata.org/wiki/Q407891","display_name":"Sodium bisulfite","level":2,"score":0.48115503787994385},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.46236446499824524},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.43838998675346375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42134231328964233},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.35013121366500854},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.23165801167488098},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17980125546455383},{"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/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2014.6863920","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2014.6863920","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1971284773","https://openalex.org/W2074231493","https://openalex.org/W2082550660","https://openalex.org/W2087064593","https://openalex.org/W2128653886","https://openalex.org/W2131374955","https://openalex.org/W2170551349","https://openalex.org/W2171777347","https://openalex.org/W2885727518"],"related_works":["https://openalex.org/W2039097638","https://openalex.org/W2087999257","https://openalex.org/W1966904860","https://openalex.org/W2156167910","https://openalex.org/W2008376810","https://openalex.org/W1965301144","https://openalex.org/W2115046713","https://openalex.org/W2028514728","https://openalex.org/W2134949149","https://openalex.org/W2094504074"],"abstract_inverted_index":{"DNA":[0,20,66,107],"methylation":[1,21,47],"is":[2,22,82],"an":[3],"important":[4],"epigenetic":[5],"mark":[6],"relevant":[7],"to":[8,17,23,29,40,44,87,102,141,149,155,163],"normal":[9],"development":[10],"and":[11,80,132,143,159],"disease":[12],"genesis.":[13],"A":[14],"common":[15],"approach":[16],"characterizing":[18],"genome-wide":[19],"use":[24],"Next":[25],"Generation":[26],"Sequencing":[27],"technology":[28,101],"sequence":[30,36],"bisulfite":[31,64,130,150,157],"treated":[32,65],"DNA.":[33],"The":[34],"short":[35,75],"reads":[37,61,76,121],"are":[38],"mapped":[39,72],"the":[41,46,60,98,113,116,129],"reference":[42],"genome":[43],"determine":[45,103],"status":[48],"of":[49,59,105,115],"Cs.":[50],"However,":[51],"despite":[52],"intense":[53],"effort,":[54],"a":[55,123],"much":[56],"smaller":[57],"proportion":[58],"derived":[62],"from":[63],"(usually":[67],"about":[68],"40-80%)":[69],"can":[70],"be":[71,136,146],"than":[73,128],"regular":[74],"mapping":[77,90,126,138],"(\u2265":[78],"90%),":[79],"it":[81],"unclear":[83],"what":[84],"factors":[85],"lead":[86],"this":[88,94],"low":[89],"efficiency.":[91],"To":[92],"address":[93],"issue,":[95],"we":[96],"used":[97,154,162],"hairpin":[99],"sequencing":[100],"sequences":[104],"both":[106],"double":[108],"strands":[109],"simultaneously.":[110],"This":[111],"enabled":[112],"recovery":[114],"original":[117],"non-bisulfite-converted":[118],"sequences.":[119],"Recovered":[120],"had":[122],"higher":[124],"unique":[125],"efficiency":[127,139],"reads,":[131,158],"one":[133],"reason":[134],"could":[135],"that":[137],"relates":[140],"entropy,":[142],"entropy":[144],"may":[145],"lost":[147],"due":[148],"treatment.":[151],"Bismark":[152],"was":[153,161],"map":[156,164],"Bowtie2":[160],"recovered":[165],"untreated":[166],"reads.":[167]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}