{"id":"https://openalex.org/W2269784461","doi":"https://doi.org/10.1155/2015/760423","title":"HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis","display_name":"HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis","publication_year":2015,"publication_date":"2015-12-20","ids":{"openalex":"https://openalex.org/W2269784461","doi":"https://doi.org/10.1155/2015/760423","mag":"2269784461","pmid":"https://pubmed.ncbi.nlm.nih.gov/26798339"},"language":"en","primary_location":{"id":"doi:10.1155/2015/760423","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2015/760423","pdf_url":"http://downloads.hindawi.com/archive/2015/760423.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":"http://downloads.hindawi.com/archive/2015/760423.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":["Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010474623","display_name":"Karthik Raja Velmurugan","orcid":null},"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":"Karthik Raja Velmurugan","raw_affiliation_strings":["Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA","Interdisciplinary Ph.D. Program in Genomics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Interdisciplinary Ph.D. Program in Genomics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030360631","display_name":"David Keimig","orcid":null},"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":"David Keimig","raw_affiliation_strings":["Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","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":true,"raw_author_name":"Hehuang Xie","raw_affiliation_strings":["Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA","Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA","Interdisciplinary Ph.D. Program in Genomics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Interdisciplinary Ph.D. Program in Genomics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5070711045"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":0.3011,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.6325456,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"2015","issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9986000061035156,"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":0.9986000061035156,"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":0.9810000061988831,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9702000021934509,"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/computational-biology","display_name":"Computational biology","score":0.6347783803939819},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6240313053131104},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.6150819659233093},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.5722379684448242},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.5173989534378052},{"id":"https://openalex.org/keywords/bisulfite","display_name":"Bisulfite","score":0.4898388087749481},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4797343313694},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3316587805747986},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2802613377571106},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12168502807617188},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11895516514778137}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6347783803939819},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6240313053131104},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.6150819659233093},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5722379684448242},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.5173989534378052},{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.4898388087749481},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4797343313694},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3316587805747986},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2802613377571106},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12168502807617188},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11895516514778137},{"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:10.1155/2015/760423","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2015/760423","pdf_url":"http://downloads.hindawi.com/archive/2015/760423.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:26798339","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26798339","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:pubmedcentral.nih.gov:4698518","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4698518","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Adv Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/78953","is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/78953","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":"Text"}],"best_oa_location":{"id":"doi:10.1155/2015/760423","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2015/760423","pdf_url":"http://downloads.hindawi.com/archive/2015/760423.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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2269784461.pdf","grobid_xml":"https://content.openalex.org/works/W2269784461.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1967495567","https://openalex.org/W1971284773","https://openalex.org/W2002322555","https://openalex.org/W2036079113","https://openalex.org/W2067130606","https://openalex.org/W2082550660","https://openalex.org/W2106889224","https://openalex.org/W2108234281","https://openalex.org/W2124985265","https://openalex.org/W2127640118","https://openalex.org/W2131374955","https://openalex.org/W2149784730","https://openalex.org/W2164214190","https://openalex.org/W2170551349"],"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":{"The":[0,131],"emerging":[1],"genome-wide":[2,70],"hairpin":[3],"bisulfite":[4,23],"sequencing":[5,24],"(hairpin-BS-Seq)":[6],"technique":[7],"enables":[8],"the":[9,12,44,62,80,90,101,105],"determination":[10],"of":[11,46,56,69],"methylation":[13,30,65,91],"pattern":[14],"for":[15,43,61,93,145],"DNA":[16,97],"double":[17],"strands":[18,98],"simultaneously.":[19],"Compared":[20],"with":[21,127,136],"traditional":[22],"(BS-Seq)":[25],"techniques,":[26],"hairpin-BS-Seq":[27,47,71,76,111],"can":[28],"determine":[29],"fidelity":[31],"and":[32,67,87,122,139],"increase":[33],"mapping":[34,100,120,124,129],"efficiency.":[35],"However,":[36],"no":[37],"computational":[38],"tool":[39],"has":[40],"been":[41],"designed":[42],"analysis":[45],"data":[48],"yet.":[49],"Here":[50],"we":[51,113],"present":[52],"HBS-tools,":[53],"a":[54,118],"set":[55],"command":[57],"line":[58],"based":[59],"tools":[60],"preprocessing,":[63],"mapping,":[64],"calling,":[66],"summarizing":[68],"data.":[72],"It":[73],"accepts":[74],"paired-end":[75],"reads":[77],"to":[78,104,110],"recover":[79],"original":[81,102],"(pre-bisulfite-converted)":[82],"sequences":[83,103],"using":[84],"global":[85],"alignment":[86],"then":[88],"calls":[89],"statuses":[92],"cytosines":[94],"on":[95],"both":[96],"after":[99],"reference":[106],"genome.":[107],"After":[108],"applying":[109],"datasets,":[112],"found":[114],"that":[115],"HBS-tools":[116,132],"have":[117],"reduced":[119],"time":[121],"improved":[123],"efficiency":[125],"compared":[126],"state-of-the-art":[128],"tools.":[130],"source":[133],"scripts,":[134],"along":[135],"user":[137],"guide":[138],"testing":[140],"data,":[141],"are":[142],"freely":[143],"available":[144],"download.":[146]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}