{"id":"https://openalex.org/W2775061293","doi":"https://doi.org/10.1093/bioinformatics/btx778","title":"Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data","display_name":"Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data","publication_year":2017,"publication_date":"2017-12-01","ids":{"openalex":"https://openalex.org/W2775061293","doi":"https://doi.org/10.1093/bioinformatics/btx778","mag":"2775061293","pmid":"https://pubmed.ncbi.nlm.nih.gov/29211825"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx778","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx778","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1414/25119980/btx778.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1414/25119980/btx778.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076376340","display_name":"Osvaldo Gra\u00f1a\u2010Castro","orcid":"https://orcid.org/0000-0003-1615-4242"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"id":"https://openalex.org/I4210089594","display_name":"Spanish National Cancer Research Centre","ror":"https://ror.org/00bvhmc43","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210089594"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Osvaldo Gra\u00f1a","raw_affiliation_strings":["Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain","Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S/N, Universidade de Vigo, Ourense, Spain"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain","institution_ids":["https://openalex.org/I4210089594"]},{"raw_affiliation_string":"Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S/N, Universidade de Vigo, Ourense, Spain","institution_ids":["https://openalex.org/I6289922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038155908","display_name":"Hugo L\u00f3pez-Fern\u00e1ndez","orcid":"https://orcid.org/0000-0002-6476-7206"},"institutions":[{"id":"https://openalex.org/I4210138594","display_name":"Rede de Qu\u00edmica e Tecnologia","ror":"https://ror.org/04j14t006","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210138594"]},{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]},{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]}],"countries":["ES","PT"],"is_corresponding":false,"raw_author_name":"Hugo L\u00f3pez-Fern\u00e1ndez","raw_affiliation_strings":["Centro de Investigaciones Biom\u00e9dicas (Centro Singular de Investigaci\u00f3n de Galicia), Campus Universitario de Vigo, Vigo, Spain","Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S/N, Universidade de Vigo, Ourense, Spain","UCIBIO-REQUIMTE, Departamento de Qu\u00edmica, Facultade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa, Lisbon, Portugal"],"affiliations":[{"raw_affiliation_string":"Centro de Investigaciones Biom\u00e9dicas (Centro Singular de Investigaci\u00f3n de Galicia), Campus Universitario de Vigo, Vigo, Spain","institution_ids":[]},{"raw_affiliation_string":"Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S/N, Universidade de Vigo, Ourense, Spain","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"UCIBIO-REQUIMTE, Departamento de Qu\u00edmica, Facultade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa, Lisbon, Portugal","institution_ids":["https://openalex.org/I83558840","https://openalex.org/I4210138594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048392452","display_name":"Florentino Fdez\u2010Riverola","orcid":"https://orcid.org/0000-0002-3943-8013"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Florentino Fdez-Riverola","raw_affiliation_strings":["Centro de Investigaciones Biom\u00e9dicas (Centro Singular de Investigaci\u00f3n de Galicia), Campus Universitario de Vigo, Vigo, Spain","Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S/N, Universidade de Vigo, Ourense, Spain"],"affiliations":[{"raw_affiliation_string":"Centro de Investigaciones Biom\u00e9dicas (Centro Singular de Investigaci\u00f3n de Galicia), Campus Universitario de Vigo, Vigo, Spain","institution_ids":[]},{"raw_affiliation_string":"Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S/N, Universidade de Vigo, Ourense, Spain","institution_ids":["https://openalex.org/I6289922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079168682","display_name":"David G. Pisano","orcid":"https://orcid.org/0000-0002-4895-4124"},"institutions":[{"id":"https://openalex.org/I4210089594","display_name":"Spanish National Cancer Research Centre","ror":"https://ror.org/00bvhmc43","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210089594"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"David Gonz\u00e1lez Pisano","raw_affiliation_strings":["Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain","institution_ids":["https://openalex.org/I4210089594"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044007257","display_name":"Daniel Glez\u2010Pe\u00f1a","orcid":"https://orcid.org/0000-0002-6129-7245"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Daniel Glez-Pe\u00f1a","raw_affiliation_strings":["Centro de Investigaciones Biom\u00e9dicas (Centro Singular de Investigaci\u00f3n de Galicia), Campus Universitario de Vigo, Vigo, Spain","Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S/N, Universidade de Vigo, Ourense, Spain"],"affiliations":[{"raw_affiliation_string":"Centro de Investigaciones Biom\u00e9dicas (Centro Singular de Investigaci\u00f3n de Galicia), Campus Universitario de Vigo, Vigo, Spain","institution_ids":[]},{"raw_affiliation_string":"Departamento de Inform\u00e1tica. ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Edificio Polit\u00e9cnico, Campus Universitario As Lagoas S/N, Universidade de Vigo, Ourense, Spain","institution_ids":["https://openalex.org/I6289922"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5044007257","https://openalex.org/A5076376340"],"corresponding_institution_ids":["https://openalex.org/I4210089594","https://openalex.org/I6289922"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.6228,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.84097572,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"34","issue":"8","first_page":"1414","last_page":"1415"},"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":0.9937999844551086,"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":0.9642000198364258,"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":0.760012686252594},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7371014356613159},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6963244676589966},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.621911883354187},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.5566608309745789},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4487433135509491},{"id":"https://openalex.org/keywords/table","display_name":"Table (database)","score":0.42952659726142883},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.3218318521976471},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1743425726890564},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.16228315234184265},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13964450359344482},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06354212760925293}],"concepts":[{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.760012686252594},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7371014356613159},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6963244676589966},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.621911883354187},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.5566608309745789},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4487433135509491},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.42952659726142883},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.3218318521976471},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1743425726890564},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.16228315234184265},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13964450359344482},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06354212760925293},{"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},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx778","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx778","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1414/25119980/btx778.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29211825","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29211825","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:www.investigo.biblioteca.uvigo.es:11093/6217","is_oa":false,"landing_page_url":"http://hdl.handle.net/11093/6217","pdf_url":null,"source":{"id":"https://openalex.org/S4377196408","display_name":"Investigo Institutional repository of UVigo (Universidade de Vigo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I6289922","host_organization_name":"Universidade de Vigo","host_organization_lineage":["https://openalex.org/I6289922"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx778","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx778","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1414/25119980/btx778.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/W2775061293.pdf","grobid_xml":"https://content.openalex.org/works/W2775061293.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1963590871","https://openalex.org/W1987557775","https://openalex.org/W1989568035","https://openalex.org/W1989573122","https://openalex.org/W2040507896","https://openalex.org/W2059099579","https://openalex.org/W2067151470","https://openalex.org/W2069796345","https://openalex.org/W2073358648","https://openalex.org/W2074746593","https://openalex.org/W2097524618","https://openalex.org/W2114970231","https://openalex.org/W2117675660","https://openalex.org/W2124985265","https://openalex.org/W2131232216","https://openalex.org/W2165541556","https://openalex.org/W2192647662"],"related_works":["https://openalex.org/W2805216920","https://openalex.org/W2619376220","https://openalex.org/W2064302386","https://openalex.org/W2134949149","https://openalex.org/W4380433113","https://openalex.org/W2035236309","https://openalex.org/W2895945844","https://openalex.org/W2033196363","https://openalex.org/W4386072068","https://openalex.org/W1964177829"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
