{"id":"https://openalex.org/W3202341299","doi":"https://doi.org/10.1093/bioinformatics/btab663","title":"RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data","display_name":"RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data","publication_year":2021,"publication_date":"2021-09-30","ids":{"openalex":"https://openalex.org/W3202341299","doi":"https://doi.org/10.1093/bioinformatics/btab663","mag":"3202341299","pmid":"https://pubmed.ncbi.nlm.nih.gov/34601556"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab663","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab663","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3934/41091705/btab663.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3934/41091705/btab663.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089751173","display_name":"Sara Hetzel","orcid":"https://orcid.org/0000-0002-4783-3814"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sara Hetzel","raw_affiliation_strings":["Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034653999","display_name":"Pay Gie\u00dfelmann","orcid":"https://orcid.org/0000-0002-1227-897X"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Pay Giesselmann","raw_affiliation_strings":["Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078948324","display_name":"Knut Reinert","orcid":"https://orcid.org/0000-0003-3078-8129"},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Knut Reinert","raw_affiliation_strings":["Department of Mathematics and Informatics, Freie Universit\u00e4t , Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Informatics, Freie Universit\u00e4t , Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031703305","display_name":"Alexander Meissner","orcid":"https://orcid.org/0000-0001-8646-7469"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Alexander Meissner","raw_affiliation_strings":["Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA","Department of Biology, Chemistry and Pharmacy, Freie Universit\u00e4t , Berlin, Germany","Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, MA 02138, USA","Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Biology, Chemistry and Pharmacy, Freie Universit\u00e4t , Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]},{"raw_affiliation_string":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, MA 02138, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089743337","display_name":"Helene Kretzmer","orcid":"https://orcid.org/0000-0002-0723-4980"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Helene Kretzmer","raw_affiliation_strings":["Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5031703305"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984","https://openalex.org/I4210142260","https://openalex.org/I75951250"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4022,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.59280485,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"37","issue":"21","first_page":"3934","last_page":"3935"},"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":0.975600004196167,"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":0.9562000036239624,"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":0.8431331515312195},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.6618868112564087},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6285207271575928},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.5719727873802185},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.5658976435661316},{"id":"https://openalex.org/keywords/data-extraction","display_name":"Data extraction","score":0.4625399112701416},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.4575954079627991},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41491782665252686},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38653457164764404},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.29920679330825806},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20857220888137817},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2045833170413971},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.19846421480178833},{"id":"https://openalex.org/keywords/medline","display_name":"MEDLINE","score":0.17772066593170166},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16082870960235596},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10609284043312073},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08943367004394531},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08845603466033936}],"concepts":[{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.8431331515312195},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.6618868112564087},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6285207271575928},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5719727873802185},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5658976435661316},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.4625399112701416},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.4575954079627991},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41491782665252686},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38653457164764404},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.29920679330825806},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20857220888137817},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2045833170413971},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.19846421480178833},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.17772066593170166},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16082870960235596},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10609284043312073},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08943367004394531},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08845603466033936},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btab663","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab663","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3934/41091705/btab663.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34601556","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34601556","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:pubmedcentral.nih.gov:8686677","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8686677","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:refubium.fu-berlin.de:fub188/33430","is_oa":true,"landing_page_url":"https://refubium.fu-berlin.de/handle/fub188/33430","pdf_url":null,"source":{"id":"https://openalex.org/S4306402444","display_name":"Refubium (Universit\u00e4tsbibliothek der Freien Universit\u00e4t Berlin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I75951250","host_organization_name":"Freie Universit\u00e4t Berlin","host_organization_lineage":["https://openalex.org/I75951250"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"doc-type:article"},{"id":"doi:10.17169/refubium-33151","is_oa":true,"landing_page_url":"https://doi.org/10.17169/refubium-33151","pdf_url":null,"source":{"id":"https://openalex.org/S7407052913","display_name":"Universit\u00e4tsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab663","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab663","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3934/41091705/btab663.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322434","display_name":"Max-Planck-Gesellschaft","ror":"https://ror.org/01hhn8329"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3202341299.pdf","grobid_xml":"https://content.openalex.org/works/W3202341299.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1979273476","https://openalex.org/W2025648894","https://openalex.org/W2046646392","https://openalex.org/W2106889224","https://openalex.org/W2122686130","https://openalex.org/W2125269686","https://openalex.org/W2131374955","https://openalex.org/W2164214190","https://openalex.org/W2164327622","https://openalex.org/W2753396470","https://openalex.org/W2792811283","https://openalex.org/W3009004192","https://openalex.org/W3038469736"],"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/W2911544435","https://openalex.org/W1991992597"],"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":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}