{"id":"https://openalex.org/W2758405313","doi":"https://doi.org/10.1093/bioinformatics/btx516","title":"<i>In silico</i> structural modeling of multiple epigenetic marks on DNA","display_name":"<i>In silico</i> structural modeling of multiple epigenetic marks on DNA","publication_year":2017,"publication_date":"2017-09-22","ids":{"openalex":"https://openalex.org/W2758405313","doi":"https://doi.org/10.1093/bioinformatics/btx516","mag":"2758405313","pmid":"https://pubmed.ncbi.nlm.nih.gov/29028987"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx516","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx516","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/1/41/25113529/btx516.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/34/1/41/25113529/btx516.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015244397","display_name":"Konrad Krawczyk","orcid":"https://orcid.org/0000-0003-0697-5522"},"institutions":[{"id":"https://openalex.org/I4210146410","display_name":"Science Oxford","ror":"https://ror.org/04j8yhy50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210146410"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Konrad Krawczyk","raw_affiliation_strings":["Department of Computer Science, Oxford University, OX1\u20093QD Oxford, UK","Department of Statistics, Oxford University, OX1\u20093LB Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Oxford University, OX1\u20093QD Oxford, UK","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210146410"]},{"raw_affiliation_string":"Department of Statistics, Oxford University, OX1\u20093LB Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025629360","display_name":"Samuel Demharter","orcid":"https://orcid.org/0000-0001-7352-3994"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210146410","display_name":"Science Oxford","ror":"https://ror.org/04j8yhy50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210146410"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Samuel Demharter","raw_affiliation_strings":["Department of Computer Science, Oxford University, OX1\u20093QD Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Oxford University, OX1\u20093QD Oxford, UK","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210146410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034280556","display_name":"Bernhard Knapp","orcid":"https://orcid.org/0000-0002-5714-7105"},"institutions":[{"id":"https://openalex.org/I3123915005","display_name":"Universitat Internacional de Catalunya","ror":"https://ror.org/00tse2b39","country_code":"ES","type":"education","lineage":["https://openalex.org/I3123915005"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Bernhard Knapp","raw_affiliation_strings":["Department of Statistics, Oxford University, OX1\u20093LB Oxford, UK","Faculty of Medicine and Health Sciences, International University of Catalonia, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Oxford University, OX1\u20093LB Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Faculty of Medicine and Health Sciences, International University of Catalonia, Barcelona, Spain","institution_ids":["https://openalex.org/I3123915005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015572211","display_name":"Charlotte M. Deane","orcid":"https://orcid.org/0000-0003-1388-2252"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Charlotte M Deane","raw_affiliation_strings":["Department of Statistics, Oxford University, OX1\u20093LB Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Oxford University, OX1\u20093LB Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022118838","display_name":"P\u00e9ter Min\u00e1ry","orcid":"https://orcid.org/0000-0002-1779-6741"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210146410","display_name":"Science Oxford","ror":"https://ror.org/04j8yhy50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210146410"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Peter Minary","raw_affiliation_strings":["Department of Computer Science, Oxford University, OX1\u20093QD Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Oxford University, OX1\u20093QD Oxford, UK","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210146410"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022118838"],"corresponding_institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210146410"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3368,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60804972,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"34","issue":"1","first_page":"41","last_page":"48"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9988999962806702,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9988999962806702,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987000226974487,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9879000186920166,"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/in-silico","display_name":"In silico","score":0.9051398038864136},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.753098726272583},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6442099809646606},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.558997392654419},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5496748685836792},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.4268264174461365},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35625022649765015},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34221357107162476},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13323262333869934}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.9051398038864136},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.753098726272583},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6442099809646606},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.558997392654419},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5496748685836792},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.4268264174461365},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35625022649765015},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34221357107162476},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13323262333869934},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"D012984","descriptor_name":"Software","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":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx516","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx516","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/1/41/25113529/btx516.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:29028987","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29028987","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx516","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx516","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/1/41/25113529/btx516.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":[{"id":"https://openalex.org/G1934935867","display_name":null,"funder_award_id":"Engineering and Physical Sciences R","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334632","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2758405313.pdf","grobid_xml":"https://content.openalex.org/works/W2758405313.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W15000766","https://openalex.org/W1554534316","https://openalex.org/W1870454962","https://openalex.org/W1983951313","https://openalex.org/W1984066495","https://openalex.org/W1989467586","https://openalex.org/W2005078564","https://openalex.org/W2006208344","https://openalex.org/W2012293288","https://openalex.org/W2018046629","https://openalex.org/W2029050314","https://openalex.org/W2029667189","https://openalex.org/W2036662877","https://openalex.org/W2042404608","https://openalex.org/W2043995349","https://openalex.org/W2053586924","https://openalex.org/W2056360984","https://openalex.org/W2056497084","https://openalex.org/W2061781938","https://openalex.org/W2062089430","https://openalex.org/W2062979058","https://openalex.org/W2067521118","https://openalex.org/W2068407171","https://openalex.org/W2072912603","https://openalex.org/W2075151834","https://openalex.org/W2080026723","https://openalex.org/W2082168427","https://openalex.org/W2094247278","https://openalex.org/W2100627460","https://openalex.org/W2114147706","https://openalex.org/W2119514855","https://openalex.org/W2130479394","https://openalex.org/W2131711535","https://openalex.org/W2132199053","https://openalex.org/W2134349183","https://openalex.org/W2136729627","https://openalex.org/W2156879354","https://openalex.org/W2157458089","https://openalex.org/W2163693609","https://openalex.org/W2164301346","https://openalex.org/W2164550220","https://openalex.org/W2171835285","https://openalex.org/W2204959575","https://openalex.org/W2237918844","https://openalex.org/W2265016423","https://openalex.org/W2340786023","https://openalex.org/W2344252179","https://openalex.org/W2433523887","https://openalex.org/W2509139507","https://openalex.org/W2513408641","https://openalex.org/W3104163644","https://openalex.org/W3104251933","https://openalex.org/W6665727307"],"related_works":["https://openalex.org/W2214376880","https://openalex.org/W3212149434","https://openalex.org/W2073893804","https://openalex.org/W2513589746","https://openalex.org/W2003194288","https://openalex.org/W2213189664","https://openalex.org/W2153919606","https://openalex.org/W2113024639","https://openalex.org/W2062254828","https://openalex.org/W2936968863"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2017-10-06T00:00:00"}
