{"id":"https://openalex.org/W2594735672","doi":"https://doi.org/10.1093/bioinformatics/btx115","title":"Computational modeling of <i>in vivo</i> and <i>in vitro</i> protein-DNA interactions by multiple instance learning","display_name":"Computational modeling of <i>in vivo</i> and <i>in vitro</i> protein-DNA interactions by multiple instance learning","publication_year":2017,"publication_date":"2017-02-27","ids":{"openalex":"https://openalex.org/W2594735672","doi":"https://doi.org/10.1093/bioinformatics/btx115","mag":"2594735672","pmid":"https://pubmed.ncbi.nlm.nih.gov/28334224"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx115","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx115","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/2097/25157171/btx115.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/33/14/2097/25157171/btx115.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100634508","display_name":"Zhen Gao","orcid":"https://orcid.org/0000-0003-3461-1910"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhen Gao","raw_affiliation_strings":["Department of Computer Science, University of Texas at San Antonio, San Antonio, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Texas at San Antonio, San Antonio, TX, USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071995180","display_name":"Jianhua Ruan","orcid":"https://orcid.org/0000-0002-5622-3137"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jianhua Ruan","raw_affiliation_strings":["Department of Computer Science, University of Texas at San Antonio, San Antonio, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Texas at San Antonio, San Antonio, TX, USA","institution_ids":["https://openalex.org/I45438204"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5071995180"],"corresponding_institution_ids":["https://openalex.org/I45438204"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8952,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.72844878,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"14","first_page":"2097","last_page":"2105"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9872000217437744,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9872000217437744,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9843000173568726,"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/T10824","display_name":"Image Retrieval and Classification Techniques","score":0.9839000105857849,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-vivo","display_name":"In vivo","score":0.65229332447052},{"id":"https://openalex.org/keywords/in-vitro","display_name":"In vitro","score":0.5864076614379883},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5380856990814209},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5357982516288757},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5324358344078064},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3430887460708618},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29857784509658813},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2672762870788574}],"concepts":[{"id":"https://openalex.org/C207001950","wikidata":"https://www.wikidata.org/wiki/Q141124","display_name":"In vivo","level":2,"score":0.65229332447052},{"id":"https://openalex.org/C202751555","wikidata":"https://www.wikidata.org/wiki/Q221681","display_name":"In vitro","level":2,"score":0.5864076614379883},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5380856990814209},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5357982516288757},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5324358344078064},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3430887460708618},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29857784509658813},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2672762870788574}],"mesh":[{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx115","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx115","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/2097/25157171/btx115.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:28334224","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28334224","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:europepmc.org:4997744","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5870851","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx115","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx115","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/2097/25157171/btx115.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/G2665795143","display_name":null,"funder_award_id":"IIS-1218201, ABI-1565076","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6035731016","display_name":null,"funder_award_id":"G12MD007591","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2594735672.pdf","grobid_xml":"https://content.openalex.org/works/W2594735672.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W90131235","https://openalex.org/W1496114027","https://openalex.org/W1498410508","https://openalex.org/W1512098439","https://openalex.org/W1518026427","https://openalex.org/W1946852907","https://openalex.org/W1975036436","https://openalex.org/W1980946495","https://openalex.org/W1996359606","https://openalex.org/W2004857965","https://openalex.org/W2014677321","https://openalex.org/W2015622114","https://openalex.org/W2033169664","https://openalex.org/W2034145535","https://openalex.org/W2038282326","https://openalex.org/W2042392223","https://openalex.org/W2058517672","https://openalex.org/W2066688766","https://openalex.org/W2068438417","https://openalex.org/W2069985409","https://openalex.org/W2089967664","https://openalex.org/W2095791120","https://openalex.org/W2096139934","https://openalex.org/W2096173332","https://openalex.org/W2104865962","https://openalex.org/W2106393550","https://openalex.org/W2115272837","https://openalex.org/W2116467413","https://openalex.org/W2118891085","https://openalex.org/W2125055259","https://openalex.org/W2129422961","https://openalex.org/W2135993011","https://openalex.org/W2141351124","https://openalex.org/W2142410561","https://openalex.org/W2144710927","https://openalex.org/W2147946837","https://openalex.org/W2151040995","https://openalex.org/W2154318594","https://openalex.org/W2157121418","https://openalex.org/W2159324718","https://openalex.org/W2159451611","https://openalex.org/W2271571451","https://openalex.org/W2292949796","https://openalex.org/W2911964244","https://openalex.org/W2999905431","https://openalex.org/W6603603545","https://openalex.org/W6630527977","https://openalex.org/W6640496116","https://openalex.org/W6674613594","https://openalex.org/W6677514038","https://openalex.org/W6677540880","https://openalex.org/W6680104626","https://openalex.org/W6683033130"],"related_works":["https://openalex.org/W2138350991","https://openalex.org/W1566729005","https://openalex.org/W2409285845","https://openalex.org/W2434195791","https://openalex.org/W1994342570","https://openalex.org/W2562771455","https://openalex.org/W2054843986","https://openalex.org/W2116210813","https://openalex.org/W2440701365","https://openalex.org/W2433842723"],"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":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2017-03-16T00:00:00"}
