{"id":"https://openalex.org/W2100918885","doi":"https://doi.org/10.1093/bioinformatics/btq360","title":"Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques","display_name":"Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques","publication_year":2010,"publication_date":"2010-07-07","ids":{"openalex":"https://openalex.org/W2100918885","doi":"https://doi.org/10.1093/bioinformatics/btq360","mag":"2100918885","pmid":"https://pubmed.ncbi.nlm.nih.gov/20610610"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq360","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq360","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/17/2116/48853991/bioinformatics_26_17_2116.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/26/17/2116/48853991/bioinformatics_26_17_2116.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058180202","display_name":"Rahul Satija","orcid":"https://orcid.org/0000-0002-1479-664X"},"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/I1336263701","display_name":"Centre for Human Genetics","ror":"https://ror.org/01rjnta51","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"R. Satija","raw_affiliation_strings":["1 Department of Statistics and 2Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Statistics and 2Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK","institution_ids":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079496228","display_name":"Jotun Hein","orcid":"https://orcid.org/0000-0002-8100-0824"},"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/I1336263701","display_name":"Centre for Human Genetics","ror":"https://ror.org/01rjnta51","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"J. Hein","raw_affiliation_strings":["1 Department of Statistics and 2Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Statistics and 2Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK","institution_ids":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062526316","display_name":"Gerton Lunter","orcid":"https://orcid.org/0000-0002-3798-2058"},"institutions":[{"id":"https://openalex.org/I1336263701","display_name":"Centre for Human Genetics","ror":"https://ror.org/01rjnta51","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]},{"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":"G. A. Lunter","raw_affiliation_strings":["1 Department of Statistics and 2Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Statistics and 2Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK","institution_ids":["https://openalex.org/I1336263701","https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5058180202"],"corresponding_institution_ids":["https://openalex.org/I1336263701","https://openalex.org/I40120149"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6777,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.69631783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"26","issue":"17","first_page":"2116","last_page":"2120"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10222","display_name":"Genomics and Chromatin Dynamics","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/T10521","display_name":"RNA and protein synthesis mechanisms","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"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8611308932304382},{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.7420469522476196},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.6976388692855835},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5770511031150818},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5763745307922363},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.564685583114624},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5045541524887085},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.4645412266254425},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4585196375846863},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4504868686199188},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.40632402896881104},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39836302399635315},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3962401747703552},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20432749390602112},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09517496824264526}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8611308932304382},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.7420469522476196},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6976388692855835},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5770511031150818},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5763745307922363},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.564685583114624},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5045541524887085},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.4645412266254425},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4585196375846863},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4504868686199188},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.40632402896881104},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39836302399635315},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3962401747703552},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20432749390602112},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09517496824264526},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018983","descriptor_name":"DNA Footprinting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018983","descriptor_name":"DNA Footprinting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018983","descriptor_name":"DNA Footprinting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018983","descriptor_name":"DNA Footprinting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq360","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq360","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/17/2116/48853991/bioinformatics_26_17_2116.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:20610610","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20610610","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:ora.ox.ac.uk:uuid:44c97612-ada4-419a-85d6-b3353b18f31f","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:44c97612-ada4-419a-85d6-b3353b18f31f","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PubMed (http://www.ncbi.nlm.nih.gov/pubmed/)","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq360","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq360","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/17/2116/48853991/bioinformatics_26_17_2116.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":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100918885.pdf","grobid_xml":"https://content.openalex.org/works/W2100918885.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1963590211","https://openalex.org/W1968256798","https://openalex.org/W1997631042","https://openalex.org/W1998745514","https://openalex.org/W2039665204","https://openalex.org/W2083201277","https://openalex.org/W2091656649","https://openalex.org/W2116790427","https://openalex.org/W2118533197","https://openalex.org/W2122820024","https://openalex.org/W2128482297","https://openalex.org/W2130325731","https://openalex.org/W2138245520","https://openalex.org/W2141395444","https://openalex.org/W2145191876","https://openalex.org/W2146974293","https://openalex.org/W2154412571","https://openalex.org/W2164863064","https://openalex.org/W2612812586","https://openalex.org/W3214380909","https://openalex.org/W4245668478","https://openalex.org/W4246084279","https://openalex.org/W6673263745"],"related_works":["https://openalex.org/W2014988381","https://openalex.org/W1989274210","https://openalex.org/W2001863853","https://openalex.org/W2144685629","https://openalex.org/W1884791383","https://openalex.org/W4281673842","https://openalex.org/W2142268426","https://openalex.org/W2024980748","https://openalex.org/W1834968294","https://openalex.org/W2100918885"],"abstract_inverted_index":{"The":[0],"GRAPeFoot":[1],"software":[2],"and":[3],"set":[4],"of":[5],"genome-wide":[6],"functional":[7],"element":[8],"predictions":[9],"are":[10],"freely":[11],"available":[12],"to":[13],"download":[14],"online":[15],"at":[16],"http://www.stats.ox.ac.uk/":[17],"approximately":[18],"satija/GRAPeFoot/.":[19]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
