{"id":"https://openalex.org/W2165958610","doi":"https://doi.org/10.1093/bioinformatics/btn664","title":"Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery","display_name":"Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery","publication_year":2009,"publication_date":"2009-01-09","ids":{"openalex":"https://openalex.org/W2165958610","doi":"https://doi.org/10.1093/bioinformatics/btn664","mag":"2165958610","pmid":"https://pubmed.ncbi.nlm.nih.gov/19136552"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn664","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn664","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/4/443/48983228/bioinformatics_25_4_443.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/25/4/443/48983228/bioinformatics_25_4_443.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088993735","display_name":"Norman E. Davey","orcid":"https://orcid.org/0000-0001-6988-4850"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]}],"countries":["GB","IE"],"is_corresponding":true,"raw_author_name":"Norman E. Davey","raw_affiliation_strings":["1 UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland and 2School of Biological Sciences, University of Southampton, Boldrewood Campus, Southampton SO16 7PX, UK"],"affiliations":[{"raw_affiliation_string":"1 UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland and 2School of Biological Sciences, University of Southampton, Boldrewood Campus, Southampton SO16 7PX, UK","institution_ids":["https://openalex.org/I100930933","https://openalex.org/I43439940"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004065601","display_name":"Denis C. Shields","orcid":"https://orcid.org/0000-0003-4015-2474"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]}],"countries":["GB","IE"],"is_corresponding":false,"raw_author_name":"Denis C. Shields","raw_affiliation_strings":["1 UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland and 2School of Biological Sciences, University of Southampton, Boldrewood Campus, Southampton SO16 7PX, UK"],"affiliations":[{"raw_affiliation_string":"1 UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland and 2School of Biological Sciences, University of Southampton, Boldrewood Campus, Southampton SO16 7PX, UK","institution_ids":["https://openalex.org/I100930933","https://openalex.org/I43439940"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054268632","display_name":"Richard J. Edwards","orcid":"https://orcid.org/0000-0002-3645-5539"},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]},{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["GB","IE"],"is_corresponding":false,"raw_author_name":"Richard J. Edwards","raw_affiliation_strings":["1 UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland and 2School of Biological Sciences, University of Southampton, Boldrewood Campus, Southampton SO16 7PX, UK"],"affiliations":[{"raw_affiliation_string":"1 UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland and 2School of Biological Sciences, University of Southampton, Boldrewood Campus, Southampton SO16 7PX, UK","institution_ids":["https://openalex.org/I100930933","https://openalex.org/I43439940"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5088993735"],"corresponding_institution_ids":["https://openalex.org/I100930933","https://openalex.org/I43439940"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.7559,"has_fulltext":true,"cited_by_count":68,"citation_normalized_percentile":{"value":0.90825063,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"4","first_page":"443","last_page":"450"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9980999827384949,"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/conserved-sequence","display_name":"Conserved sequence","score":0.6575802564620972},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6457999348640442},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5908728241920471},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5757405757904053},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48250699043273926},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4101752042770386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3400399088859558},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3060804605484009},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.24527403712272644},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20246228575706482}],"concepts":[{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.6575802564620972},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6457999348640442},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5908728241920471},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5757405757904053},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48250699043273926},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4101752042770386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3400399088859558},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3060804605484009},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.24527403712272644},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20246228575706482},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn664","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn664","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/4/443/48983228/bioinformatics_25_4_443.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:19136552","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19136552","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:eprints.soton.ac.uk:143455","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401019","display_name":"ePrints Soton (University of Southampton)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn664","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn664","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/4/443/48983228/bioinformatics_25_4_443.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":[{"score":0.6700000166893005,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2165958610.pdf","grobid_xml":"https://content.openalex.org/works/W2165958610.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W121768123","https://openalex.org/W196004681","https://openalex.org/W1214546200","https://openalex.org/W1965582988","https://openalex.org/W1967293793","https://openalex.org/W1974703047","https://openalex.org/W1975121208","https://openalex.org/W1984164188","https://openalex.org/W1986751941","https://openalex.org/W1987200512","https://openalex.org/W2007016963","https://openalex.org/W2030779556","https://openalex.org/W2036511353","https://openalex.org/W2041449172","https://openalex.org/W2043816461","https://openalex.org/W2046407284","https://openalex.org/W2050284387","https://openalex.org/W2052033556","https://openalex.org/W2083259406","https://openalex.org/W2096988908","https://openalex.org/W2099111195","https://openalex.org/W2102956364","https://openalex.org/W2105788709","https://openalex.org/W2110371871","https://openalex.org/W2111909811","https://openalex.org/W2132926880","https://openalex.org/W2137239190","https://openalex.org/W2144252381","https://openalex.org/W2146950091","https://openalex.org/W2147610376","https://openalex.org/W2155657795","https://openalex.org/W2156407548","https://openalex.org/W2158714788","https://openalex.org/W2168514491","https://openalex.org/W2916288174","https://openalex.org/W4210580032","https://openalex.org/W6628147189"],"related_works":["https://openalex.org/W2770593030","https://openalex.org/W4281727072","https://openalex.org/W2560201613","https://openalex.org/W3154990682","https://openalex.org/W2171975302","https://openalex.org/W2022352247","https://openalex.org/W1532073221","https://openalex.org/W2377538627","https://openalex.org/W2107220315","https://openalex.org/W1996543580"],"abstract_inverted_index":{"All":[0],"data":[1],"and":[2],"tools":[3],"in":[4],"this":[5],"article":[6],"are":[7],"available":[8],"at":[9],"http://bioware.ucd.ie/~slimdisc/slimfinder/conmasking/.":[10]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}