{"id":"https://openalex.org/W2158559404","doi":"https://doi.org/10.1093/bioinformatics/btm576","title":"An assessment of the uses of homologous interactions","display_name":"An assessment of the uses of homologous interactions","publication_year":2007,"publication_date":"2007-11-27","ids":{"openalex":"https://openalex.org/W2158559404","doi":"https://doi.org/10.1093/bioinformatics/btm576","mag":"2158559404","pmid":"https://pubmed.ncbi.nlm.nih.gov/18042554"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm576","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm576","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/689/16885251/btm576.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/24/5/689/16885251/btm576.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005669639","display_name":"Ramazan Saeed","orcid":null},"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":true,"raw_author_name":"Ramazan Saeed","raw_affiliation_strings":["Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","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 Deane","raw_affiliation_strings":["Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5005669639"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.9064,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.85652537,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"24","issue":"5","first_page":"689","last_page":"695"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9616000056266785,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9616000056266785,"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":0.013799999840557575,"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":0.006500000134110451,"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/computer-science","display_name":"Computer science","score":0.5949362516403198},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.5653767585754395},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39498990774154663},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19973403215408325},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19054272770881653},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06343913078308105}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5949362516403198},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.5653767585754395},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39498990774154663},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19973403215408325},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19054272770881653},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06343913078308105}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btm576","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm576","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/689/16885251/btm576.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:18042554","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18042554","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":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.560.12","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.560.12","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2007/11/27/bioinformatics.btm576.full.pdf","raw_type":"text"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:16491068-20d9-42be-b870-9391c020f510","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:16491068-20d9-42be-b870-9391c020f510","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/btm576","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm576","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/689/16885251/btm576.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":0.44999998807907104}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2158559404.pdf","grobid_xml":"https://content.openalex.org/works/W2158559404.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1486817521","https://openalex.org/W1513501940","https://openalex.org/W1771060896","https://openalex.org/W1918391659","https://openalex.org/W1967638691","https://openalex.org/W1976952616","https://openalex.org/W1989034333","https://openalex.org/W2027439534","https://openalex.org/W2037036397","https://openalex.org/W2042613054","https://openalex.org/W2045131140","https://openalex.org/W2057993196","https://openalex.org/W2065304353","https://openalex.org/W2071062657","https://openalex.org/W2079818352","https://openalex.org/W2084619201","https://openalex.org/W2099913238","https://openalex.org/W2103017472","https://openalex.org/W2104315543","https://openalex.org/W2106336008","https://openalex.org/W2112947018","https://openalex.org/W2113019448","https://openalex.org/W2113654464","https://openalex.org/W2123500593","https://openalex.org/W2124354935","https://openalex.org/W2127637605","https://openalex.org/W2130687290","https://openalex.org/W2132666556","https://openalex.org/W2133548874","https://openalex.org/W2136280642","https://openalex.org/W2136957665","https://openalex.org/W2144344817","https://openalex.org/W2147774652","https://openalex.org/W2149310258","https://openalex.org/W2154662648","https://openalex.org/W2158714788","https://openalex.org/W2163736554","https://openalex.org/W2166020074","https://openalex.org/W2167869241","https://openalex.org/W2168708357","https://openalex.org/W2170778160","https://openalex.org/W2172049947","https://openalex.org/W4238742598","https://openalex.org/W4239029175","https://openalex.org/W6657524342","https://openalex.org/W6680534649","https://openalex.org/W6681875201"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein-protein":[1],"interactions":[2,27,60,183,212,273],"have":[3,21,100],"proved":[4],"to":[5,34,165],"be":[6,291],"a":[7,162,170,185,264],"valuable":[8],"starting":[9],"point":[10],"for":[11,92,130,142,181,204,256,285],"understanding":[12],"the":[13,17,56,109,112,118,125,146,167,177,195,275,287],"inner":[14],"workings":[15],"of":[16,58,96,111,120,128,148,169,187,210,247,266,271],"cell.":[18],"Computational":[19],"methodologies":[20],"been":[22],"built":[23,233],"which":[24,97],"both":[25],"predict":[26,35],"and":[28,46,54,66,84,133,144,159,216,269,282],"use":[29,119,147],"interaction":[30,49,68,74,83,131,140,172,278],"datasets":[31,122,284],"in":[32,61,245],"order":[33],"other":[36,152],"protein":[37,153,267],"features.":[38],"Such":[39],"methods":[40],"require":[41],"gold":[42],"standard":[43,243],"positive":[44,65],"(GSP)":[45],"negative":[47,67,171,182],"(GSN)":[48],"sets.":[50,279],"Here":[51],"we":[52,137,174,217,262],"examine":[53,145],"demonstrate":[55,218],"usefulness":[57],"homologous":[59,211,236,272],"predicting":[62],"good":[63],"quality":[64,277],"datasets.":[69],"RESULTS:":[70],"We":[71,87,114,250],"generate":[72,138],"GSP":[73,231,254,281],"sets":[75,91,141,232,244,255],"as":[76,156],"subsets":[77],"from":[78,293],"experimental":[79],"data":[80],"using":[81,193,234],"only":[82],"sequence":[85],"information.":[86],"can":[88,251,290],"therefore":[89],"produce":[90],"several":[93,257],"species":[94,226,289],"(many":[95],"at":[98],"present":[99],"no":[101],"identified":[102],"GSPs).":[103],"Comprehensive":[104],"error":[105],"rate":[106],"testing":[107],"demonstrates":[108],"power":[110,127],"method.":[113],"also":[115,214],"show":[116,263],"how":[117],"our":[121,235],"significantly":[123],"improves":[124],"predictive":[126,248],"algorithms":[129],"prediction":[132],"function":[134],"prediction.":[135],"Furthermore,":[136],"GSN":[139,206,283],"yeast":[143],"homology":[149],"along":[150],"with":[151],"properties":[154],"such":[155,253],"localization,":[157],"expression":[158],"function.":[160],"Using":[161],"novel":[163],"method":[164,192,203,238],"assess":[166],"accuracy":[168],"set,":[173],"find":[175],"that":[176,219],"best":[178],"single":[179],"selector":[180],"is":[184,213],"lack":[186,270],"co-function.":[188],"However,":[189],"an":[190],"integrated":[191],"all":[194,286],"characteristics":[196],"shows":[197],"significant":[198],"improvement":[199],"over":[200],"any":[201],"current":[202],"identifying":[205],"interactions.":[207],"The":[208],"nature":[209],"examined":[215],"interologs":[220],"are":[221,239],"found":[222],"more":[223],"commonly":[224],"within":[225],"than":[227,242],"across":[228],"species.":[229,258],"CONCLUSION:":[230],"verification":[237],"demonstrably":[240],"better":[241],"terms":[246],"ability.":[249],"build":[252],"When":[259],"generating":[260],"GSNs":[261],"combination":[265],"features":[268],"gives":[274],"highest":[276],"AVAILABILITY:":[280],"studied":[288],"downloaded":[292],"http://www.stats.ox.ac.uk/~deane/HPIV.":[294]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":5}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
