{"id":"https://openalex.org/W2159247826","doi":"https://doi.org/10.1186/1471-2105-14-154","title":"Reconstituting protein interaction networks using parameter-dependent domain-domain interactions","display_name":"Reconstituting protein interaction networks using parameter-dependent domain-domain interactions","publication_year":2013,"publication_date":"2013-05-07","ids":{"openalex":"https://openalex.org/W2159247826","doi":"https://doi.org/10.1186/1471-2105-14-154","mag":"2159247826","pmid":"https://pubmed.ncbi.nlm.nih.gov/23651452"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-154","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-154","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-154","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-154","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004210800","display_name":"Vesna Memi\u0161evi\u0107","orcid":null},"institutions":[{"id":"https://openalex.org/I2800986571","display_name":"Telemedicine & Advanced Technology Research Center","ror":"https://ror.org/014pvr265","country_code":"US","type":"other","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2800986571","https://openalex.org/I2802581893"]},{"id":"https://openalex.org/I2802581893","display_name":"United States Army Medical Research and Development Command","ror":"https://ror.org/03cd02q50","country_code":"US","type":"facility","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vesna Memi\u0161evi\u0107","raw_affiliation_strings":["Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA","Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA","institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"]},{"raw_affiliation_string":"Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA","institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030271505","display_name":"Anders Wallqvist","orcid":"https://orcid.org/0000-0002-9775-7469"},"institutions":[{"id":"https://openalex.org/I2800986571","display_name":"Telemedicine & Advanced Technology Research Center","ror":"https://ror.org/014pvr265","country_code":"US","type":"other","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2800986571","https://openalex.org/I2802581893"]},{"id":"https://openalex.org/I2802581893","display_name":"United States Army Medical Research and Development Command","ror":"https://ror.org/03cd02q50","country_code":"US","type":"facility","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anders Wallqvist","raw_affiliation_strings":["Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA","institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020594190","display_name":"Jaques Reifman","orcid":"https://orcid.org/0000-0001-7292-2029"},"institutions":[{"id":"https://openalex.org/I2800986571","display_name":"Telemedicine & Advanced Technology Research Center","ror":"https://ror.org/014pvr265","country_code":"US","type":"other","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2800986571","https://openalex.org/I2802581893"]},{"id":"https://openalex.org/I2802581893","display_name":"United States Army Medical Research and Development Command","ror":"https://ror.org/03cd02q50","country_code":"US","type":"facility","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jaques Reifman","raw_affiliation_strings":["Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA","institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020594190"],"corresponding_institution_ids":["https://openalex.org/I2800986571","https://openalex.org/I2802581893"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.2381,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.79222368,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"14","issue":"1","first_page":"154","last_page":"154"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.991100013256073,"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":0.991100013256073,"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":0.0027000000700354576,"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":0.0013000000035390258,"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":0.7469667196273804},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.7222820520401001},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.7105058431625366},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6139777302742004},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5521032214164734},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.511022686958313},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4823564887046814},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.4642987847328186},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43745946884155273},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41925176978111267},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22999006509780884},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20637047290802002},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.12831911444664001},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12015831470489502},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10066491365432739}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7469667196273804},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.7222820520401001},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.7105058431625366},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6139777302742004},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5521032214164734},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.511022686958313},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4823564887046814},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.4642987847328186},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43745946884155273},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41925176978111267},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22999006509780884},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20637047290802002},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.12831911444664001},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12015831470489502},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10066491365432739},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-14-154","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-154","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-154","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23651452","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23651452","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2657523","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3660195","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-154","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-154","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-154","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320338280","display_name":"Medical Research and Materiel Command","ror":"https://ror.org/03cd02q50"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2159247826.pdf","grobid_xml":"https://content.openalex.org/works/W2159247826.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1559606743","https://openalex.org/W1879637501","https://openalex.org/W1973897761","https://openalex.org/W1977922844","https://openalex.org/W1986512768","https://openalex.org/W1988422871","https://openalex.org/W1993591356","https://openalex.org/W2002468235","https://openalex.org/W2008116827","https://openalex.org/W2014719716","https://openalex.org/W2016685368","https://openalex.org/W2023587449","https://openalex.org/W2037993016","https://openalex.org/W2045131140","https://openalex.org/W2060770414","https://openalex.org/W2067305633","https://openalex.org/W2077997913","https://openalex.org/W2080922074","https://openalex.org/W2085963663","https://openalex.org/W2090076432","https://openalex.org/W2099946731","https://openalex.org/W2101330776","https://openalex.org/W2104239076","https://openalex.org/W2109248504","https://openalex.org/W2109715166","https://openalex.org/W2109867978","https://openalex.org/W2112792893","https://openalex.org/W2113654464","https://openalex.org/W2114374137","https://openalex.org/W2116423958","https://openalex.org/W2117035344","https://openalex.org/W2117815893","https://openalex.org/W2122274181","https://openalex.org/W2130581715","https://openalex.org/W2131094547","https://openalex.org/W2141885858","https://openalex.org/W2143973712","https://openalex.org/W2145427519","https://openalex.org/W2146312020","https://openalex.org/W2151006472","https://openalex.org/W2153294290","https://openalex.org/W2157346087","https://openalex.org/W2160232999","https://openalex.org/W2161563546","https://openalex.org/W2161811112","https://openalex.org/W2168708357","https://openalex.org/W2753765968","https://openalex.org/W4210623056","https://openalex.org/W4242156070","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2045131140","https://openalex.org/W2010825547","https://openalex.org/W2095910716","https://openalex.org/W1980334039","https://openalex.org/W1973695911","https://openalex.org/W1970034234","https://openalex.org/W1993087844","https://openalex.org/W2107811186","https://openalex.org/W1987582651","https://openalex.org/W2027811431"],"abstract_inverted_index":{"BACKGROUND:":[0],"We":[1,93,119,216],"can":[2,180],"describe":[3],"protein-protein":[4],"interactions":[5,12,18,318,326],"(PPIs)":[6],"as":[7],"sets":[8],"of":[9,40,46,70,78,100,137,153,170,176,185,198,249,255,289,297,310,312,324],"distinct":[10],"domain-domain":[11],"(DDIs)":[13],"that":[14,24,38,121,179],"mediate":[15],"the":[16,36,76,98,134,149,182,252,287,290,295,305,308,313],"physical":[17],"between":[19],"proteins.":[20],"Experimental":[21],"data":[22,64,115,225],"confirm":[23],"DDIs":[25,41,210,250,272],"are":[26,336],"more":[27,207],"consistent":[28,232],"than":[29,211],"their":[30],"corresponding":[31],"PPIs,":[32,171],"lending":[33],"support":[34],"to":[35,50,97,111,143,148,190,221,244,263,285],"notion":[37],"analyses":[39],"may":[42],"improve":[43],"our":[44,203,266],"understanding":[45],"PPIs":[47,73,199,256],"and":[48,57,231,257,334],"lead":[49],"further":[51],"insights":[52],"into":[53],"cellular":[54],"function,":[55],"disease,":[56],"evolution.":[58],"However,":[59],"currently":[60],"available":[61],"experimental":[62],"DDI":[63,84,163],"cover":[65],"only":[66],"a":[67,90,107,158,168,173,196,219,242,246],"small":[68,174,247],"fraction":[69],"all":[71,329],"existing":[72,212,264],"and,":[74],"in":[75,261],"absence":[77],"structural":[79],"data,":[80],"determining":[81],"which":[82],"particular":[83],"mediates":[85],"any":[86,236],"given":[87,167,237,337],"PPI":[88],"is":[89],"challenge.":[91],"RESULTS:":[92],"present":[94],"two":[95,283],"contributions":[96],"field":[99],"domain":[101,113,126,177,223,233,325],"interaction":[102],"analysis.":[103],"First,":[104],"we":[105,123,132,156,240,258,280],"introduce":[106,157],"novel":[108,159],"computational":[109,160,213],"strategy":[110],"merge":[112,222],"annotation":[114,130,224,234,292],"from":[116,128,141,200,226,251],"multiple":[117,201,227],"databases.":[118],"show":[120],"when":[122],"merged":[124],"yeast":[125],"annotations":[127,302],"six":[129],"databases":[131],"increased":[133,301],"average":[135,151],"number":[136],"domains":[138],"per":[139],"protein":[140,186,330],"1.05":[142],"2.44,":[144],"bringing":[145],"it":[146],"closer":[147],"estimated":[150],"value":[152],"3.":[154],"Second,":[155],"method,":[161],"parameter-dependent":[162],"selection":[164],"(PADDS),":[165],"which,":[166],"set":[169,175,184,197,248,254],"extracts":[172],"pairs":[178],"reconstruct":[181],"original":[183],"interactions,":[187],"while":[188],"attempting":[189],"minimize":[191],"false":[192,316],"positives.":[193],"Based":[194],"on":[195,294],"organisms,":[202],"method":[204,220,243,267],"extracted":[205,298],"27%":[206],"experimentally":[208],"detected":[209],"approaches.":[214],"CONCLUSIONS:":[215],"have":[217],"provided":[218,241],"sources,":[228],"ensuring":[229],"large":[230],"for":[235,328],"organism.":[238],"Moreover,":[239],"extract":[245],"underlying":[253,291],"showed":[259],"that,":[260],"contrast":[262],"approaches,":[265],"was":[268],"not":[269],"biased":[270],"towards":[271],"with":[273],"low":[274],"or":[275],"high":[276],"occurrence":[277],"counts.":[278],"Finally,":[279],"used":[281],"these":[282],"methods":[284],"highlight":[286],"influence":[288],"density":[293],"characteristics":[296],"DDIs.":[299],"Although":[300],"greatly":[303],"expanded":[304],"possible":[306],"DDIs,":[307],"lack":[309],"knowledge":[311],"true":[314],"biological":[315],"positive":[317],"still":[319],"prevents":[320],"an":[321],"unambiguous":[322],"assignment":[323],"responsible":[327],"network":[331],"interactions.Executable":[332],"files":[333],"examples":[335],"at:":[338],"http://www.bhsai.org/downloads/padds/":[339]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
