{"id":"https://openalex.org/W2147330086","doi":"https://doi.org/10.1093/bioinformatics/btt208","title":"Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding","display_name":"Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding","publication_year":2013,"publication_date":"2013-06-19","ids":{"openalex":"https://openalex.org/W2147330086","doi":"https://doi.org/10.1093/bioinformatics/btt208","mag":"2147330086","pmid":"https://pubmed.ncbi.nlm.nih.gov/23812985"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt208","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt208","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i199/50702379/bioinformatics_29_13_i199.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i199/50702379/bioinformatics_29_13_i199.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007730744","display_name":"Carlo Vittorio Cannistraci","orcid":"https://orcid.org/0000-0003-0100-8410"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Carlo Vittorio Cannistraci","raw_affiliation_strings":["Integrative Systems Biology Laboratory, Biological and Environmental Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia. kalokagathos.agon@gmail.com","Integrative Systems Biology Laboratory, Biological and Environmental Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Integrative Systems Biology Laboratory, Biological and Environmental Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia. kalokagathos.agon@gmail.com","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Integrative Systems Biology Laboratory, Biological and Environmental Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027888740","display_name":"Gregorio Alanis\u2010Lobato","orcid":"https://orcid.org/0000-0001-9339-4229"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Gregorio Alanis-Lobato","raw_affiliation_strings":["King Abdullah University of Science and Technology, Jeddah, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Jeddah, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009690319","display_name":"Timothy Ravasi","orcid":"https://orcid.org/0000-0002-9950-465X"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Timothy Ravasi","raw_affiliation_strings":["King Abdullah University of Science and Technology, Jeddah, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Jeddah, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.0148,"has_fulltext":false,"cited_by_count":128,"citation_normalized_percentile":{"value":0.96210159,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"29","issue":"13","first_page":"i199","last_page":"i209"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9620000123977661,"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":0.9620000123977661,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.009499999694526196,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.005100000184029341,"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/embedding","display_name":"Embedding","score":0.6889944672584534},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5062898397445679},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.47647377848625183},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.42453616857528687},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.29547446966171265},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18335333466529846},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.13123184442520142},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.1049090325832367}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6889944672584534},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5062898397445679},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.47647377848625183},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.42453616857528687},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.29547446966171265},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18335333466529846},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.13123184442520142},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.1049090325832367}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btt208","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt208","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i199/50702379/bioinformatics_29_13_i199.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23812985","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23812985","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:2688190","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3694668","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3694668","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3694668","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:repository.kaust.edu.sa:10754/325437","is_oa":true,"landing_page_url":"http://hdl.handle.net/10754/325437","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt208","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt208","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i199/50702379/bioinformatics_29_13_i199.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2147330086.pdf"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W1533120515","https://openalex.org/W1647729745","https://openalex.org/W1659833910","https://openalex.org/W1883660207","https://openalex.org/W1956694423","https://openalex.org/W1965680834","https://openalex.org/W1993229737","https://openalex.org/W2001141328","https://openalex.org/W2008620264","https://openalex.org/W2019963189","https://openalex.org/W2022980325","https://openalex.org/W2037933327","https://openalex.org/W2043469923","https://openalex.org/W2043508111","https://openalex.org/W2045729458","https://openalex.org/W2045843285","https://openalex.org/W2049240645","https://openalex.org/W2050583899","https://openalex.org/W2057545775","https://openalex.org/W2060079687","https://openalex.org/W2066506515","https://openalex.org/W2066692087","https://openalex.org/W2076022280","https://openalex.org/W2077293181","https://openalex.org/W2084809122","https://openalex.org/W2099862356","https://openalex.org/W2099913238","https://openalex.org/W2100761975","https://openalex.org/W2101420429","https://openalex.org/W2107710781","https://openalex.org/W2112090702","https://openalex.org/W2115465732","https://openalex.org/W2128049108","https://openalex.org/W2133465414","https://openalex.org/W2134312057","https://openalex.org/W2135132400","https://openalex.org/W2135526239","https://openalex.org/W2139556877","https://openalex.org/W2140221871","https://openalex.org/W2140280811","https://openalex.org/W2144344817","https://openalex.org/W2147370995","https://openalex.org/W2148762636","https://openalex.org/W2155004936","https://openalex.org/W2157444450","https://openalex.org/W2158217645","https://openalex.org/W2162730790","https://openalex.org/W2163736554","https://openalex.org/W2168708357","https://openalex.org/W2187089797","https://openalex.org/W2496323672","https://openalex.org/W2770983033","https://openalex.org/W2953332543","https://openalex.org/W3008070742","https://openalex.org/W3099514962","https://openalex.org/W3143219376","https://openalex.org/W6639546282","https://openalex.org/W6680351982","https://openalex.org/W6680590460","https://openalex.org/W6683161245"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2081900870","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/W4391913857","https://openalex.org/W2350741829"],"abstract_inverted_index":{"MOTIVATION:":[0],"Most":[1],"functions":[2],"within":[3],"the":[4,55,101,131,167,171,191,197,217,222],"cell":[5],"emerge":[6],"thanks":[7],"to":[8,72,104,108,190],"protein-protein":[9],"interactions":[10,32],"(PPIs),":[11],"yet":[12],"experimental":[13],"determination":[14],"of":[15,27,119,193,200,262],"PPIs":[16,237],"is":[17,39,47,181,208,214],"both":[18],"expensive":[19],"and":[20,29,94,135,152,157,211,226,260],"time-consuming.":[21],"PPI":[22],"networks":[23,195],"present":[24],"significant":[25],"levels":[26],"noise":[28],"incompleteness.":[30],"Predicting":[31],"using":[33],"only":[34],"PPI-network":[35],"topology":[36],"(topological":[37],"prediction)":[38],"difficult":[40],"but":[41],"essential":[42],"when":[43],"prior":[44],"biological":[45,210],"knowledge":[46],"absent":[48],"or":[49,246],"unreliable.":[50],"METHODS:":[51],"Network":[52],"embedding":[53,92,133,155,192],"emphasizes":[54],"relations":[56],"between":[57],"network":[58,81,224],"proteins":[59],"embedded":[60],"in":[61,65,100,174,216,243,249],"a":[62,115,182],"low-dimensional":[63],"space,":[64],"which":[66,83],"protein":[67,194,223,233],"pairs":[68],"that":[69,186,209],"are":[70,272],"closer":[71],"each":[73],"other":[74],"represent":[75,238],"good":[76,239],"candidate":[77,109],"interactions.":[78,110],"To":[79],"achieve":[80],"denoising,":[82],"boosts":[84],"prediction":[85,199,261],"performance,":[86],"we":[87,112,187],"first":[88],"applied":[89,189],"minimum":[90],"curvilinear":[91],"(MCE),":[93],"then":[95],"adopted":[96],"shortest":[97],"path":[98],"(SP)":[99],"reduced":[102],"space":[103],"assign":[105],"likelihood":[106],"scores":[107],"Furthermore,":[111],"introduce":[113],"(i)":[114],"new":[116,138,232],"valid":[117],"variation":[118],"MCE,":[120],"named":[121],"non-centred":[122],"MCE":[123],"(ncMCE);":[124],"(ii)":[125],"two":[126,137],"automatic":[127],"strategies":[128],"for":[129,141,196,205,230,241,247,257],"selecting":[130],"appropriate":[132],"dimension;":[134],"(iii)":[136],"randomized":[139],"procedures":[140],"evaluating":[142],"predictions.":[143],"RESULTS:":[144],"We":[145],"compared":[146],"our":[147,206],"method":[148],"against":[149],"several":[150],"unsupervised":[151,198],"supervisedly":[153],"tuned":[154],"approaches":[156],"node":[158],"neighbourhood":[159],"techniques.":[160],"Despite":[161],"its":[162],"computational":[163],"simplicity,":[164],"ncMCE-SP":[165],"was":[166],"overall":[168],"leader,":[169],"outperforming":[170],"current":[172],"methods":[173],"topological":[175],"link":[176],"prediction.":[177],"CONCLUSION:":[178],"Minimum":[179],"curvilinearity":[180],"valuable":[183],"non-linear":[184,218],"framework":[185],"successfully":[188],"novel":[201],"PPIs.":[202],"The":[203,235],"rationale":[204],"approach":[207],"evolutionary":[212],"information":[213],"imprinted":[215],"patterns":[219],"hidden":[220],"behind":[221],"topology,":[225],"can":[227],"be":[228],"exploited":[229],"predicting":[231],"links.":[234],"predicted":[236],"candidates":[240],"testing":[242],"high-throughput":[244],"experiments":[245],"exploitation":[248],"systems":[250],"biology":[251],"tools":[252],"such":[253],"as":[254],"those":[255],"used":[256],"network-based":[258],"inference":[259],"disease-related":[263],"functional":[264],"modules.":[265],"AVAILABILITY:":[266],"https://sites.google.com/site/carlovittoriocannistraci/home.":[267],"SUPPLEMENTARY":[268],"INFORMATION:":[269],"Supplementary":[270],"data":[271],"available":[273],"at":[274],"Bioinformatics":[275],"online.":[276]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":19},{"year":2017,"cited_by_count":15},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}
