{"id":"https://openalex.org/W2620714699","doi":"https://doi.org/10.1109/tcbb.2017.2710129","title":"Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks","display_name":"Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks","publication_year":2017,"publication_date":"2017-05-31","ids":{"openalex":"https://openalex.org/W2620714699","doi":"https://doi.org/10.1109/tcbb.2017.2710129","mag":"2620714699","pmid":"https://pubmed.ncbi.nlm.nih.gov/30102599"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2017.2710129","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2017.2710129","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5097388117","display_name":"Md Abdul Alim","orcid":"https://orcid.org/0000-0002-8453-0871"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Md Abdul Alim","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL"],"raw_orcid":"https://orcid.org/0000-0002-8453-0871","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033580922","display_name":"Ahmet Ay","orcid":"https://orcid.org/0000-0002-0726-5461"},"institutions":[{"id":"https://openalex.org/I39660569","display_name":"Colgate University","ror":"https://ror.org/05d23ve83","country_code":"US","type":"education","lineage":["https://openalex.org/I39660569"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ahmet Ay","raw_affiliation_strings":["Department of Biology and Mathematics, Colgate University, Hamilton, NY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology and Mathematics, Colgate University, Hamilton, NY","institution_ids":["https://openalex.org/I39660569"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100326701","display_name":"Md Mahmudul Hasan","orcid":"https://orcid.org/0000-0002-2061-6641"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Md Mahmudul Hasan","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005663679","display_name":"My T. Thai","orcid":"https://orcid.org/0000-0003-0503-2012"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"My T. Thai","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL"],"raw_orcid":"https://orcid.org/0000-0003-0503-2012","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091769289","display_name":"Tamer Kahveci","orcid":"https://orcid.org/0000-0002-4403-8612"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tamer Kahveci","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL"],"raw_orcid":"https://orcid.org/0000-0002-4403-8612","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5097388117"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":0.1123,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.50118597,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"15","issue":"4","first_page":"1079","last_page":"1091"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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/T10885","display_name":"Gene expression and cancer classification","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"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.7285655736923218},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.65155428647995},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6131390333175659},{"id":"https://openalex.org/keywords/gene-knockdown","display_name":"Gene knockdown","score":0.4960845410823822},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.4730462431907654},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46922311186790466},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.37709322571754456},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2769268751144409},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.2690931558609009},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23631566762924194},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12052309513092041},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.09133276343345642}],"concepts":[{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.7285655736923218},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.65155428647995},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6131390333175659},{"id":"https://openalex.org/C173396325","wikidata":"https://www.wikidata.org/wiki/Q1501275","display_name":"Gene knockdown","level":3,"score":0.4960845410823822},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.4730462431907654},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46922311186790466},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.37709322571754456},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2769268751144409},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.2690931558609009},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23631566762924194},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12052309513092041},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.09133276343345642},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"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":"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2017.2710129","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2017.2710129","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30102599","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30102599","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1499476884","https://openalex.org/W1546639740","https://openalex.org/W1588133965","https://openalex.org/W1647075334","https://openalex.org/W1969941684","https://openalex.org/W1972129511","https://openalex.org/W1974482866","https://openalex.org/W1976441097","https://openalex.org/W1984222668","https://openalex.org/W1989129192","https://openalex.org/W1992361007","https://openalex.org/W1996405087","https://openalex.org/W1999922265","https://openalex.org/W2003652380","https://openalex.org/W2006339308","https://openalex.org/W2024027099","https://openalex.org/W2027439534","https://openalex.org/W2036454804","https://openalex.org/W2038863154","https://openalex.org/W2042629507","https://openalex.org/W2046675213","https://openalex.org/W2053087839","https://openalex.org/W2055173338","https://openalex.org/W2055396579","https://openalex.org/W2061505806","https://openalex.org/W2066060839","https://openalex.org/W2066113694","https://openalex.org/W2067803871","https://openalex.org/W2096182373","https://openalex.org/W2102526951","https://openalex.org/W2106882534","https://openalex.org/W2119740363","https://openalex.org/W2124637492","https://openalex.org/W2137412574","https://openalex.org/W2137896695","https://openalex.org/W2145848202","https://openalex.org/W2146812359","https://openalex.org/W2161623098","https://openalex.org/W2197611285","https://openalex.org/W2494863456","https://openalex.org/W4233359534","https://openalex.org/W4294216483","https://openalex.org/W6629754406","https://openalex.org/W6687530929","https://openalex.org/W7007883154"],"related_works":["https://openalex.org/W4391126805","https://openalex.org/W2093213574","https://openalex.org/W2076785949","https://openalex.org/W2129321041","https://openalex.org/W2167306613","https://openalex.org/W1963563485","https://openalex.org/W2810831330","https://openalex.org/W1974857950","https://openalex.org/W3132602097","https://openalex.org/W1982914007"],"abstract_inverted_index":{"Signaling":[0],"networks":[1,20,46,60,82,136,190,222,275],"are":[2,105,117,174,276],"involved":[3,43],"in":[4,44,57,170,258],"almost":[5],"all":[6],"major":[7],"diseases":[8],"such":[9,35],"as":[10,36,68,92,157],"cancer.":[11],"As":[12],"a":[13,129,193],"result":[14],"of":[15,80,144,162,223,225,231,260,279],"this,":[16],"understanding":[17],"how":[18],"signaling":[19,59,81,135,147,208,221,287],"function":[21,268],"is":[22,65,72,155],"vital":[23],"for":[24,28],"finding":[25,158],"new":[26,206],"treatments":[27],"many":[29,41],"diseases.":[30],"Using":[31],"gene":[32],"knockdown":[33,200],"assays":[34],"RNA":[37],"interference":[38],"(RNAi)":[39],"technology,":[40],"genes":[42,56],"these":[45,55,232],"can":[47,300],"be":[48,301],"identified.":[49],"However,":[50,101],"determining":[51],"the":[52,58,102,142,145,152,159,181,188,198,229,235,252,283,290],"interactions":[53,293,298],"between":[54],"using":[61,86],"only":[62],"experimental":[63],"techniques":[64,88],"very":[66,73],"challenging,":[67],"performing":[69],"extensive":[70],"experiments":[71],"expensive":[74],"and":[75,137,216,245,285,294],"sometimes,":[76],"even":[77,270],"impractical.":[78],"Construction":[79],"from":[83],"RNAi":[84,125,199],"data":[85,126],"computational":[87],"have":[89],"been":[90],"proposed":[91,253],"an":[93],"alternative":[94],"way":[95],"to":[96,109,140,180,192,219,234,282],"solve":[97],"this":[98,121],"challenging":[99],"problem.":[100],"earlier":[103],"approaches":[104,233],"either":[106],"not":[107,118],"scalable":[108],"large":[110],"scale":[111,217],"networks,":[112,169],"or":[113],"their":[114,172,177],"accuracy":[115],"levels":[116],"satisfactory.":[119],"In":[120,149],"study,":[122],"we":[123,203,263],"integrate":[124],"given":[127,166],"on":[128,165,187,242],"target":[130,146,182,194],"network":[131,153,195,209,238],"with":[132],"multiple":[133,167],"reference":[134,168,189,274],"phylogenetic":[138,178],"trees":[139],"construct":[141],"topology":[143],"network.":[148,183],"our":[150,266,280],"work,":[151],"construction":[154,210,239],"considered":[156],"minimum":[160],"number":[161],"edit":[163,185],"operations":[164,186],"which":[171],"contributions":[173],"weighted":[175],"by":[176],"distances":[179],"The":[184],"lead":[191],"that":[196,212,251,265,299],"satisfies":[197],"observations.":[201],"Here,":[202],"propose":[204],"two":[205],"reference-based":[207,237],"methods":[211,254,267,281],"provide":[213],"optimal":[214],"results":[215],"well":[218,269],"large-scale":[220],"hundreds":[224],"components.":[226],"We":[227],"compare":[228],"performance":[230],"state-of-the-art":[236],"method":[240,257],"SiNeC":[241,256],"synthetic,":[243],"semi-synthetic,":[244],"real":[246],"datasets.":[247],"Our":[248],"analyses":[249],"show":[250,264],"outperform":[255],"terms":[259],"accuracy.":[261],"Furthermore,":[262],"if":[271],"evolutionarily":[272],"distant":[273],"used.":[277],"Application":[278],"Apoptosis":[284],"Wnt":[286],"pathways":[288],"recovers":[289],"known":[291],"protein-protein":[292],"suggests":[295],"additional":[296],"relevant":[297],"tested":[302],"experimentally.":[303]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
