{"id":"https://openalex.org/W4413412856","doi":"https://doi.org/10.1093/bib/bbaf432","title":"LncPTPred: predicting lncRNA\u2013protein interaction based on crosslinking and immunoprecipitation (CLIP-Seq) data","display_name":"LncPTPred: predicting lncRNA\u2013protein interaction based on crosslinking and immunoprecipitation (CLIP-Seq) data","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4413412856","doi":"https://doi.org/10.1093/bib/bbaf432","pmid":"https://pubmed.ncbi.nlm.nih.gov/40838786"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf432","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf432/64100863/bbaf432.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf432/64100863/bbaf432.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102768753","display_name":"Gourab Das","orcid":"https://orcid.org/0009-0002-1205-6530"},"institutions":[{"id":"https://openalex.org/I152754861","display_name":"Bose Institute","ror":"https://ror.org/01a5mqy88","country_code":"IN","type":"facility","lineage":["https://openalex.org/I152754861"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Gourab Das","raw_affiliation_strings":["Department of Biological Sciences, Bose Institute , Unified Academic Campus, Kolkata 700 091, West Bengal ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Bose Institute , Unified Academic Campus, Kolkata 700 091, West Bengal ,","institution_ids":["https://openalex.org/I152754861"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049350672","display_name":"Troyee Das","orcid":"https://orcid.org/0000-0002-0774-7022"},"institutions":[{"id":"https://openalex.org/I152754861","display_name":"Bose Institute","ror":"https://ror.org/01a5mqy88","country_code":"IN","type":"facility","lineage":["https://openalex.org/I152754861"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Troyee Das","raw_affiliation_strings":["Department of Biological Sciences, Bose Institute , Unified Academic Campus, Kolkata 700 091, West Bengal ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Bose Institute , Unified Academic Campus, Kolkata 700 091, West Bengal ,","institution_ids":["https://openalex.org/I152754861"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045445946","display_name":"Zhumur Ghosh","orcid":null},"institutions":[{"id":"https://openalex.org/I152754861","display_name":"Bose Institute","ror":"https://ror.org/01a5mqy88","country_code":"IN","type":"facility","lineage":["https://openalex.org/I152754861"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Zhumur Ghosh","raw_affiliation_strings":["Department of Biological Sciences, Bose Institute , Unified Academic Campus, Kolkata 700 091, West Bengal ,"],"raw_orcid":"https://orcid.org/0000-0002-4877-7551","affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Bose Institute , Unified Academic Campus, Kolkata 700 091, West Bengal ,","institution_ids":["https://openalex.org/I152754861"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102768753"],"corresponding_institution_ids":["https://openalex.org/I152754861"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.7827,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.76022013,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"26","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10604","display_name":"RNA Research and Splicing","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/T11482","display_name":"RNA modifications and cancer","score":0.9979000091552734,"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":0.8329378366470337},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5800087451934814},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5343486666679382},{"id":"https://openalex.org/keywords/immunoprecipitation","display_name":"Immunoprecipitation","score":0.5212072134017944},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4946689307689667},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4534884989261627},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44918522238731384},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.1157437264919281},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.104277104139328},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0955541729927063}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8329378366470337},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5800087451934814},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5343486666679382},{"id":"https://openalex.org/C71829478","wikidata":"https://www.wikidata.org/wiki/Q901305","display_name":"Immunoprecipitation","level":3,"score":0.5212072134017944},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4946689307689667},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4534884989261627},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44918522238731384},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.1157437264919281},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.104277104139328},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0955541729927063},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D047468","descriptor_name":"Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047468","descriptor_name":"Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf432","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf432/64100863/bbaf432.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40838786","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40838786","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12368852","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12368852","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf432","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf432/64100863/bbaf432.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4587460391","display_name":null,"funder_award_id":"RBMH/FW/2020/10","funder_id":"https://openalex.org/F4320320720","funder_display_name":"Indian Council of Medical Research"}],"funders":[{"id":"https://openalex.org/F4320320720","display_name":"Indian Council of Medical Research","ror":"https://ror.org/0492wrx28"},{"id":"https://openalex.org/F4320327938","display_name":"Indian Statistical Institute","ror":"https://ror.org/00q2w1j53"},{"id":"https://openalex.org/F4320329061","display_name":"Bose Institute","ror":"https://ror.org/01a5mqy88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413412856.pdf","grobid_xml":"https://content.openalex.org/works/W4413412856.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1975304761","https://openalex.org/W2001619934","https://openalex.org/W2008468705","https://openalex.org/W2019217933","https://openalex.org/W2020746805","https://openalex.org/W2025150647","https://openalex.org/W2038413819","https://openalex.org/W2038438413","https://openalex.org/W2044117548","https://openalex.org/W2049631297","https://openalex.org/W2052938279","https://openalex.org/W2053003053","https://openalex.org/W2064515831","https://openalex.org/W2072394638","https://openalex.org/W2086561953","https://openalex.org/W2101071606","https://openalex.org/W2103375140","https://openalex.org/W2103683291","https://openalex.org/W2119501676","https://openalex.org/W2131241448","https://openalex.org/W2160697532","https://openalex.org/W2245239316","https://openalex.org/W2291340556","https://openalex.org/W2507804718","https://openalex.org/W2519231134","https://openalex.org/W2523076424","https://openalex.org/W2539087954","https://openalex.org/W2794896638","https://openalex.org/W2912083425","https://openalex.org/W2921372942","https://openalex.org/W2971759641","https://openalex.org/W2995997429","https://openalex.org/W3003593479","https://openalex.org/W3028467496","https://openalex.org/W3036197410","https://openalex.org/W3046003662","https://openalex.org/W3094758468","https://openalex.org/W3134329288","https://openalex.org/W3163379025","https://openalex.org/W3193881848","https://openalex.org/W3217643826","https://openalex.org/W4205247356","https://openalex.org/W4205705151","https://openalex.org/W4206995041","https://openalex.org/W4386209142","https://openalex.org/W6678911119","https://openalex.org/W6750010280"],"related_works":["https://openalex.org/W1976739589","https://openalex.org/W7949606","https://openalex.org/W2526890363","https://openalex.org/W121381176","https://openalex.org/W2000239818","https://openalex.org/W3129816939","https://openalex.org/W626095004","https://openalex.org/W2081832690","https://openalex.org/W150314098","https://openalex.org/W2912862995"],"abstract_inverted_index":{"Long":[0],"noncoding":[1],"RNA":[2],"(lncRNA)-protein":[3],"Interaction":[4],"(LPI)":[5],"across":[6],"diverse":[7],"biological":[8],"systems,":[9],"directly":[10],"and":[11,30,76,100],"indirectly,":[12],"regulates":[13],"various":[14],"cellular":[15],"processes.":[16],"Experimental":[17],"assays":[18],"to":[19,44,86,111,127],"recognize":[20],"the":[21,48,58,68,97,101,117,134,138,147,152,161,165],"protein":[22],"binding":[23],"partners":[24],"of":[25,70,92,119,129,140,149,164,176],"lncRNAs":[26],"are":[27],"highly":[28],"time-consuming":[29],"expensive.":[31],"In":[32],"silico":[33],"predictive":[34],"approaches":[35],"involving":[36],"pattern":[37],"recognition":[38],"techniques":[39],"provide":[40],"a":[41,72,79,158,177,183],"promising":[42],"alternative":[43],"it":[45,144],"by":[46],"reducing":[47],"search":[49],"space.":[50],"Our":[51],"work":[52,94],"identifies":[53],"such":[54],"hidden":[55],"patterns":[56],"within":[57,151],"cross-linking":[59],"immunoprecipitation":[60],"sequencing":[61],"(CLIP-Seq)":[62],"data,":[63],"which":[64,155],"aid":[65],"in":[66,174],"overcoming":[67],"problem":[69],"obtaining":[71],"real":[73],"negative":[74],"dataset":[75],"thus":[77],"offer":[78],"state-of-the-art":[80],"machine":[81],"learning":[82],"(ML)-based":[83],"prediction":[84,113,131],"algorithm":[85],"predict":[87],"LPI.":[88],"The":[89,168],"initial":[90],"phase":[91,103],"this":[93],"involves":[95],"preparing":[96],"training":[98],"dataset,":[99],"next":[102],"is":[104],"devoted":[105],"towards":[106],"developing":[107],"an":[108],"ML-based":[109],"model":[110],"perform":[112],"operations.":[114],"To":[115],"demonstrate":[116],"efficacy":[118],"our":[120,141],"model,":[121],"its":[122],"performance":[123],"has":[124,171],"been":[125,172],"compared":[126],"that":[128],"contemporary":[130],"tools,":[132],"with":[133],"result":[135],"clearly":[136],"showing":[137],"outperformance":[139],"model.":[142],"Moreover,":[143],"also":[145],"provides":[146],"segments":[148],"interaction":[150],"lncRNA":[153],"loci,":[154],"act":[156],"as":[157,180,182],"roadmap":[159],"for":[160],"precise":[162],"design":[163],"validation":[166],"experiment.":[167],"LncPTPred":[169],"tool":[170],"provided":[173],"terms":[175],"web":[178],"server":[179,189],"well":[181],"standalone":[184],"version":[185],"on":[186],"GitHub.":[187],"Web":[188],"Link:":[190,193],"http://bicresources.jcbose.ac.in/zhumur/lncptpred/.":[191],"Github":[192],"https://github.com/zglabDIB/lncptpred.git.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-12T08:28:47.272897","created_date":"2025-10-10T00:00:00"}
