{"id":"https://openalex.org/W2135500958","doi":"https://doi.org/10.1142/s0219720014500267","title":"Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts","display_name":"Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts","publication_year":2014,"publication_date":"2014-08-20","ids":{"openalex":"https://openalex.org/W2135500958","doi":"https://doi.org/10.1142/s0219720014500267","mag":"2135500958","pmid":"https://pubmed.ncbi.nlm.nih.gov/25245144"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720014500267","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720014500267","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5039299193","display_name":"Harshal Inamdar","orcid":null},"institutions":[{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]},{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Harshal Inamdar","raw_affiliation_strings":["Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune 411007, India"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune 411007, India","institution_ids":["https://openalex.org/I878213199","https://openalex.org/I1331500379"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020270902","display_name":"Avik Datta","orcid":"https://orcid.org/0000-0002-1411-8638"},"institutions":[{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]},{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Avik Datta","raw_affiliation_strings":["Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune 411007, India"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune 411007, India","institution_ids":["https://openalex.org/I878213199","https://openalex.org/I1331500379"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018369824","display_name":"Sunitha Manjari K","orcid":null},"institutions":[{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]},{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sunitha Manjari K","raw_affiliation_strings":["Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune 411007, India"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune 411007, India","institution_ids":["https://openalex.org/I878213199","https://openalex.org/I1331500379"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041136744","display_name":"Rajendra Joshi","orcid":"https://orcid.org/0000-0003-1299-0091"},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]},{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Rajendra Joshi","raw_affiliation_strings":["Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune 411007, India"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune 411007, India","institution_ids":["https://openalex.org/I878213199","https://openalex.org/I1331500379"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5039299193"],"corresponding_institution_ids":["https://openalex.org/I1331500379","https://openalex.org/I878213199"],"apc_list":null,"apc_paid":null,"fwci":0.1092,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.53403064,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"12","issue":"05","first_page":"1450026","last_page":"1450026"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9995999932289124,"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":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7234096527099609},{"id":"https://openalex.org/keywords/spurious-relationship","display_name":"Spurious relationship","score":0.6825350522994995},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.656705379486084},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5680388808250427},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5676487684249878},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5115657448768616},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5073303580284119},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4473162293434143},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4334696829319},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4278145432472229},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3847028613090515},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.2462652623653412},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.15842047333717346},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14506664872169495}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7234096527099609},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.6825350522994995},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.656705379486084},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5680388808250427},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5676487684249878},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5115657448768616},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5073303580284119},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4473162293434143},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4334696829319},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4278145432472229},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3847028613090515},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2462652623653412},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.15842047333717346},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14506664872169495},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720014500267","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720014500267","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:25245144","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25245144","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.5,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320729","display_name":"Department of Information Technology, Ministry of Communications and Information Technology","ror":"https://ror.org/02z31cn83"},{"id":"https://openalex.org/F4320321071","display_name":"Department of Electronics and Information Technology, Ministry of Communications and Information Technology","ror":"https://ror.org/02z31cn83"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1969491708","https://openalex.org/W1981509058","https://openalex.org/W2006559366","https://openalex.org/W2021341670","https://openalex.org/W2024976844","https://openalex.org/W2040770546","https://openalex.org/W2052918843","https://openalex.org/W2053514780","https://openalex.org/W2055043387","https://openalex.org/W2095691309","https://openalex.org/W2097065948","https://openalex.org/W2098832713","https://openalex.org/W2102304447","https://openalex.org/W2110957978","https://openalex.org/W2126144698","https://openalex.org/W2141458291","https://openalex.org/W2150695488","https://openalex.org/W2156841387","https://openalex.org/W2160969485","https://openalex.org/W4210450218"],"related_works":["https://openalex.org/W2162899405","https://openalex.org/W3113091479","https://openalex.org/W941090075","https://openalex.org/W2044987316","https://openalex.org/W3134374554","https://openalex.org/W2237480245","https://openalex.org/W2075065631","https://openalex.org/W2519167559","https://openalex.org/W4288358396","https://openalex.org/W4311248832"],"abstract_inverted_index":{"Recent":[0],"evidences":[1],"suggest":[2],"that":[3,13,139],"a":[4,19,54],"substantial":[5],"amount":[6],"of":[7,22,28,70,77,98,115,120,126,129,156],"genome":[8],"is":[9,124,159],"transcribed":[10],"more":[11],"than":[12],"was":[14],"anticipated,":[15],"giving":[16],"rise":[17],"to":[18,57,66,150],"large":[20],"number":[21,69,128],"unknown":[23],"or":[24,131],"novel":[25,29,59,78,92,99,103,135,154],"transcripts.":[26,100,116,136],"Identification":[27],"transcripts":[30,79,104,155],"can":[31],"provide":[32],"key":[33],"insights":[34],"into":[35],"understanding":[36],"important":[37],"cellular":[38],"functions":[39],"as":[40,42,53,86],"well":[41],"molecular":[43],"mechanisms":[44],"underlying":[45],"complex":[46],"diseases":[47],"like":[48],"cancer.":[49],"RNA-Seq":[50],"has":[51],"emerged":[52],"powerful":[55],"tool":[56],"detect":[58],"transcripts,":[60],"which":[61,94],"previous":[62],"profiling":[63],"techniques":[64],"failed":[65],"identify.":[67],"A":[68,117],"tools":[71,123],"are":[72,95],"available":[73],"for":[74],"enabling":[75],"identification":[76],"at":[80],"different":[81],"levels.":[82],"Read":[83],"mappers":[84],"such":[85],"TopHat,":[87],"MapSplice,":[88],"and":[89,109,146],"SOAPsplice":[90],"predict":[91],"junctions,":[93],"the":[96],"indicators":[97],"Cufflinks":[101],"assembles":[102],"based":[105],"on":[106],"alignment":[107],"information":[108,141],"Oases":[110],"performs":[111],"de":[112],"novo":[113],"construction":[114],"common":[118],"limitation":[119],"all":[121,143],"these":[122],"prediction":[125],"sizable":[127],"spurious":[130],"false":[132],"positive":[133],"(FP)":[134],"An":[137],"approach":[138],"integrates":[140],"from":[142],"above":[144],"sources":[145],"simultaneously":[147],"scrutinizes":[148],"FPs":[149],"correctly":[151],"identify":[152],"authentic":[153],"high":[157],"confidence":[158],"proposed.":[160]},"counts_by_year":[{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}