{"id":"https://openalex.org/W2122690812","doi":"https://doi.org/10.3233/isb-2012-0459","title":"Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations","display_name":"Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W2122690812","doi":"https://doi.org/10.3233/isb-2012-0459","mag":"2122690812","pmid":"https://pubmed.ncbi.nlm.nih.gov/23202426"},"language":"en","primary_location":{"id":"doi:10.3233/isb-2012-0459","is_oa":true,"landing_page_url":"https://doi.org/10.3233/isb-2012-0459","pdf_url":"https://content.iospress.com:443/download/in-silico-biology/isb459?id=in-silico-biology%2Fisb459","source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://content.iospress.com:443/download/in-silico-biology/isb459?id=in-silico-biology%2Fisb459","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017101305","display_name":"Serghei Mangul","orcid":"https://orcid.org/0000-0003-4770-3443"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Serghei Mangul","raw_affiliation_strings":["Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009449784","display_name":"Adrian Caciula","orcid":null},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adrian Caciula","raw_affiliation_strings":["Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046953828","display_name":"Olga Glebova","orcid":"https://orcid.org/0000-0002-7566-0471"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olga Glebova","raw_affiliation_strings":["Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","institution_ids":["https://openalex.org/I181565077"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014788373","display_name":"Ion M\u0103ndoiu","orcid":"https://orcid.org/0000-0002-4818-0237"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ion Mandoiu","raw_affiliation_strings":["Department of Computer Science &amp; Engineering, University of Connecticut,\r          Storrs, CT, USA, E-mail: ion@engr.uconn.edu","Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA, E-mail: ion@engr.uconn.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science &amp; Engineering, University of Connecticut,\r          Storrs, CT, USA, E-mail: ion@engr.uconn.edu","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA, E-mail: ion@engr.uconn.edu","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072751459","display_name":"Alex Zelikovsky","orcid":"https://orcid.org/0000-0003-4424-4691"},"institutions":[{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex Zelikovsky","raw_affiliation_strings":["Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r          E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA,\r E-mails: {serghei, acaciula, glebova, alexz}@cs.gsu.edu","institution_ids":["https://openalex.org/I181565077"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017101305"],"corresponding_institution_ids":["https://openalex.org/I181565077"],"apc_list":null,"apc_paid":null,"fwci":0.3973,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.62475298,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"11","issue":"5-6","first_page":"251","last_page":"261"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9993000030517578,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9973999857902527,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.8277864456176758},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.7696361541748047},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6044782400131226},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4615699052810669},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3696601390838623},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36685487627983093},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.173595130443573},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17141348123550415},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14579805731773376}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.8277864456176758},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7696361541748047},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6044782400131226},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4615699052810669},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3696601390838623},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36685487627983093},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.173595130443573},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17141348123550415},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14579805731773376}],"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.3233/isb-2012-0459","is_oa":true,"landing_page_url":"https://doi.org/10.3233/isb-2012-0459","pdf_url":"https://content.iospress.com:443/download/in-silico-biology/isb459?id=in-silico-biology%2Fisb459","source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation","raw_type":"journal-article"},{"id":"pmid:23202426","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23202426","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":"In silico biology","raw_type":null}],"best_oa_location":{"id":"doi:10.3233/isb-2012-0459","is_oa":true,"landing_page_url":"https://doi.org/10.3233/isb-2012-0459","pdf_url":"https://content.iospress.com:443/download/in-silico-biology/isb459?id=in-silico-biology%2Fisb459","source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2096208076","display_name":"III: Small:  Collaborative Research:  Reconstruction of Haplotype Spectra from High-Throughput Sequencing Data","funder_award_id":"0916948","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2624405081","display_name":"CAREER: Combinatorial Algorithms for High-Throughput Collection and Analysis of Genomic Diversity Data","funder_award_id":"0546457","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3754485978","display_name":"III: Small:  Collaborative Research:  Reconstruction of Haplotype Spectra from High-Throughput Sequencing Data","funder_award_id":"0916401","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5649101056","display_name":null,"funder_award_id":"IIS-0916401","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G6136016438","display_name":null,"funder_award_id":"IIS-0916401","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7144931082","display_name":null,"funder_award_id":"IIS-0916401","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G8524297662","display_name":null,"funder_award_id":"2011-67016-30331","funder_id":"https://openalex.org/F4320332299","funder_display_name":"National Institute of Food and Agriculture"},{"id":"https://openalex.org/G8643431141","display_name":"Bioinformatics Tools Enabling Large-Scale DNA Barcoding","funder_award_id":"0543365","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320310607","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18"},{"id":"https://openalex.org/F4320332299","display_name":"National Institute of Food and Agriculture","ror":"https://ror.org/05qx3fv49"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2122690812.pdf","grobid_xml":"https://content.openalex.org/works/W2122690812.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1493192698","https://openalex.org/W1981509058","https://openalex.org/W1988929438","https://openalex.org/W1989729446","https://openalex.org/W2000875411","https://openalex.org/W2030914835","https://openalex.org/W2037809979","https://openalex.org/W2055770801","https://openalex.org/W2086323500","https://openalex.org/W2093253451","https://openalex.org/W2097065948","https://openalex.org/W2098832713","https://openalex.org/W2100448568","https://openalex.org/W2101735289","https://openalex.org/W2107564978","https://openalex.org/W2112888168","https://openalex.org/W2114504176","https://openalex.org/W2122789575","https://openalex.org/W2124985265","https://openalex.org/W2126419817","https://openalex.org/W2127640118","https://openalex.org/W2141458291","https://openalex.org/W2154431984","https://openalex.org/W2160164696","https://openalex.org/W2255028219"],"related_works":["https://openalex.org/W4394359997","https://openalex.org/W4362511652","https://openalex.org/W4362511917","https://openalex.org/W4362511922","https://openalex.org/W4362485688","https://openalex.org/W4362530184","https://openalex.org/W4362530193","https://openalex.org/W2904597490","https://openalex.org/W4362485661","https://openalex.org/W4394365953"],"abstract_inverted_index":{"The":[0],"paper":[1],"addresses":[2],"the":[3,82],"problem":[4],"of":[5,61,99,104],"how":[6],"to":[7,68,79],"use":[8],"RNA-Seq":[9],"data":[10],"for":[11,33],"transcriptome":[12,34,51,71],"reconstruction":[13,36,100],"and":[14,37,43,49,59,101],"quantification,":[15],"as":[16,18,57,74,76,78],"well":[17,77],"novel":[19,29],"transcript":[20,83],"discovery":[21],"in":[22,39],"partially":[23,40],"annotated":[24,41],"genomes.":[25],"We":[26],"present":[27],"a":[28],"annotation-guided":[30,48],"general":[31],"framework":[32],"discovery,":[35],"quantification":[38],"genomes":[42],"compare":[44],"it":[45],"with":[46],"existing":[47,70],"genome-guided":[50],"assembly":[52],"methods.":[53],"Our":[54],"method,":[55],"referred":[56],"Discovery":[58],"Reconstruction":[60],"Unannotated":[62],"Transcripts":[63],"(DRUT),":[64],"can":[65],"be":[66],"used":[67],"enhance":[69],"assemblers,":[72],"such":[73],"Cufflinks,":[75],"accurately":[80],"estimate":[81],"frequencies.":[84],"Empirical":[85],"analysis":[86],"on":[87],"synthetic":[88],"datasets":[89],"confirms":[90],"that":[91],"Cufflinks":[92],"enhanced":[93],"by":[94],"DRUT":[95],"has":[96],"superior":[97],"quality":[98],"frequency":[102],"estimation":[103],"transcripts.":[105]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
