{"id":"https://openalex.org/W2143819684","doi":"https://doi.org/10.1109/iccabs.2011.5729924","title":"Workshop: Using a transcript catalog and paired-end RNA-Seq data to identify differential alternative splicing","display_name":"Workshop: Using a transcript catalog and paired-end RNA-Seq data to identify differential alternative splicing","publication_year":2011,"publication_date":"2011-02-01","ids":{"openalex":"https://openalex.org/W2143819684","doi":"https://doi.org/10.1109/iccabs.2011.5729924","mag":"2143819684"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2011.5729924","doi":"https://doi.org/10.1109/iccabs.2011.5729924","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2011.5729924","pdf_url":null,"source":{"id":"https://openalex.org/S4393918246","display_name":"IEEE International Conference on Computational Advances in Bio and Medical Sciences","issn_l":"2164-229X","issn":["2164-229X"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref"],"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/A5011043085","display_name":"Brian E. Howard","orcid":"https://orcid.org/0000-0002-6123-7090","observed_orcids":["https://orcid.org/0000-0002-6123-7090"]},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian E. Howard","raw_affiliation_strings":["Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066019402","display_name":"Xiaoping Tan","orcid":"https://orcid.org/0000-0002-3256-392X","observed_orcids":["https://orcid.org/0000-0002-3256-392X"]},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoping Tan","raw_affiliation_strings":["Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA","Department of Plant Pathology, North Carolina State University, Raleigh, 27606, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Department of Plant Pathology, North Carolina State University, Raleigh, 27606, USA#TAB#","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Paola Veronese","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paola Veronese","raw_affiliation_strings":["Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA","Department of Plant Pathology, North Carolina State University, Raleigh, 27606, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Department of Plant Pathology, North Carolina State University, Raleigh, 27606, USA#TAB#","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058462301","display_name":"Steffen Heber","orcid":"https://orcid.org/0000-0002-1050-3635","observed_orcids":["https://orcid.org/0000-0002-1050-3635"]},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steffen Heber","raw_affiliation_strings":["Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, 27606, USA","institution_ids":["https://openalex.org/I137902535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I137902535"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.21435346,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"270","last_page":"270"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.923799991607666,"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/T10604","display_name":"RNA Research and Splicing","score":0.923799991607666,"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":0.06790000200271606,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0019000000320374966,"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/alternative-splicing","display_name":"alternative splicing","score":0.9879999756813049},{"id":"https://openalex.org/keywords/differential-splicing","display_name":"differential splicing","score":0.8349999785423279},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.9259999990463257},{"id":"https://openalex.org/keywords/pseudomonas-syringae","display_name":"Pseudomonas syringae","score":1.0},{"id":"https://openalex.org/keywords/host-pathogen-interaction","display_name":"host-pathogen interaction","score":0.9380000233650208},{"id":"https://openalex.org/keywords/isoform-quantification","display_name":"isoform quantification","score":0.9430000185966492},{"id":"https://openalex.org/keywords/linear-models","display_name":"linear models","score":0.7179999947547913}],"concepts":[{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.7651925086975098},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6979883909225464},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6805248260498047},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.6477638483047485},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6084473133087158},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6051579713821411},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5069878101348877},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.49650174379348755},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4747077524662018},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.43778523802757263},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.42009884119033813},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3297349810600281},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.3215644359588623},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3117867112159729}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2011.5729924","doi":"https://doi.org/10.1109/iccabs.2011.5729924","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2011.5729924","pdf_url":null,"source":{"id":"https://openalex.org/S4393918246","display_name":"IEEE International Conference on Computational Advances in Bio and Medical Sciences","issn_l":"2164-229X","issn":["2164-229X"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W1986113553","https://openalex.org/W2001952613","https://openalex.org/W2116348004","https://openalex.org/W2157080481","https://openalex.org/W2157770058"],"related_works":["https://openalex.org/W2904939684","https://openalex.org/W2321791250","https://openalex.org/W4213427798","https://openalex.org/W2012312817","https://openalex.org/W2081598294","https://openalex.org/W2056672569","https://openalex.org/W2090969926","https://openalex.org/W4385462331","https://openalex.org/W2564462691","https://openalex.org/W2023199111"],"abstract_inverted_index":{"The":[0,61,149],"purpose":[1],"of":[2,12,19,56,74,86,155,158,171,179,187,190,201,209,217],"this":[3,48,50],"NSF-Eager":[4],"grant":[5],"is":[6],"to":[7,15,70,100,109,121,141,184],"use":[8,137],"high-throughput":[9],"RNA":[10],"sequencing":[11,103],"the":[13,17,23,72,84,90,94,118,156,177,188,204,207],"transcriptome":[14],"assess":[16],"role":[18,43],"alternative":[20,38,160,173],"splicing":[21,39,58,161],"in":[22,77,98,203],"host-pathogen":[24],"interaction":[25],"between":[26],"Arabidopsis":[27],"thaliana":[28],"and":[29,135,162],"Pseudomonas":[30],"syringae.":[31],"Although":[32],"previous":[33],"studies":[34],"have":[35,223],"demonstrated":[36],"that":[37,129,220],"plays":[40],"an":[41],"important":[42],"for":[44,132,146,167,197],"individual":[45],"genes":[46,182,212,219],"during":[47],"interaction,":[49],"whole-genome":[51],"approach":[52],"will":[53],"investigate":[54],"thousands":[55],"potential":[57],"events":[59],"simultaneously.":[60],"method":[62,95],"presented":[63],"here":[64],"employs":[65],"a":[66,78,110,138,152,168,198,214],"linear":[67,139],"models":[68],"framework":[69],"estimate":[71,142],"ratios":[73,145],"known":[75],"isoforms":[76],"given":[79],"sample,":[80],"taking":[81],"into":[82],"account":[83],"non-uniformity":[85],"RNA-sequencing":[87],"reads":[88,106,119,128],"along":[89],"targeted":[91],"transcripts.":[92,174],"Recently,":[93],"was":[96],"adapted":[97],"order":[99],"accommodate":[101],"paired-end":[102],"technology.":[104],"Briefly,":[105],"are":[107,130],"mapped":[108],"transcript":[111],"catalog":[112],"(TAIR":[113],"10":[114],"gene":[115,231],"models),":[116],"partition":[117],"according":[120],"their":[122],"compatibility":[123],"with":[124],"these":[125],"models,":[126],"identify":[127],"informative":[131],"isoform":[133,143],"quantification,":[134],"then":[136],"model":[140],"expression":[144],"each":[147],"gene.":[148],"results":[150],"provide":[151],"first":[153],"approximation":[154],"extent":[157],"pathogen-induced":[159],"so":[163],"far":[164],"indicate":[165],"evidence":[166,196],"wide":[169],"variety":[170],"novel":[172],"In":[175],"addition,":[176],"set":[178,189,208,216],"differentially":[180,191,210],"spliced":[181,211],"appears":[183],"be":[185],"independent":[186],"expressed":[192],"genes,":[193],"providing":[194],"new":[195],"hidden":[199],"layer":[200],"regulation":[202],"transcriptome.":[205],"Hence,":[206],"provides":[213],"promising":[215],"candidate":[218],"researchers":[221],"may":[222],"previously":[224],"overlooked":[225],"by":[226],"focusing":[227],"solely":[228],"on":[229],"differential":[230],"expression.":[232]},"counts_by_year":[],"updated_date":"2026-10-06T10:28:23.643775","created_date":"2025-10-10T00:00:00"}