{"id":"https://openalex.org/W1497400772","doi":"https://doi.org/10.1186/1471-2105-13-s17-s24","title":"TranSeqAnnotator: large-scale analysis of transcriptomic data","display_name":"TranSeqAnnotator: large-scale analysis of transcriptomic data","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W1497400772","doi":"https://doi.org/10.1186/1471-2105-13-s17-s24","mag":"1497400772","pmid":"https://pubmed.ncbi.nlm.nih.gov/23282024"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s17-s24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s17-s24","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S17-S24","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S17-S24","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017106773","display_name":"Ranjeeta Menon","orcid":"https://orcid.org/0000-0002-8509-2543"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Ranjeeta Menon","raw_affiliation_strings":["Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, NSW 2109, Australia","Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, NSW 2109, Australia","institution_ids":["https://openalex.org/I99043593"]},{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, Australia","institution_ids":["https://openalex.org/I99043593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081296622","display_name":"Gagan Garg","orcid":"https://orcid.org/0000-0002-9523-6360"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Gagan Garg","raw_affiliation_strings":["Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, NSW, 2109, Australia","Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, NSW, 2109, Australia","institution_ids":["https://openalex.org/I99043593"]},{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, Australia","institution_ids":["https://openalex.org/I99043593"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085039675","display_name":"Robin B. Gasser","orcid":"https://orcid.org/0000-0002-4423-1690"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Robin B Gasser","raw_affiliation_strings":["Department of Veterinary Sciences, The University of Melbourne, Werribee, VIC, 3030, Australia","Department of Veterinary Sciences, The University of Melbourne, Werribee, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Veterinary Sciences, The University of Melbourne, Werribee, VIC, 3030, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Veterinary Sciences, The University of Melbourne, Werribee, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083278600","display_name":"Shoba Ranganathan","orcid":"https://orcid.org/0000-0002-8290-813X"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]},{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["AU","SG"],"is_corresponding":false,"raw_author_name":"Shoba Ranganathan","raw_affiliation_strings":["Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597","Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, NSW, 2109, Australia","Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore","Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, NSW, 2109, Australia","institution_ids":["https://openalex.org/I99043593"]},{"raw_affiliation_string":"Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence, Macquarie University, Sydney, Australia","institution_ids":["https://openalex.org/I99043593"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5017106773"],"corresponding_institution_ids":["https://openalex.org/I99043593"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.8044,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.69975526,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"13","issue":"S17","first_page":"S24","last_page":"S24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","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"}},"topics":[{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9977999925613403,"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":0.992900013923645,"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/scale","display_name":"Scale (ratio)","score":0.5756061673164368},{"id":"https://openalex.org/keywords/scale-analysis","display_name":"Scale analysis (mathematics)","score":0.5124688744544983},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4461812674999237},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3691713809967041},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3687204122543335},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2515740990638733},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.2144177258014679},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.13810110092163086}],"concepts":[{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5756061673164368},{"id":"https://openalex.org/C2775879016","wikidata":"https://www.wikidata.org/wiki/Q2845204","display_name":"Scale analysis (mathematics)","level":2,"score":0.5124688744544983},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4461812674999237},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3691713809967041},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3687204122543335},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2515740990638733},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.2144177258014679},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.13810110092163086},{"id":"https://openalex.org/C153294291","wikidata":"https://www.wikidata.org/wiki/Q25261","display_name":"Meteorology","level":1,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-13-s17-s24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s17-s24","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S17-S24","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23282024","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23282024","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:jupiter.its.unimelb.edu.au:11343/264922","is_oa":true,"landing_page_url":"http://hdl.handle.net/11343/264922","pdf_url":"http://hdl.handle.net/11343/264922","source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:a106419124f2434cbf954805e3a9d3f7","is_oa":true,"landing_page_url":"https://doaj.org/article/a106419124f2434cbf954805e3a9d3f7","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 13, Iss Suppl 17, p S24 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2521586","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3521237","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s17-s24","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s17-s24","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S17-S24","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320591","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1497400772.pdf","grobid_xml":"https://content.openalex.org/works/W1497400772.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1509786727","https://openalex.org/W1545357297","https://openalex.org/W1573617710","https://openalex.org/W1606826621","https://openalex.org/W1963568761","https://openalex.org/W1970621669","https://openalex.org/W1971248527","https://openalex.org/W1974584611","https://openalex.org/W1981740050","https://openalex.org/W1987545661","https://openalex.org/W1991307293","https://openalex.org/W2001798854","https://openalex.org/W2010247691","https://openalex.org/W2023317028","https://openalex.org/W2024312710","https://openalex.org/W2025399116","https://openalex.org/W2026997856","https://openalex.org/W2027847170","https://openalex.org/W2039971761","https://openalex.org/W2041352234","https://openalex.org/W2041956242","https://openalex.org/W2044965398","https://openalex.org/W2047399443","https://openalex.org/W2052084054","https://openalex.org/W2054943596","https://openalex.org/W2063495059","https://openalex.org/W2074538482","https://openalex.org/W2077961169","https://openalex.org/W2088333455","https://openalex.org/W2089220247","https://openalex.org/W2094448442","https://openalex.org/W2103717317","https://openalex.org/W2105406701","https://openalex.org/W2109348952","https://openalex.org/W2111433116","https://openalex.org/W2115933717","https://openalex.org/W2116423958","https://openalex.org/W2117490274","https://openalex.org/W2120457919","https://openalex.org/W2125973903","https://openalex.org/W2130687290","https://openalex.org/W2134485438","https://openalex.org/W2144428663","https://openalex.org/W2149585737","https://openalex.org/W2152770371","https://openalex.org/W2153274876","https://openalex.org/W2156362263","https://openalex.org/W2159033700","https://openalex.org/W2163769388","https://openalex.org/W2164124971","https://openalex.org/W2165674132","https://openalex.org/W2402088633","https://openalex.org/W2782267736","https://openalex.org/W2917375902","https://openalex.org/W2917431650"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2365350080","https://openalex.org/W2394388677"],"abstract_inverted_index":{"TranSeqAnnotator":[0,19],"has":[1],"been":[2],"developed":[3],"in":[4,26],"a":[5],"Linux":[6],"cluster,":[7],"to":[8,30,40,45],"perform":[9],"an":[10],"exhaustive":[11],"and":[12,15,33,49,56],"reliable":[13],"analysis":[14],"provide":[16],"detailed":[17],"annotation.":[18],"outputs":[20],"gene":[21],"ontologies,":[22],"protein":[23,31],"functional":[24],"identifications":[25],"terms":[27],"of":[28],"mapping":[29],"domains":[32],"metabolic":[34],"pathways.":[35],"The":[36],"pipeline":[37],"is":[38,66],"applied":[39],"annotate":[41],"large":[42],"EST":[43],"datasets":[44],"identify":[46],"several":[47],"novel":[48],"known":[50],"genes":[51],"with":[52],"therapeutic":[53],"experimental":[54],"validations":[55],"could":[57],"serve":[58],"as":[59],"potential":[60],"targets":[61],"for":[62,69],"parasite":[63],"intervention.":[64],"TransSeqAnnotator":[65],"freely":[67],"available":[68],"the":[70],"scientific":[71],"community":[72],"at":[73],"http://estexplorer.biolinfo.org/TranSeqAnnotator/.":[74]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-17T17:19:04.345684","created_date":"2025-10-10T00:00:00"}
