{"id":"https://openalex.org/W4401441207","doi":"https://doi.org/10.1093/bioinformatics/btae475","title":"TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups","display_name":"TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups","publication_year":2024,"publication_date":"2024-08-01","ids":{"openalex":"https://openalex.org/W4401441207","doi":"https://doi.org/10.1093/bioinformatics/btae475","pmid":"https://pubmed.ncbi.nlm.nih.gov/39120880"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae475","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae475","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae475","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106555999","display_name":"Pallavi Surana","orcid":"https://orcid.org/0009-0004-4241-9181"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pallavi Surana","raw_affiliation_strings":["Department of Biomedical Informatics, Stony Brook University , Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook University , Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007048284","display_name":"Pratik Dutta","orcid":"https://orcid.org/0000-0002-1579-8946"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pratik Dutta","raw_affiliation_strings":["Department of Biomedical Informatics, Stony Brook University , Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook University , Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017429478","display_name":"Ramana V. Davuluri","orcid":"https://orcid.org/0000-0002-7053-1064"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ramana V Davuluri","raw_affiliation_strings":["Department of Biomedical Informatics, Stony Brook University , Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook University , Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5106555999"],"corresponding_institution_ids":["https://openalex.org/I59553526"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7309,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.85161555,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"40","issue":"8","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":0.9998000264167786,"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":0.9998000264167786,"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":0.9995999932289124,"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":0.9995999932289124,"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/transcriptome","display_name":"Transcriptome","score":0.8030291795730591},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5960095524787903},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5611962676048279},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45690053701400757},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3386354446411133},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3202987313270569},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2922302782535553},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20142728090286255},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15314945578575134}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.8030291795730591},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5960095524787903},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5611962676048279},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45690053701400757},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3386354446411133},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3202987313270569},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2922302782535553},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20142728090286255},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15314945578575134},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":"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":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","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":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":"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":"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":"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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae475","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae475","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39120880","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39120880","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11319638","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11319638","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11319638/pdf/btae475.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae475","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae475","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.699999988079071}],"awards":[{"id":"https://openalex.org/G6647179965","display_name":null,"funder_award_id":"R01LM013722","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1533942137","https://openalex.org/W1884519301","https://openalex.org/W1978695171","https://openalex.org/W1981409633","https://openalex.org/W1986553481","https://openalex.org/W2009329319","https://openalex.org/W2058972518","https://openalex.org/W2084468230","https://openalex.org/W2094074349","https://openalex.org/W2095521407","https://openalex.org/W2104005232","https://openalex.org/W2104224685","https://openalex.org/W2129097232","https://openalex.org/W2131478115","https://openalex.org/W2132132957","https://openalex.org/W2137582063","https://openalex.org/W2145825942","https://openalex.org/W2150901760","https://openalex.org/W2155804510","https://openalex.org/W2155839154","https://openalex.org/W2280788332","https://openalex.org/W2293607291","https://openalex.org/W2469916682","https://openalex.org/W2591757282","https://openalex.org/W2757254843","https://openalex.org/W2806989085","https://openalex.org/W2890528557","https://openalex.org/W2949475756","https://openalex.org/W3042292144","https://openalex.org/W3083914502","https://openalex.org/W3105507774","https://openalex.org/W3133859624","https://openalex.org/W3135817634","https://openalex.org/W3155911001","https://openalex.org/W3175752499","https://openalex.org/W3201129361","https://openalex.org/W3217192868","https://openalex.org/W4224993560","https://openalex.org/W4282926069","https://openalex.org/W4283749730","https://openalex.org/W4296605715","https://openalex.org/W4297457060","https://openalex.org/W4311292859","https://openalex.org/W4376872864","https://openalex.org/W6695120148","https://openalex.org/W6797786779"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"TransTEx":[0],"database:":[1],"https://bmi.cewit.stonybrook.edu/transtexdb/":[2],"and":[3],"the":[4],"R":[5],"package":[6],"is":[7],"available":[8],"via":[9],"GitHub:":[10],"https://github.com/pallavisurana1/TransTEx.":[11]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2025-10-10T00:00:00"}
