{"id":"https://openalex.org/W3045595303","doi":"https://doi.org/10.1093/bib/bbaa137","title":"Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS","display_name":"Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS","publication_year":2020,"publication_date":"2020-06-08","ids":{"openalex":"https://openalex.org/W3045595303","doi":"https://doi.org/10.1093/bib/bbaa137","mag":"3045595303","pmid":"https://pubmed.ncbi.nlm.nih.gov/32728687"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa137","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa137","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5023034408","display_name":"Zhixu Qiu","orcid":"https://orcid.org/0000-0003-1979-5272"},"institutions":[{"id":"https://openalex.org/I4210156609","display_name":"L'Alliance Boviteq","ror":"https://ror.org/05asf4e91","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210156609"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Zhixu Qiu","raw_affiliation_strings":["Ma\u2019s Lab","Ma's Lab"],"affiliations":[{"raw_affiliation_string":"Ma\u2019s Lab","institution_ids":["https://openalex.org/I4210156609"]},{"raw_affiliation_string":"Ma's Lab","institution_ids":["https://openalex.org/I4210156609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100429250","display_name":"Siyuan Chen","orcid":"https://orcid.org/0009-0001-8475-0305"},"institutions":[{"id":"https://openalex.org/I4210156609","display_name":"L'Alliance Boviteq","ror":"https://ror.org/05asf4e91","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210156609"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Siyuan Chen","raw_affiliation_strings":["Ma\u2019s Lab","Ma's Lab"],"affiliations":[{"raw_affiliation_string":"Ma\u2019s Lab","institution_ids":["https://openalex.org/I4210156609"]},{"raw_affiliation_string":"Ma's Lab","institution_ids":["https://openalex.org/I4210156609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002842332","display_name":"Yuhong Qi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210156609","display_name":"L'Alliance Boviteq","ror":"https://ror.org/05asf4e91","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210156609"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yuhong Qi","raw_affiliation_strings":["Ma\u2019s Lab","Ma's Lab"],"affiliations":[{"raw_affiliation_string":"Ma\u2019s Lab","institution_ids":["https://openalex.org/I4210156609"]},{"raw_affiliation_string":"Ma's Lab","institution_ids":["https://openalex.org/I4210156609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090110899","display_name":"Chunni Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210156609","display_name":"L'Alliance Boviteq","ror":"https://ror.org/05asf4e91","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210156609"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Chunni Liu","raw_affiliation_strings":["Ma\u2019s Lab","Ma's Lab"],"affiliations":[{"raw_affiliation_string":"Ma\u2019s Lab","institution_ids":["https://openalex.org/I4210156609"]},{"raw_affiliation_string":"Ma's Lab","institution_ids":["https://openalex.org/I4210156609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012757323","display_name":"Jingjing Zhai","orcid":"https://orcid.org/0000-0002-1535-3103"},"institutions":[{"id":"https://openalex.org/I4210156609","display_name":"L'Alliance Boviteq","ror":"https://ror.org/05asf4e91","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210156609"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jingjing Zhai","raw_affiliation_strings":["Ma\u2019s Lab","Ma's Lab"],"affiliations":[{"raw_affiliation_string":"Ma\u2019s Lab","institution_ids":["https://openalex.org/I4210156609"]},{"raw_affiliation_string":"Ma's Lab","institution_ids":["https://openalex.org/I4210156609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030207354","display_name":"Shang Xie","orcid":"https://orcid.org/0000-0002-9751-1418"},"institutions":[{"id":"https://openalex.org/I4210156609","display_name":"L'Alliance Boviteq","ror":"https://ror.org/05asf4e91","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210156609"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shang Xie","raw_affiliation_strings":["Ma\u2019s Lab","Ma's Lab"],"affiliations":[{"raw_affiliation_string":"Ma\u2019s Lab","institution_ids":["https://openalex.org/I4210156609"]},{"raw_affiliation_string":"Ma's Lab","institution_ids":["https://openalex.org/I4210156609"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018556396","display_name":"Chuang Ma","orcid":"https://orcid.org/0000-0001-9612-7898"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chuang Ma","raw_affiliation_strings":["Bioinformatics Laboratory at Northwest A&F University"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Laboratory at Northwest A&F University","institution_ids":["https://openalex.org/I89652312"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5018556396"],"corresponding_institution_ids":["https://openalex.org/I89652312"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.3314,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.56715059,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"22","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9970999956130981,"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":0.9950000047683716,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.7309458255767822},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.7294838428497314},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5953487157821655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5707406997680664},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5624266862869263},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5281201601028442},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4440154433250427},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38000303506851196},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33006495237350464},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.25569796562194824},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25451892614364624},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22844195365905762},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15144866704940796}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7309458255767822},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7294838428497314},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5953487157821655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5707406997680664},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5624266862869263},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5281201601028442},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4440154433250427},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38000303506851196},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33006495237350464},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.25569796562194824},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25451892614364624},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22844195365905762},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15144866704940796},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa137","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa137","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32728687","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32728687","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7170841796","display_name":null,"funder_award_id":"31570371","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W1968239355","https://openalex.org/W1971899779","https://openalex.org/W1978829017","https://openalex.org/W1978937741","https://openalex.org/W2045204781","https://openalex.org/W2047749683","https://openalex.org/W2049446938","https://openalex.org/W2050345155","https://openalex.org/W2055253589","https://openalex.org/W2096192437","https://openalex.org/W2100137396","https://openalex.org/W2101613178","https://openalex.org/W2102278945","https://openalex.org/W2103690822","https://openalex.org/W2104005232","https://openalex.org/W2105434771","https://openalex.org/W2106678197","https://openalex.org/W2109322710","https://openalex.org/W2122760939","https://openalex.org/W2122968580","https://openalex.org/W2126419817","https://openalex.org/W2138207763","https://openalex.org/W2141458291","https://openalex.org/W2154860326","https://openalex.org/W2160420391","https://openalex.org/W2161633633","https://openalex.org/W2165405863","https://openalex.org/W2169353806","https://openalex.org/W2184055070","https://openalex.org/W2215156857","https://openalex.org/W2313931749","https://openalex.org/W2333082097","https://openalex.org/W2463761386","https://openalex.org/W2464084885","https://openalex.org/W2521382392","https://openalex.org/W2536657235","https://openalex.org/W2553838260","https://openalex.org/W2557547067","https://openalex.org/W2594035655","https://openalex.org/W2605929552","https://openalex.org/W2606335523","https://openalex.org/W2612976808","https://openalex.org/W2615786037","https://openalex.org/W2624572223","https://openalex.org/W2651264916","https://openalex.org/W2761430568","https://openalex.org/W2761771578","https://openalex.org/W2767042318","https://openalex.org/W2802396666","https://openalex.org/W2811434510","https://openalex.org/W2883511460","https://openalex.org/W2889374441","https://openalex.org/W2890879010","https://openalex.org/W2903241977","https://openalex.org/W2918528086","https://openalex.org/W2919891976","https://openalex.org/W2946711137","https://openalex.org/W2946950751","https://openalex.org/W2947667722","https://openalex.org/W2948535302","https://openalex.org/W2949317881","https://openalex.org/W2949324846","https://openalex.org/W2949631739","https://openalex.org/W2951912016","https://openalex.org/W2952615074","https://openalex.org/W2955079935","https://openalex.org/W2967881004","https://openalex.org/W4230096730","https://openalex.org/W6702740663"],"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":{"Transcriptional":[0],"switch":[1],"(TS)":[2],"is":[3,41],"a":[4,45,66,72],"widely":[5],"observed":[6],"phenomenon":[7],"caused":[8],"by":[9,44],"changes":[10],"in":[11,21],"the":[12,18,121,130],"relative":[13],"expression":[14],"of":[15,47,80,123,134,149,160],"transcripts":[16],"from":[17,87],"same":[19],"gene,":[20],"spatial,":[22],"temporal":[23,89,136],"or":[24,112],"other":[25],"dimensions.":[26],"TS":[27,54,81,100,132,158],"has":[28],"been":[29],"associated":[30],"with":[31,111],"human":[32],"diseases,":[33],"plant":[34],"development":[35],"and":[36,52,78,90,105,108,125,137,156],"stress":[37],"responses.":[38],"Its":[39],"investigation":[40],"often":[42],"hampered":[43],"lack":[46],"suitable":[48],"tools":[49],"allowing":[50],"comprehensive":[51],"flexible":[53],"analysis":[55,79,101,133],"for":[56,83,102,109,129],"high-throughput":[57],"RNA":[58],"sequencing":[59],"(RNA-Seq)":[60],"data.":[61,140,163],"Here,":[62],"we":[63],"present":[64],"deepTS,":[65],"user-friendly":[67],"web-based":[68],"implementation":[69],"that":[70],"enables":[71],"fully":[73],"interactive,":[74],"multifunctional":[75],"identification,":[76],"visualization":[77],"events":[82],"large-scale":[84,161],"RNA-Seq":[85,139,162],"datasets":[86],"pairwise,":[88,135],"population":[91,138],"experiments.":[92],"deepTS":[93,124,143],"offers":[94],"rich":[95],"functionality":[96],"to":[97],"streamline":[98],"RNA-Seq-based":[99],"both":[103],"model":[104],"non-model":[106],"organisms":[107],"those":[110],"without":[113],"reference":[114],"transcriptome.":[115],"The":[116],"presented":[117],"case":[118],"studies":[119],"highlight":[120],"capabilities":[122],"demonstrate":[126],"its":[127],"potential":[128],"transcriptome-wide":[131],"We":[141],"believe":[142],"will":[144],"help":[145],"research":[146],"groups,":[147],"regardless":[148],"their":[150],"informatics":[151],"expertise,":[152],"perform":[153],"accessible,":[154],"reproducible":[155],"collaborative":[157],"analyses":[159]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
