{"id":"https://openalex.org/W2944987874","doi":"https://doi.org/10.1093/bioinformatics/btz405","title":"Estimating the strength of expression conservation from high throughput RNA-seq data","display_name":"Estimating the strength of expression conservation from high throughput RNA-seq data","publication_year":2019,"publication_date":"2019-05-16","ids":{"openalex":"https://openalex.org/W2944987874","doi":"https://doi.org/10.1093/bioinformatics/btz405","mag":"2944987874","pmid":"https://pubmed.ncbi.nlm.nih.gov/31114853"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz405","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz405","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/A5080712092","display_name":"Xun Gu","orcid":"https://orcid.org/0000-0001-9845-6986"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xun Gu","raw_affiliation_strings":["Department of Genetics, Development, and Cell Biology, Iowa State University , Ames, IA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Development, and Cell Biology, Iowa State University , Ames, IA, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030927081","display_name":"Hang Ruan","orcid":"https://orcid.org/0000-0001-7506-3805"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Hang Ruan","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, McGovern Medical School , The University of Texas Health Science Center at Houston, Houston, TX, USA","MOE Key Laboratory of Contemporary Anthropology, Fudan University , Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, McGovern Medical School , The University of Texas Health Science Center at Houston, Houston, TX, USA","institution_ids":["https://openalex.org/I919571938"]},{"raw_affiliation_string":"MOE Key Laboratory of Contemporary Anthropology, Fudan University , Shanghai, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100378741","display_name":"H. J. Yang","orcid":"https://orcid.org/0009-0004-8274-9863"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingwen Yang","raw_affiliation_strings":["Human Phenome Institute, Fudan University , Shanghai, China","MOE Key Laboratory of Contemporary Anthropology, Fudan University , Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Phenome Institute, Fudan University , Shanghai, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"MOE Key Laboratory of Contemporary Anthropology, Fudan University , Shanghai, China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5080712092"],"corresponding_institution_ids":["https://openalex.org/I173911158"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.58,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.65556959,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"35","issue":"23","first_page":"5030","last_page":"5038"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.37229999899864197,"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":0.37229999899864197,"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/T10885","display_name":"Gene expression and cancer classification","score":0.07829999923706055,"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":0.07339999824762344,"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/expression","display_name":"Expression (computer science)","score":0.6507835388183594},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6061080098152161},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5624626278877258},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5183923840522766},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5004072189331055},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4800228178501129},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.46800246834754944},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4215911328792572},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.26790598034858704},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2180837094783783},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14724400639533997},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07271414995193481}],"concepts":[{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6507835388183594},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6061080098152161},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5624626278877258},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5183923840522766},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5004072189331055},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4800228178501129},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.46800246834754944},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4215911328792572},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26790598034858704},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2180837094783783},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14724400639533997},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07271414995193481},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz405","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz405","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31114853","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31114853","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.7599999904632568}],"awards":[{"id":"https://openalex.org/G5015279867","display_name":null,"funder_award_id":"2017YFC0908600","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6311218165","display_name":null,"funder_award_id":"31571355","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"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1966206981","https://openalex.org/W1967752350","https://openalex.org/W1970270474","https://openalex.org/W1971977350","https://openalex.org/W1981509058","https://openalex.org/W1983275320","https://openalex.org/W1986376668","https://openalex.org/W2000495354","https://openalex.org/W2014279841","https://openalex.org/W2020208273","https://openalex.org/W2040618467","https://openalex.org/W2054755820","https://openalex.org/W2068872007","https://openalex.org/W2076469310","https://openalex.org/W2090803844","https://openalex.org/W2093477772","https://openalex.org/W2095178364","https://openalex.org/W2103320667","https://openalex.org/W2114104545","https://openalex.org/W2128969076","https://openalex.org/W2129558874","https://openalex.org/W2143492752","https://openalex.org/W2145359428","https://openalex.org/W2148899381","https://openalex.org/W2149641002","https://openalex.org/W2150989284","https://openalex.org/W2157274247","https://openalex.org/W2166117746","https://openalex.org/W2168258419","https://openalex.org/W2168513406","https://openalex.org/W2258109946","https://openalex.org/W2278336807","https://openalex.org/W2326475460","https://openalex.org/W2542145069","https://openalex.org/W2556374950","https://openalex.org/W4230304092","https://openalex.org/W4243261323","https://openalex.org/W4244432582","https://openalex.org/W6650371812","https://openalex.org/W6682122819","https://openalex.org/W6730173538"],"related_works":["https://openalex.org/W2136583354","https://openalex.org/W2111238207","https://openalex.org/W2760721665","https://openalex.org/W4205762803","https://openalex.org/W330130819","https://openalex.org/W2288610023","https://openalex.org/W2392243736","https://openalex.org/W2112044895","https://openalex.org/W2535856026","https://openalex.org/W86652014"],"abstract_inverted_index":{"MOTIVATION:":[0],"Evolution":[1],"of":[2,52,70,115],"gene":[3],"across":[4],"species":[5,42],"is":[6,21,132,153],"usually":[7],"subject":[8],"to":[9,13,40,65,95,110],"the":[10,15,25,68,80,112,127],"stabilizing":[11],"selection":[12],"maintain":[14],"optimal":[16],"expression":[17,27,71,116],"level.":[18],"While":[19],"it":[20],"generally":[22],"accepted":[23],"that":[24,105],"resulting":[26],"conservation":[28,72],"may":[29,161],"vary":[30],"considerably":[31],"among":[32,77],"genes,":[33],"statistically":[34],"reliable":[35],"estimation":[36],"remains":[37],"challenging,":[38],"due":[39],"few":[41],"included":[43],"in":[44,126],"current":[45],"comparative":[46],"RNA-seq":[47,83],"data":[48],"with":[49],"high":[50,81],"number":[51],"unknown":[53],"parameters.":[54],"RESULTS:":[55],"In":[56],"this":[57],"paper,":[58],"we":[59,88],"develop":[60,137],"a":[61],"gamma":[62],"distribution":[63],"model":[64],"describe":[66],"how":[67],"strength":[69],"(denoted":[73],"by":[74],"W)":[75],"varies":[76],"genes.":[78],"Given":[79],"throughput":[82],"datasets":[84],"from":[85],"multiple":[86],"species,":[87],"then":[89],"formulate":[90],"an":[91],"empirical":[92],"Bayesian":[93],"procedure":[94],"estimate":[96],"W":[97],"for":[98,150],"each":[99],"gene.":[100],"Our":[101,121],"case":[102],"studies":[103],"showed":[104],"those":[106],"W-estimates":[107],"are":[108],"useful":[109],"study":[111],"evolutionary":[113],"pattern":[114],"conservation.":[117],"AVAILABILITY":[118],"AND":[119],"IMPLEMENTATION:":[120],"method":[122],"has":[123],"been":[124],"implemented":[125],"R-package":[128],"software,":[129],"TreeExp,":[130],"which":[131],"publically":[133],"available":[134,154],"at":[135,155],"Github":[136],"site":[138],"https://github.com/hr1912/TreeExp.":[139],"It":[140],"involves":[141],"three":[142],"functions:":[143],"estParaGamma,":[144],"estParaQ":[145],"and":[146],"estParaWBayesian.":[147],"The":[148],"manual":[149],"software":[151],"TreeExp":[152],"https://github.com/hr1912/TreeExp/tree/master/vignettes.":[156],"For":[157],"any":[158],"question,":[159],"one":[160],"contact":[162],"Dr":[163],"Hang":[164],"Ruan":[165],"(Hang.Ruan@uth.tmc.edu).":[166]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
