{"id":"https://openalex.org/W1542869991","doi":null,"title":"Computational Analysis of an Evolutionarily Conserved Vertebrate Muscle Alternative Splicing Program","display_name":"Computational Analysis of an Evolutionarily Conserved Vertebrate Muscle Alternative Splicing Program","publication_year":2006,"publication_date":"2006-06-15","ids":{"openalex":"https://openalex.org/W1542869991","mag":"1542869991"},"language":"en","primary_location":{"id":"pmh:oai:osti.gov:923004","doi":null,"is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/923004","pdf_url":"https://www.osti.gov/biblio/923004","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.osti.gov/biblio/923004","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045721045","display_name":"Debopriya Das","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Debopriya Das","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029268107","display_name":"Tyson A. Clark","orcid":"https://orcid.org/0000-0002-7779-3227","observed_orcids":["https://orcid.org/0000-0002-7779-3227"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tyson A. Clark","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-7779-3227","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024936558","display_name":"Anthony C. Schweitzer","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Anthony Schweitzer","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008632337","display_name":"Henry Marr","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Henry Marr","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111571077","display_name":"Miki L. Yamamoto","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Miki Yamamoto","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113788794","display_name":"Marilyn Parra","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Marilyn Parra","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035138804","display_name":"Josh Arribere","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Josh Arribere","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048467633","display_name":"Simon Minovitsky","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Simon Minovitsky","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107834893","display_name":"Inna L Dubchak","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Inna Dubchak","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024545644","display_name":"John E. Blume","orcid":"https://orcid.org/0000-0003-3026-953X","observed_orcids":["https://orcid.org/0000-0003-3026-953X"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"John E. Blume","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5037151010","display_name":"John G. Conboy","orcid":"https://orcid.org/0000-0001-6541-7606","observed_orcids":["https://orcid.org/0000-0001-6541-7606"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"John G. Conboy","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-6541-7606","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"35","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":1.0,"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":1.0,"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/T10441","display_name":"Muscle Physiology and Disorders","score":0.0,"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":0.0,"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/exon-microarrays","display_name":"exon microarrays","score":0.8080000281333923},{"id":"https://openalex.org/keywords/cytoskeletal-proteins","display_name":"cytoskeletal proteins","score":0.9710000157356262},{"id":"https://openalex.org/keywords/muscle-cell-differentiation","display_name":"muscle cell differentiation","score":0.8420000076293945},{"id":"https://openalex.org/keywords/phylogenetic-conservation","display_name":"phylogenetic conservation","score":0.8700000047683716},{"id":"https://openalex.org/keywords/vertebrate-muscle","display_name":"vertebrate muscle","score":0.6600000262260437}],"concepts":[{"id":"https://openalex.org/C2778961482","wikidata":"https://www.wikidata.org/wiki/Q25241","display_name":"Vertebrate","level":3,"score":0.8074243068695068},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.6915872693061829},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.6886144280433655},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.597149133682251},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.558605432510376},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5287886261940002},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.51670241355896},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4433271586894989},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.4336230754852295},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33929210901260376},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23621001839637756},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.082996666431427},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:osti.gov:923004","doi":null,"is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/923004","pdf_url":"https://www.osti.gov/biblio/923004","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:info:ark/67531/metadc900357","doi":null,"is_oa":false,"landing_page_url":"https://digital.library.unt.edu/ark:/67531/metadc900357/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400792","display_name":"University of North Texas Digital Library (University of North Texas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I123534392","host_organization_name":"University of North Texas","host_organization_lineage":["https://openalex.org/I123534392"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal Name: Nucleic Acids Research; Journal Volume: 35; Related Information: Journal Publication Date: 2007","raw_type":"Article"},{"id":"mag:1542869991","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/content/qt54698760/qt54698760.pdf?t=lnqzpc","pdf_url":null,"source":{"id":"https://openalex.org/S2764971142","display_name":"Lawrence Berkeley National Laboratory","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":"https://openalex.org/P4320800592","host_organization_name":"United States Department of Energy","host_organization_lineage":["https://openalex.org/P4320800592"],"host_organization_lineage_names":["United States Department of Energy"],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"Lawrence Berkeley National Laboratory","raw_type":null},{"id":"mag:3021681867","doi":null,"is_oa":true,"landing_page_url":"https://www.osti.gov/servlets/purl/923004","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":null,"is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research","raw_type":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:923004","doi":null,"is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/923004","pdf_url":"https://www.osti.gov/biblio/923004","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1398330795","display_name":null,"funder_award_id":"DE-AC03-?","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1643223109","display_name":null,"funder_award_id":"AC03-76SF00098","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G193590374","display_name":null,"funder_award_id":"DEAC03-76SF00098","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7444770027","display_name":null,"funder_award_id":"DE-AC03- 76SF00098","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306101","display_name":"National Aeronautics and Space Administration","ror":"https://ror.org/027ka1x80"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1542869991.pdf","grobid_xml":"https://content.openalex.org/works/W1542869991.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1480376833","https://openalex.org/W1498410508","https://openalex.org/W1514379483","https://openalex.org/W1555409852","https://openalex.org/W1560913816","https://openalex.org/W1699218328","https://openalex.org/W1963918734","https://openalex.org/W1971158461","https://openalex.org/W1986113553","https://openalex.org/W1993780097","https://openalex.org/W2008836144","https://openalex.org/W2012145036","https://openalex.org/W2019518393","https://openalex.org/W2020334159","https://openalex.org/W2024853196","https://openalex.org/W2038903837","https://openalex.org/W2045300068","https://openalex.org/W2053998703","https://openalex.org/W2059293195","https://openalex.org/W2060286924","https://openalex.org/W2070340804","https://openalex.org/W2072088482","https://openalex.org/W2081748748","https://openalex.org/W2089346704","https://openalex.org/W2092831145","https://openalex.org/W2093506762","https://openalex.org/W2096940705","https://openalex.org/W2099117011","https://openalex.org/W2102887078","https://openalex.org/W2103116226","https://openalex.org/W2108317489","https://openalex.org/W2110901570","https://openalex.org/W2114066176","https://openalex.org/W2116178342","https://openalex.org/W2118667823","https://openalex.org/W2118823143","https://openalex.org/W2120900302","https://openalex.org/W2124169580","https://openalex.org/W2125487242","https://openalex.org/W2126558916","https://openalex.org/W2127230663","https://openalex.org/W2127997124","https://openalex.org/W2128016314","https://openalex.org/W2128195632","https://openalex.org/W2128319725","https://openalex.org/W2129071328","https://openalex.org/W2137057460","https://openalex.org/W2139703939","https://openalex.org/W2141124826","https://openalex.org/W2144710927","https://openalex.org/W2149038500","https://openalex.org/W2152941241","https://openalex.org/W2158433767","https://openalex.org/W2159958242","https://openalex.org/W2161879263","https://openalex.org/W2167616277","https://openalex.org/W2168909179","https://openalex.org/W2169361401","https://openalex.org/W2171605197","https://openalex.org/W2171805190","https://openalex.org/W2172189627"],"related_works":["https://openalex.org/W4302389332","https://openalex.org/W2121816001","https://openalex.org/W2079643255","https://openalex.org/W2093506762","https://openalex.org/W2072088482","https://openalex.org/W2057774013","https://openalex.org/W7096764543","https://openalex.org/W324535036","https://openalex.org/W2106696739","https://openalex.org/W2289893284"],"abstract_inverted_index":{"A":[0,26],"novel":[1,109],"exon":[2,11],"microarray":[3,218],"format":[4],"that":[5,138,166],"probes":[6],"gene":[7],"expression":[8,156,212],"with":[9,67],"single":[10],"resolution":[12],"was":[13,124],"employed":[14],"to":[15,42,56,169],"elucidate":[16],"critical":[17,168],"features":[18],"of":[19,28,45,75,81,93,116,132,157,160,163,213],"a":[20,98,108,145,158],"vertebrate":[21,77],"muscle":[22,47,68,170],"alternative":[23,152],"splicing":[24,48,105,121,142,153],"program.":[25,49],"dataset":[27],"56":[29],"microarray-defined,":[30],"muscle-enriched":[31,64,192,211],"exons":[32,214],"and":[33,70,112,140,180,194],"their":[34],"flanking":[35,201],"introns":[36],"were":[37,54,84],"examined":[38],"computationally":[39],"in":[40,86,129,148,199],"order":[41],"investigate":[43],"coordination":[44],"the":[46,87,94,150,191,200,210,217],"Candidate":[50],"intron":[51],"regulatory":[52,82],"motifs":[53,83],"required":[55],"meet":[57],"several":[58,76],"stringent":[59],"criteria:":[60],"significant":[61],"over-representation":[62],"near":[63],"exons,":[65],"correlation":[66],"expression,":[69],"phylogenetic":[71],"conservation":[72],"among":[73],"genomes":[74],"orders.":[78],"Three":[79],"classes":[80],"identified":[85],"proximal":[88],"downstream":[89],"intron,":[90],"within":[91],"200nt":[92],"target":[95],"exons:":[96],"UGCAUG,":[97],"specific":[99],"binding":[100,117],"site":[101],"for":[102,119],"Fox-1":[103],"related":[104],"factors;":[106],"ACUAAC,":[107],"branchpoint-like":[110],"element;":[111],"UG-/UGC-rich":[113],"elements":[114],"characteristic":[115],"sites":[118],"CELF":[120,141],"factors.":[122],"UGCAUG":[123],"remarkably":[125],"enriched,":[126],"being":[127],"present":[128],"nearly":[130],"one-half":[131],"all":[133],"cases.":[134],"These":[135],"studies":[136],"suggest":[137],"Fox":[139],"factors":[143],"play":[144],"major":[146],"role":[147],"enforcing":[149],"muscle-specific":[151],"program,":[154],"facilitating":[155],"set":[159],"unique":[161],"isoforms":[162],"cytoskeletal":[164],"proteins":[165],"are":[167,176],"cell":[171],"differentiation.":[172],"Supplementary":[173],"materials:":[174],"There":[175],"four":[177],"supplementary":[178,182,204],"tables":[179,185],"one":[181],"figure.":[183],"The":[184,203],"provide":[186],"additional":[187],"detailed":[188],"information":[189],"concerning":[190],"datasets,":[193],"about":[195],"over-represented":[196],"oligonucleotide":[197],"sequences":[198],"introns.":[202],"figure":[205],"shows":[206],"RT-PCR":[207],"data":[208],"confirming":[209],"predicted":[215],"from":[216],"analysis.":[219]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
