{"id":"https://openalex.org/W4409295056","doi":"https://doi.org/10.3389/fbinf.2025.1532981","title":"Transcripts derived from AmnSINE1 repetitive sequences are depleted in the cortex of autism spectrum disorder patients","display_name":"Transcripts derived from AmnSINE1 repetitive sequences are depleted in the cortex of autism spectrum disorder patients","publication_year":2025,"publication_date":"2025-04-09","ids":{"openalex":"https://openalex.org/W4409295056","doi":"https://doi.org/10.3389/fbinf.2025.1532981","pmid":"https://pubmed.ncbi.nlm.nih.gov/40270680"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1532981","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1532981","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1532981/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1532981/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066478742","display_name":"Nicolina Sciaraffa","orcid":"https://orcid.org/0000-0002-3380-0181"},"institutions":[{"id":"https://openalex.org/I4210150906","display_name":"Ri.MED","ror":"https://ror.org/05qetrn02","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210150906"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Nicolina Sciaraffa","raw_affiliation_strings":["Advanced Data Analysis Group, Ri. MED Foundation, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Data Analysis Group, Ri. MED Foundation, Palermo, Italy","institution_ids":["https://openalex.org/I4210150906"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015205454","display_name":"Daniele Santoni","orcid":"https://orcid.org/0000-0003-1898-5285"},"institutions":[{"id":"https://openalex.org/I4210115688","display_name":"Institute for Systems Analysis","ror":"https://ror.org/02kmet255","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210115688"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Daniele Santoni","raw_affiliation_strings":["Institute for System Analysis and Computer Science \"Antonio Ruberti\", National Research Council of Italy (IASI-CNR), Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for System Analysis and Computer Science \"Antonio Ruberti\", National Research Council of Italy (IASI-CNR), Rome, Italy","institution_ids":["https://openalex.org/I4210115688"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048110554","display_name":"Andrea Li Greci","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150906","display_name":"Ri.MED","ror":"https://ror.org/05qetrn02","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210150906"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Li Greci","raw_affiliation_strings":["Advanced Data Analysis Group, Ri. MED Foundation, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Data Analysis Group, Ri. MED Foundation, Palermo, Italy","institution_ids":["https://openalex.org/I4210150906"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006034069","display_name":"Swonild Ilenia Genovese","orcid":"https://orcid.org/0000-0001-6302-5879"},"institutions":[{"id":"https://openalex.org/I900890020","display_name":"University of Palermo","ror":"https://ror.org/044k9ta02","country_code":"IT","type":"education","lineage":["https://openalex.org/I900890020"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Swonild Ilenia Genovese","raw_affiliation_strings":["Independent Researcher, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Independent Researcher, Palermo, Italy","institution_ids":["https://openalex.org/I900890020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026545305","display_name":"Claudia Coronnello","orcid":"https://orcid.org/0000-0001-5962-8642"},"institutions":[{"id":"https://openalex.org/I4210150906","display_name":"Ri.MED","ror":"https://ror.org/05qetrn02","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210150906"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Claudia Coronnello","raw_affiliation_strings":["Advanced Data Analysis Group, Ri. MED Foundation, Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Data Analysis Group, Ri. MED Foundation, Palermo, Italy","institution_ids":["https://openalex.org/I4210150906"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063657176","display_name":"Walter Arancio","orcid":"https://orcid.org/0000-0002-6736-7734"},"institutions":[{"id":"https://openalex.org/I4210130743","display_name":"Institute for Biomedical Research and Innovation","ror":"https://ror.org/03byxpq91","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210130743"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Walter Arancio","raw_affiliation_strings":["Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Palermo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Palermo, Italy","institution_ids":["https://openalex.org/I4210130743","https://openalex.org/I4210155236"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5063657176"],"corresponding_institution_ids":["https://openalex.org/I4210130743","https://openalex.org/I4210155236"],"apc_list":{"value":2125,"currency":"USD","value_usd":2125},"apc_paid":{"value":2125,"currency":"USD","value_usd":2125},"fwci":0.7048,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.6645971,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"5","issue":null,"first_page":"1532981","last_page":"1532981"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10106","display_name":"Autism Spectrum Disorder Research","score":0.8816999793052673,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10106","display_name":"Autism Spectrum Disorder Research","score":0.8816999793052673,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11772","display_name":"Genetics and Neurodevelopmental Disorders","score":0.02370000071823597,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.01600000075995922,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/autism-spectrum-disorder","display_name":"Autism spectrum disorder","score":0.8155432939529419},{"id":"https://openalex.org/keywords/spectrum","display_name":"Spectrum (functional analysis)","score":0.46391168236732483},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.4615471661090851},{"id":"https://openalex.org/keywords/cortex","display_name":"Cortex (anatomy)","score":0.41915449500083923},{"id":"https://openalex.org/keywords/autism","display_name":"Autism","score":0.40366625785827637},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.3754608929157257},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3397608697414398},{"id":"https://openalex.org/keywords/psychiatry","display_name":"Psychiatry","score":0.2296489179134369},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12727153301239014}],"concepts":[{"id":"https://openalex.org/C2778538070","wikidata":"https://www.wikidata.org/wiki/Q1436063","display_name":"Autism spectrum disorder","level":3,"score":0.8155432939529419},{"id":"https://openalex.org/C156778621","wikidata":"https://www.wikidata.org/wiki/Q1365748","display_name":"Spectrum (functional analysis)","level":2,"score":0.46391168236732483},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.4615471661090851},{"id":"https://openalex.org/C2777348757","wikidata":"https://www.wikidata.org/wiki/Q2346577","display_name":"Cortex (anatomy)","level":2,"score":0.41915449500083923},{"id":"https://openalex.org/C205778803","wikidata":"https://www.wikidata.org/wiki/Q38404","display_name":"Autism","level":2,"score":0.40366625785827637},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.3754608929157257},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3397608697414398},{"id":"https://openalex.org/C118552586","wikidata":"https://www.wikidata.org/wiki/Q7867","display_name":"Psychiatry","level":1,"score":0.2296489179134369},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12727153301239014},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1532981","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1532981","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1532981/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40270680","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40270680","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12015672","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12015672","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:e9cc57273958404a89dbbccca9b18315","is_oa":true,"landing_page_url":"https://doaj.org/article/e9cc57273958404a89dbbccca9b18315","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1532981","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1532981","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1532981/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F7311471023","display_name":"NextGenerationEU","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4409295056.pdf"},"referenced_works_count":73,"referenced_works":["https://openalex.org/W1976400666","https://openalex.org/W1984535493","https://openalex.org/W1986601943","https://openalex.org/W1994518469","https://openalex.org/W2009022397","https://openalex.org/W2017628468","https://openalex.org/W2032679533","https://openalex.org/W2036652203","https://openalex.org/W2037930474","https://openalex.org/W2046387002","https://openalex.org/W2054217796","https://openalex.org/W2079190867","https://openalex.org/W2083381199","https://openalex.org/W2096105837","https://openalex.org/W2098734267","https://openalex.org/W2098941203","https://openalex.org/W2102278945","https://openalex.org/W2120456037","https://openalex.org/W2123500593","https://openalex.org/W2128016314","https://openalex.org/W2129867386","https://openalex.org/W2130388134","https://openalex.org/W2131271579","https://openalex.org/W2134913157","https://openalex.org/W2138207763","https://openalex.org/W2139480055","https://openalex.org/W2149785901","https://openalex.org/W2149959145","https://openalex.org/W2168950294","https://openalex.org/W2170551349","https://openalex.org/W2179438025","https://openalex.org/W2305236534","https://openalex.org/W2346917834","https://openalex.org/W2421217190","https://openalex.org/W2524626331","https://openalex.org/W2529943579","https://openalex.org/W2566339083","https://openalex.org/W2590099042","https://openalex.org/W2613763984","https://openalex.org/W2788010503","https://openalex.org/W2910033056","https://openalex.org/W2917207851","https://openalex.org/W2954482542","https://openalex.org/W2981275956","https://openalex.org/W3014345105","https://openalex.org/W3029928583","https://openalex.org/W3036923110","https://openalex.org/W3097766161","https://openalex.org/W3119240720","https://openalex.org/W3158052545","https://openalex.org/W3162898217","https://openalex.org/W3163012943","https://openalex.org/W3188425922","https://openalex.org/W3203396323","https://openalex.org/W3208232274","https://openalex.org/W4210782186","https://openalex.org/W4211227988","https://openalex.org/W4291392232","https://openalex.org/W4292114232","https://openalex.org/W4294733470","https://openalex.org/W4304630325","https://openalex.org/W4306946976","https://openalex.org/W4308722562","https://openalex.org/W4312085035","https://openalex.org/W4313327172","https://openalex.org/W4320490649","https://openalex.org/W4321236378","https://openalex.org/W4323663741","https://openalex.org/W4362639600","https://openalex.org/W4366599198","https://openalex.org/W4367320428","https://openalex.org/W4386244163","https://openalex.org/W4387341749"],"related_works":["https://openalex.org/W4280602684","https://openalex.org/W4310092953","https://openalex.org/W2227393071","https://openalex.org/W4402326599","https://openalex.org/W1995350144","https://openalex.org/W2082102603","https://openalex.org/W2166141227","https://openalex.org/W3133980636","https://openalex.org/W4378085486","https://openalex.org/W4366602711"],"abstract_inverted_index":{"Aims:":[0],"Autism":[1],"spectrum":[2],"disorder":[3],"(ASD)":[4],"is":[5,32,46],"a":[6,11,66,91,157,200,233],"brain":[7,188],"developmental":[8],"disability":[9],"with":[10,145],"not-fully":[12],"clarified":[13],"etiogenesis.":[14],"Current":[15],"ASD":[16,41,101,122,129,173,196,238],"research":[17],"largely":[18,47],"focuses":[19],"on":[20],"coding":[21],"regions":[22],"of":[23,37,49,73,99,126,166,204],"the":[24,35,116,138,167,217],"genome,":[25],"but":[26,190],"up":[27],"to":[28,40,84],"date":[29],"much":[30],"less":[31],"known":[33],"about":[34],"contribution":[36],"non-coding":[38,44,206],"elements":[39],"risk.":[42],"The":[43,124],"genome":[45],"made":[48],"DNA":[50],"repetitive":[51],"sequences":[52],"(RS).":[53],"Although":[54],"RS":[55,64,87,118],"were":[56,108],"considered":[57],"slightly":[58],"more":[59],"than":[60],"\"junk":[61],"DNA\",":[62],"today":[63],"have":[65],"recognized":[67],"role":[68,92,125,203,234],"in":[69,77,93,110,121,128,156,163,187,195,208,224,237],"almost":[70],"every":[71],"aspect":[72],"human":[74,79,168],"biology,":[75],"especially":[76],"developing":[78],"brain.":[80],"Our":[81,227],"aim":[82],"was":[83,115],"test":[85],"if":[86],"transcription":[88],"may":[89,215],"play":[90],"ASD.":[94],"Methods:":[95],"dorsolateral":[96],"prefrontal":[97],"cortex":[98],"13":[100],"patients":[102],"and":[103,149,182],"39":[104],"matched":[105],"controls.":[106],"Results":[107],"validated":[109],"independent":[111],"datasets.":[112],"Results:":[113],"AmnSINE1":[114,127,142,176,205,213,236],"only":[117,186],"significantly":[119],"downregulated":[120],"specimens.":[123],"has":[130,153],"been":[131,154],"investigated":[132],"at":[133],"multiple":[134],"levels,":[135],"showing":[136],"that":[137,212],"1,416":[139],"genes":[140,178,222],"containing":[141],"are":[143,179,183],"associated":[144],"nervous":[146],"system":[147],"development":[148],"autism":[150],"susceptibility.":[151],"This":[152],"confirmed":[155],"different":[158,172],"experimental":[159],"setting,":[160],"such":[161],"as":[162],"organoid":[164],"models":[165],"cerebral":[169],"cortex,":[170],"harboring":[171],"causative":[174],"mutations.":[175],"related":[177],"transcriptionally":[180],"co-regulated":[181],"involved":[184,194,223],"not":[185],"formation":[189],"can":[191],"specifically":[192],"be":[193],"development.":[197,239],"Looking":[198],"for":[199,221,235],"possible":[201],"direct":[202],"transcripts":[207,214],"ASD,":[209],"we":[210],"report":[211],"alter":[216],"miRNA":[218],"regulatory":[219],"landscape":[220],"neurogenesis.":[225],"Conclusion:":[226],"findings":[228],"provide":[229],"preliminary":[230],"evidence":[231],"supporting":[232]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
