{"id":"https://openalex.org/W7205637320","doi":null,"title":"Novel Integrated Galaxy Workflow Suites for comprehensive small non coding RNA Analysis","display_name":"Novel Integrated Galaxy Workflow Suites for comprehensive small non coding RNA Analysis","publication_year":2026,"publication_date":"2026-06-22","ids":{"openalex":"https://openalex.org/W7205637320"},"language":"en","primary_location":{"id":"pmh:oai:HAL:hal-05688981v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-05688981v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Galaxy Community Conference 2026, Jun 2026, Clermont - Ferrand, France","raw_type":"info:eu-repo/semantics/conferenceObject"},"volume":null,"type":"conference-paper","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.science/hal-05688981v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080750618","display_name":"Joe Ueda","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210107326","display_name":"Institut de Biologie Paris-Seine","ror":"https://ror.org/01c2cjg59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210107326"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ueda, Joe","raw_affiliation_strings":["IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","InforBio - Bioinformatique [IBPS] (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","institution_ids":["https://openalex.org/I4210107326"]},{"raw_affiliation_string":"InforBio - Bioinformatique [IBPS] (France)","institution_ids":["https://openalex.org/I4210107326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078634979","display_name":"Lorette Noiret","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210107326","display_name":"Institut de Biologie Paris-Seine","ror":"https://ror.org/01c2cjg59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210107326"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Noiret, Lorette","raw_affiliation_strings":["IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","InforBio - Bioinformatique [IBPS] (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","institution_ids":["https://openalex.org/I4210107326"]},{"raw_affiliation_string":"InforBio - Bioinformatique [IBPS] (France)","institution_ids":["https://openalex.org/I4210107326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089138210","display_name":"Antoine Boivin","orcid":"https://orcid.org/0000-0001-8671-1599","observed_orcids":["https://orcid.org/0000-0001-8671-1599"]},"institutions":[{"id":"https://openalex.org/I4210107326","display_name":"Institut de Biologie Paris-Seine","ror":"https://ror.org/01c2cjg59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210107326"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Boivin, Antoine","raw_affiliation_strings":["IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","TErBio - \u00c9pig\u00e9n\u00e9tique transg\u00e9n\u00e9rationelle et biologie des petits ARN = Transgenerational Epigenetics & small RNA biology (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","institution_ids":["https://openalex.org/I4210107326"]},{"raw_affiliation_string":"TErBio - \u00c9pig\u00e9n\u00e9tique transg\u00e9n\u00e9rationelle et biologie des petits ARN = Transgenerational Epigenetics & small RNA biology (France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065810212","display_name":"Laure Teysset","orcid":"https://orcid.org/0000-0002-7413-1850","observed_orcids":["https://orcid.org/0000-0002-7413-1850"]},"institutions":[{"id":"https://openalex.org/I4210107326","display_name":"Institut de Biologie Paris-Seine","ror":"https://ror.org/01c2cjg59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210107326"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Teysset, Laure","raw_affiliation_strings":["IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","TErBio - \u00c9pig\u00e9n\u00e9tique transg\u00e9n\u00e9rationelle et biologie des petits ARN = Transgenerational Epigenetics & small RNA biology (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","institution_ids":["https://openalex.org/I4210107326"]},{"raw_affiliation_string":"TErBio - \u00c9pig\u00e9n\u00e9tique transg\u00e9n\u00e9rationelle et biologie des petits ARN = Transgenerational Epigenetics & small RNA biology (France)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041164066","display_name":"Cl\u00e9ment Carr\u00e9","orcid":"https://orcid.org/0000-0002-9668-4288","observed_orcids":["https://orcid.org/0000-0002-9668-4288"]},"institutions":[{"id":"https://openalex.org/I4210107326","display_name":"Institut de Biologie Paris-Seine","ror":"https://ror.org/01c2cjg59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210107326"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Carr\u00e9, Cl\u00e9ment","raw_affiliation_strings":["IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","TErBio - \u00c9pig\u00e9n\u00e9tique transg\u00e9n\u00e9rationelle et biologie des petits ARN = Transgenerational Epigenetics & small RNA biology (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","institution_ids":["https://openalex.org/I4210107326"]},{"raw_affiliation_string":"TErBio - \u00c9pig\u00e9n\u00e9tique transg\u00e9n\u00e9rationelle et biologie des petits ARN = Transgenerational Epigenetics & small RNA biology (France)","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069276927","display_name":"Na\u00efra Naouar","orcid":"https://orcid.org/0000-0003-2161-8603","observed_orcids":["https://orcid.org/0000-0003-2161-8603"]},"institutions":[{"id":"https://openalex.org/I4210107326","display_name":"Institut de Biologie Paris-Seine","ror":"https://ror.org/01c2cjg59","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210107326"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Naouar, Na\u00efra","raw_affiliation_strings":["IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","IBPS-Artbio - Bioinformatique [IBPS] (France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBPS - Institut de Biologie Paris Seine (Quai Saint-Bernard75252 PARIS CEDEX 05 - France)","institution_ids":["https://openalex.org/I4210107326"]},{"raw_affiliation_string":"IBPS-Artbio - Bioinformatique [IBPS] (France)","institution_ids":["https://openalex.org/I4210107326"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210107326"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"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":null,"issue":null,"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":0.4535999894142151,"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":0.4535999894142151,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.15610000491142273,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.05620000138878822,"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/small-rna","display_name":"small RNA","score":0.9319999814033508},{"id":"https://openalex.org/keywords/piwi-interacting-rnas","display_name":"piRNA","score":0.871999979019165},{"id":"https://openalex.org/keywords/pirna-clusters","display_name":"piRNA clusters","score":0.9449999928474426},{"id":"https://openalex.org/keywords/trna-derived-fragments","display_name":"tRNA-derived fragments","score":0.9269999861717224},{"id":"https://openalex.org/keywords/histone-modifications","display_name":"histone modifications","score":0.9309999942779541},{"id":"https://openalex.org/keywords/chip-seq","display_name":"ChIP-seq","score":0.9089999794960022},{"id":"https://openalex.org/keywords/small-rna-sequencing","display_name":"small RNA sequencing","score":0.9980000257492065},{"id":"https://openalex.org/keywords/bioinformatics-pipeline","display_name":"bioinformatics pipeline","score":0.8270000219345093},{"id":"https://openalex.org/keywords/galaxy-platform","display_name":"Galaxy platform","score":0.7480000257492065},{"id":"https://openalex.org/keywords/transposon-silencing","display_name":"transposon silencing","score":0.7250000238418579},{"id":"https://openalex.org/keywords/gene-expression-regulation","display_name":"gene expression regulation","score":0.41200000047683716}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7275000214576721},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.689300000667572},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.5544999837875366},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4309000074863434},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.40720000863075256},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36320000886917114},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3398999869823456},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.28679999709129333},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26969999074935913},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.2565000057220459},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.25380000472068787}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:HAL:hal-05688981v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-05688981v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Galaxy Community Conference 2026, Jun 2026, Clermont - Ferrand, France","raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-05688981v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-05688981v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Galaxy Community Conference 2026, Jun 2026, Clermont - Ferrand, France","raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2571119285","https://openalex.org/W2996823043","https://openalex.org/W4256320612","https://openalex.org/W2887110521","https://openalex.org/W4223461291","https://openalex.org/W2067634674","https://openalex.org/W7220846218","https://openalex.org/W2612843518","https://openalex.org/W2799571658","https://openalex.org/W2414286129"],"abstract_inverted_index":{"Small":[0],"non-coding":[1],"RNAs":[2,9,49],"(sncRNAs)":[3],"are":[4,133,142],"a":[5,12,44],"class":[6],"of":[7,31,54,74,104,226,236,242,253],"regulatory":[8],"that":[10],"play":[11],"central":[13],"role":[14,59],"in":[15,60],"gene":[16,186],"expression":[17],"and":[18,41,72,129,218,245,268],"genome":[19],"stability.":[20],"Although":[21,57],"this":[22,210],"field":[23],"has":[24],"recently":[25],"gained":[26],"significant":[27],"attention,":[28],"many":[29],"aspects":[30,225],"sncRNA":[32,55,158,169,227,254],"biology":[33],"remain":[34,82],"poorly":[35],"understood,":[36],"especially":[37],"regarding":[38],"their":[39,58,92],"emergence":[40,71],"functional":[42],"interactions.As":[43],"representative":[45],"use":[46],"case,":[47],"PIWI-interacting":[48],"(piRNAs)":[50],"illustrate":[51],"the":[52,67,70,102,137,234,240,246,251,272],"challenges":[53],"analysis.":[56],"transposable":[61],"element":[62],"silencing":[63],"is":[64,200,231],"well":[65],"characterized,":[66],"processes":[68],"governing":[69],"activation":[73,86],"piRNA-producing":[75],"genomic":[76],"regions,":[77],"known":[78],"as":[79,108,120,149,172],"piRNA":[80],"clusters,":[81],"less":[83],"understood.":[84],"Their":[85],"can":[87],"be":[88],"assessed":[89],"by":[90,101],"quantifying":[91],"abundance":[93],"using":[94],"small":[95,257],"RNA-seq":[96,258],"across":[97],"different":[98,224],"conditions,":[99],"complemented":[100],"analysis":[103,117,235],"epigenetic":[105],"markers,":[106],"such":[107,119,148,171],"histone":[109,243],"modifications,":[110],"through":[111,256,271],"ChIP-seq":[112,237],"experiments.":[113],"While":[114],"several":[115],"individual":[116],"tools":[118,147],"FastQC":[121],"for":[122,126,131,195,207,239],"quality":[123],"control,":[124],"Bowtie":[125],"sequence":[127],"alignment,":[128],"MACS3":[130],"peak-calling":[132],"already":[134],"available":[135,201],"within":[136,202],"Galaxy":[138,273],"platform,":[139],"important":[140],"components":[141],"still":[143],"missing,":[144],"including":[145,189],"visualization":[146],"Enhanced":[150],"heatmap.":[151],"More":[152],"importantly,":[153],"dedicated":[154,232],"workflows":[155,220],"tailored":[156],"to":[157,167,182,222,233],"have":[159,179],"not":[160],"been":[161,180],"developed":[162],"yet.":[163],"This":[164],"limitation":[165],"applies":[166],"other":[168,184],"classes":[170],"tRNA-derived":[173],"fragments":[174],"(tRFs),":[175],"whose":[176],"elevated":[177],"levels":[178],"shown":[181],"disrupt":[183],"sncRNA-mediated":[185],"repression":[187],"pathways,":[188],"piRNAs.":[190],"However,":[191],"no":[192],"specialized":[193],"tool":[194,216],"tRF":[196],"quantification,":[197],"like":[198],"MINTmap,":[199],"Galaxy,":[203],"further":[204],"limiting":[205],"accessibility":[206,270],"non-computational":[208],"users.In":[209],"context,":[211],"we":[212],"present":[213],"two":[214],"bioinformatics":[215],"suites":[217],"associated":[219],"designed":[221],"investigate":[223],"biology.":[228],"One":[229],"workflow":[230],"data":[238],"profiling":[241],"modifications":[244],"second":[247],"one":[248],"focuses":[249],"on":[250],"characterization":[252],"population":[255],"data.":[259],"They":[260],"will":[261],"integrate":[262],"existing":[263],"tools,":[264],"introduce":[265],"missing":[266],"functionalities,":[267],"improve":[269],"framework.":[274]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-09-02T00:00:00"}