{"id":"https://openalex.org/W7117155555","doi":"https://doi.org/10.1093/bioinformatics/btaf673","title":"PARANOiD: Pipeline for Automated Read ANalysis of iCLIP Data","display_name":"PARANOiD: Pipeline for Automated Read ANalysis of iCLIP Data","publication_year":2025,"publication_date":"2025-12-23","ids":{"openalex":"https://openalex.org/W7117155555","doi":"https://doi.org/10.1093/bioinformatics/btaf673","pmid":"https://pubmed.ncbi.nlm.nih.gov/41437628"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf673","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf673","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf673/66121160/btaf673.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf673/66121160/btaf673.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023115063","display_name":"Patrick Barth","orcid":"https://orcid.org/0000-0002-9156-9694"},"institutions":[{"id":"https://openalex.org/I200763008","display_name":"Justus-Liebig-Universit\u00e4t Gie\u00dfen","ror":"https://ror.org/033eqas34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200763008"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Patrick Barth","raw_affiliation_strings":["Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,"],"raw_orcid":"https://orcid.org/0000-0002-9156-9694","affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,","institution_ids":["https://openalex.org/I200763008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054737574","display_name":"Frank F\u00f6rster","orcid":"https://orcid.org/0000-0003-4166-5423"},"institutions":[{"id":"https://openalex.org/I200763008","display_name":"Justus-Liebig-Universit\u00e4t Gie\u00dfen","ror":"https://ror.org/033eqas34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200763008"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Frank F\u00f6rster","raw_affiliation_strings":["Bioinformatics Core Facility, Justus Liebig University Giessen , 35392 Giessen,","Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,"],"raw_orcid":"https://orcid.org/0000-0003-4166-5423","affiliations":[{"raw_affiliation_string":"Bioinformatics Core Facility, Justus Liebig University Giessen , 35392 Giessen,","institution_ids":["https://openalex.org/I200763008"]},{"raw_affiliation_string":"Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,","institution_ids":["https://openalex.org/I200763008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010804745","display_name":"Sebastian Jaenicke","orcid":null},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]},{"id":"https://openalex.org/I200763008","display_name":"Justus-Liebig-Universit\u00e4t Gie\u00dfen","ror":"https://ror.org/033eqas34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200763008"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sebastian Jaenicke","raw_affiliation_strings":["Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,","ELIXIR Germany, Institute of Bio- and Geosciences (IBG-5)\u2013Computational Metagenomics, Forschungszentrum J\u00fclich GmbH , 52425 J\u00fclich,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,","institution_ids":["https://openalex.org/I200763008"]},{"raw_affiliation_string":"ELIXIR Germany, Institute of Bio- and Geosciences (IBG-5)\u2013Computational Metagenomics, Forschungszentrum J\u00fclich GmbH , 52425 J\u00fclich,","institution_ids":["https://openalex.org/I171892758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115044615","display_name":"Fabienne Thelen","orcid":"https://orcid.org/0009-0008-9890-6228"},"institutions":[{"id":"https://openalex.org/I200763008","display_name":"Justus-Liebig-Universit\u00e4t Gie\u00dfen","ror":"https://ror.org/033eqas34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200763008"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fabienne Thelen","raw_affiliation_strings":["Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,"],"raw_orcid":"https://orcid.org/0009-0008-9890-6228","affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,","institution_ids":["https://openalex.org/I200763008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095903377","display_name":"Oliver Rossbach","orcid":null},"institutions":[{"id":"https://openalex.org/I200763008","display_name":"Justus-Liebig-Universit\u00e4t Gie\u00dfen","ror":"https://ror.org/033eqas34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200763008"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Oliver Rossbach","raw_affiliation_strings":["Institute of Biochemistry, Faculty of Biology and Chemistry (FB08), Justus Liebig University Giessen , 35392 Giessen,"],"raw_orcid":"https://orcid.org/0000-0002-1172-0359","affiliations":[{"raw_affiliation_string":"Institute of Biochemistry, Faculty of Biology and Chemistry (FB08), Justus Liebig University Giessen , 35392 Giessen,","institution_ids":["https://openalex.org/I200763008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088808959","display_name":"Friedemann Weber","orcid":"https://orcid.org/0000-0001-9737-337X"},"institutions":[{"id":"https://openalex.org/I200763008","display_name":"Justus-Liebig-Universit\u00e4t Gie\u00dfen","ror":"https://ror.org/033eqas34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200763008"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Friedemann Weber","raw_affiliation_strings":["German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen , 35392 Giessen,"],"raw_orcid":"https://orcid.org/0000-0001-9737-337X","affiliations":[{"raw_affiliation_string":"German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen , 35392 Giessen,","institution_ids":["https://openalex.org/I200763008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030020118","display_name":"Lyudmila Shalamova","orcid":"https://orcid.org/0000-0002-4393-1281"},"institutions":[{"id":"https://openalex.org/I200763008","display_name":"Justus-Liebig-Universit\u00e4t Gie\u00dfen","ror":"https://ror.org/033eqas34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200763008"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lyudmila Shalamova","raw_affiliation_strings":["German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen , 35392 Giessen,"],"raw_orcid":"https://orcid.org/0000-0002-4393-1281","affiliations":[{"raw_affiliation_string":"German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen , 35392 Giessen,","institution_ids":["https://openalex.org/I200763008"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088085534","display_name":"Alexander Goesmann","orcid":"https://orcid.org/0000-0002-7086-2568"},"institutions":[{"id":"https://openalex.org/I200763008","display_name":"Justus-Liebig-Universit\u00e4t Gie\u00dfen","ror":"https://ror.org/033eqas34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200763008"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alexander Goesmann","raw_affiliation_strings":["Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,"],"raw_orcid":"https://orcid.org/0000-0002-7086-2568","affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, Justus Liebig University Giessen , 35392 Giessen,","institution_ids":["https://openalex.org/I200763008"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.56816291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.5012000203132629,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.5012000203132629,"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/T10604","display_name":"RNA Research and Splicing","score":0.09200000017881393,"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":0.05570000037550926,"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/pipeline","display_name":"Pipeline (software)","score":0.7562000155448914},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5378999710083008},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.374099999666214},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.31850001215934753},{"id":"https://openalex.org/keywords/automated-method","display_name":"Automated method","score":0.28290000557899475}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7738999724388123},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7562000155448914},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5378999710083008},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.374099999666214},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3702999949455261},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.34540000557899475},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.31850001215934753},{"id":"https://openalex.org/C3019060180","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automated method","level":2,"score":0.28290000557899475},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.2793000042438507},{"id":"https://openalex.org/C138827492","wikidata":"https://www.wikidata.org/wiki/Q6661985","display_name":"Data processing","level":2,"score":0.2581999897956848},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2563000023365021},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.2540999948978424},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2524999976158142},{"id":"https://openalex.org/C199639397","wikidata":"https://www.wikidata.org/wiki/Q1788588","display_name":"Engineering drawing","level":1,"score":0.2502000033855438}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D047468","descriptor_name":"Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D047468","descriptor_name":"Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D047468","descriptor_name":"Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf673","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf673","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf673/66121160/btaf673.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41437628","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41437628","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},{"id":"pmh:oai:pubmedcentral.nih.gov:13020903","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13020903/","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf673","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf673","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf673/66121160/btaf673.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6361542036","display_name":"GRK 2355: Regulatorische Netzwerke im mRNALebenszyklus:\nvon kodierenden zu nichtkodierenden RNAs","funder_award_id":"325443116","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320311010","display_name":"Justus Liebig Universit\u00e4t Gie\u00dfen","ror":"https://ror.org/033eqas34"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7117155555.pdf","grobid_xml":"https://content.openalex.org/works/W7117155555.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA-protein":[1],"interactions":[2],"play":[3],"essential":[4],"roles":[5],"in":[6],"every":[7],"living":[8],"organism,":[9],"with":[10],"RNA":[11],"transcription,":[12],"processing,":[13],"and":[14,50,94,109,142,166],"translation":[15],"being":[16],"just":[17],"a":[18,53,85,139],"few":[19],"examples.":[20],"Therefore,":[21],"determining":[22],"the":[23,37,41,63,79,104,163],"set":[24],"of":[25,40,62,78,92,106],"RNAs":[26],"that":[27],"are":[28,133],"bound":[29],"by":[30],"individual":[31],"RNA-binding":[32],"proteins,":[33],"as":[34,36,135,143],"well":[35],"precise":[38],"location":[39],"interaction,":[42],"is":[43,52,84,160,167,173],"crucial":[44],"for":[45,88,102,138,152],"biological":[46],"understanding.":[47],"CLIP":[48,64],"(UV-cross-linking":[49],"immunoprecipitation)":[51],"method":[54],"developed":[55],"to":[56,117],"study":[57],"these":[58],"interactions.":[59],"Several":[60],"variations":[61],"protocol":[65],"have":[66],"been":[67],"developed,":[68],"e.g.":[69,121],"iCLIP":[70,93],"(individual-nucleotide":[71],"resolution":[72,77],"CLIP),":[73],"which":[74,113,148],"offers":[75],"nucleotide-precise":[76],"cross-linking":[80],"event.":[81],"RESULTS:":[82],"PARANOiD":[83,159],"versatile":[86],"software":[87],"fully":[89],"automated":[90],"analysis":[91,154],"iCLIP2":[95],"data.":[96],"It":[97],"contains":[98],"all":[99],"steps":[100],"necessary":[101],"preprocessing,":[103],"determination":[105],"cross-link":[107,125],"locations,":[108],"several":[110],"additional":[111],"steps,":[112],"can":[114,149],"be":[115,150],"used":[116,151],"detect":[118],"specific":[119],"characteristics,":[120],"definite":[122],"distances":[123],"between":[124],"events":[126],"or":[127],"identify":[128],"binding":[129],"motifs.":[130],"Additionally,":[131],"results":[132],"visualized":[134],"statistical":[136],"plots":[137],"quick":[140],"overview":[141],"standardized":[144],"bioinformatics":[145],"file":[146],"formats,":[147],"further":[153],"steps.":[155],"AVAILABILITY":[156],"AND":[157],"IMPLEMENTATION:":[158],"published":[161],"under":[162],"MIT":[164],"license":[165],"available":[168,174],"from":[169],"https://github.com/patrick-barth/PARANOiD.":[170],"The":[171],"documentation":[172],"at":[175],"https://paranoid.readthedocs.io/en/latest/index.html.":[176]},"counts_by_year":[],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-12-24T00:00:00"}
