{"id":"https://openalex.org/W3209768589","doi":"https://doi.org/10.1093/bioinformatics/btab755","title":"Peakhood: individual site context extraction for CLIP-seq peak regions","display_name":"Peakhood: individual site context extraction for CLIP-seq peak regions","publication_year":2021,"publication_date":"2021-10-29","ids":{"openalex":"https://openalex.org/W3209768589","doi":"https://doi.org/10.1093/bioinformatics/btab755","mag":"3209768589","pmid":"https://pubmed.ncbi.nlm.nih.gov/34734974"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab755","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab755","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":"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":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btab755","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041266113","display_name":"Micha\u00ebl Uhl","orcid":"https://orcid.org/0000-0002-9563-4991"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michael Uhl","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9563-4991","affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000223586","display_name":"Dominik Rabsch","orcid":"https://orcid.org/0000-0001-6701-7753"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dominik Rabsch","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany"],"raw_orcid":"https://orcid.org/0000-0001-6701-7753","affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063976174","display_name":"Florian Eggenhofer","orcid":"https://orcid.org/0000-0001-9564-7525"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Florian Eggenhofer","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany"],"raw_orcid":"https://orcid.org/0000-0001-9564-7525","affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017672883","display_name":"Rolf Backofen","orcid":"https://orcid.org/0000-0001-8231-3323"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rolf Backofen","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany","Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg im Breisgau, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8231-3323","affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science, University of Freiburg , Freiburg im Breisgau, Germany","institution_ids":["https://openalex.org/I161046081"]},{"raw_affiliation_string":"Signalling Research Centres BIOSS and CIBSS, University of Freiburg , Freiburg im Breisgau, Germany","institution_ids":["https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"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":0.0814,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.45193246,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"38","issue":"4","first_page":"1139","last_page":"1140"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9243999719619751,"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":0.9243999719619751,"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":0.025699999183416367,"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/T12610","display_name":"RNA regulation and disease","score":0.013399999588727951,"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/context","display_name":"Context (archaeology)","score":0.7424185872077942},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6194890141487122},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.5531253218650818},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38767969608306885},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.151189386844635},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.08975797891616821},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.08727827668190002},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.0834985077381134}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.7424185872077942},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6194890141487122},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.5531253218650818},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38767969608306885},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.151189386844635},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.08975797891616821},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.08727827668190002},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0834985077381134}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab755","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab755","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":"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:34734974","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34734974","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:8796379","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8796379","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/btab755","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab755","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":"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/G6057495830","display_name":null,"funder_award_id":"BA2168/11-2 SPP 1738","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7005732762","display_name":null,"funder_award_id":"BA 2168/11-1 SPP 1738,","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7077404544","display_name":null,"funder_award_id":"RNAProNet-031L0164B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1985217779","https://openalex.org/W2044117548","https://openalex.org/W2053003053","https://openalex.org/W2114532236","https://openalex.org/W2167866392","https://openalex.org/W2307041907","https://openalex.org/W2951377271","https://openalex.org/W3014747614","https://openalex.org/W3046003662","https://openalex.org/W3113169150"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"MOTIVATION:":[0],"CLIP-seq":[1,26,73,86,96],"is":[2,65,148],"by":[3,29,90],"far":[4],"the":[5,54,68,81,121],"most":[6,122],"widely":[7],"used":[8],"method":[9],"to":[10,37,72,102,115,134],"determine":[11,103],"transcriptome-wide":[12],"binding":[13,20,61,142],"sites":[14,113],"of":[15,132,139],"RNA-binding":[16],"proteins":[17],"(RBPs).":[18],"The":[19],"site":[21],"locations":[22],"are":[23,160],"identified":[24,89],"from":[25],"read":[27,97],"data":[28,159],"tools":[30],"termed":[31],"peak":[32,48,74,87,91,110],"callers.":[33],"Many":[34],"RBPs":[35],"bind":[36],"a":[38,63,136],"spliced":[39],"RNA":[40],"(i.e.":[41],"transcript)":[42],"context,":[43,117],"but":[44],"all":[45],"currently":[46],"available":[47,150,161],"callers":[49],"only":[50],"consider":[51],"and":[52,99,126],"report":[53],"genomic":[55,100],"context.":[56],"To":[57],"accurately":[58],"model":[59],"protein":[60],"behavior,":[62],"tool":[64,83],"needed":[66],"for":[67,108,129],"individual":[69],"context":[70,105,141],"assignment":[71],"regions.":[75],"RESULTS:":[76],"Here":[77],"we":[78],"present":[79],"Peakhood,":[80],"first":[82],"that":[84],"utilizes":[85],"regions":[88],"callers,":[92],"in":[93],"tandem":[94],"with":[95],"information":[98],"annotations,":[101],"which":[104],"applies,":[106],"individually":[107],"each":[109],"region.":[111],"For":[112],"assigned":[114],"transcript":[116,140],"it":[118],"further":[119],"determines":[120],"likely":[123],"splice":[124],"variant,":[125],"merges":[127],"results":[128],"any":[130],"number":[131],"datasets":[133],"obtain":[135],"comprehensive":[137],"collection":[138],"sites.":[143],"AVAILABILITY":[144],"AND":[145],"IMPLEMENTATION:":[146],"Peakhood":[147],"freely":[149],"under":[151],"MIT":[152],"license":[153],"at:":[154],"https://github.com/BackofenLab/Peakhood.":[155],"SUPPLEMENTARY":[156],"INFORMATION:":[157],"Supplementary":[158],"at":[162],"Bioinformatics":[163],"online.":[164]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
