{"id":"https://openalex.org/W3026015559","doi":"https://doi.org/10.1093/bioinformatics/btaa493","title":"HALPER facilitates the identification of regulatory element orthologs across species","display_name":"HALPER facilitates the identification of regulatory element orthologs across species","publication_year":2020,"publication_date":"2020-05-08","ids":{"openalex":"https://openalex.org/W3026015559","doi":"https://doi.org/10.1093/bioinformatics/btaa493","mag":"3026015559","pmid":"https://pubmed.ncbi.nlm.nih.gov/32407523"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa493","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa493","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/15/4339/35285102/btaa493.pdf","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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/15/4339/35285102/btaa493.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100419423","display_name":"Xiaoyu Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiaoyu Zhang","raw_affiliation_strings":["Department of Computer Science"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010714171","display_name":"Irene M. Kaplow","orcid":"https://orcid.org/0000-0002-8924-8269"},"institutions":[{"id":"https://openalex.org/I4210113153","display_name":"Neuroscience Institute","ror":"https://ror.org/0240rwx68","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210113153","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Irene M Kaplow","raw_affiliation_strings":["Department of Computational Biology","Neuroscience Institute"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology","institution_ids":[]},{"raw_affiliation_string":"Neuroscience Institute","institution_ids":["https://openalex.org/I4210113153"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038619849","display_name":"Morgan Wirthlin","orcid":"https://orcid.org/0000-0001-7967-7070"},"institutions":[{"id":"https://openalex.org/I4210113153","display_name":"Neuroscience Institute","ror":"https://ror.org/0240rwx68","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210113153","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Morgan Wirthlin","raw_affiliation_strings":["Department of Computational Biology","Neuroscience Institute"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology","institution_ids":[]},{"raw_affiliation_string":"Neuroscience Institute","institution_ids":["https://openalex.org/I4210113153"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052773902","display_name":"Tae Yoon Park","orcid":"https://orcid.org/0000-0001-6358-9375"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tae Yoon Park","raw_affiliation_strings":["Department of Biology, Carnegie Mellon University , Pittsburgh, PA 15213,","Department of Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Carnegie Mellon University , Pittsburgh, PA 15213,","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Department of Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079371001","display_name":"Andreas Pfenning","orcid":"https://orcid.org/0000-0002-7390-5041"},"institutions":[{"id":"https://openalex.org/I4210113153","display_name":"Neuroscience Institute","ror":"https://ror.org/0240rwx68","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210113153","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Andreas R Pfenning","raw_affiliation_strings":["Department of Computational Biology","Neuroscience Institute"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology","institution_ids":[]},{"raw_affiliation_string":"Neuroscience Institute","institution_ids":["https://openalex.org/I4210113153"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5052773902","https://openalex.org/A5079371001"],"corresponding_institution_ids":["https://openalex.org/I4210113153","https://openalex.org/I74973139"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.254,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.78853928,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"36","issue":"15","first_page":"4339","last_page":"4340"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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":0.9950000047683716,"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":0.9934999942779541,"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/identification","display_name":"Identification (biology)","score":0.8437508344650269},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5724884271621704},{"id":"https://openalex.org/keywords/element","display_name":"Element (criminal law)","score":0.5511125326156616},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4359395205974579},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3948584198951721},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.1272728145122528}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.8437508344650269},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5724884271621704},{"id":"https://openalex.org/C200288055","wikidata":"https://www.wikidata.org/wiki/Q2621792","display_name":"Element (criminal law)","level":2,"score":0.5511125326156616},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4359395205974579},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3948584198951721},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.1272728145122528},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa493","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa493","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/15/4339/35285102/btaa493.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32407523","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32407523","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:7520040","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7520040","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa493","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa493","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/15/4339/35285102/btaa493.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.75,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G3449623593","display_name":null,"funder_award_id":"DP1DA046585","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3026015559.pdf","grobid_xml":"https://content.openalex.org/works/W3026015559.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1866488244","https://openalex.org/W2039176012","https://openalex.org/W2112132489","https://openalex.org/W2114416522","https://openalex.org/W2122598328","https://openalex.org/W2128969076","https://openalex.org/W2166825456","https://openalex.org/W2259938310","https://openalex.org/W2867000904","https://openalex.org/W2901874671"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3}],"updated_date":"2026-04-19T08:26:33.389920","created_date":"2025-10-10T00:00:00"}
