{"id":"https://openalex.org/W4412556089","doi":"https://doi.org/10.1093/nargab/lqaf098","title":"Loopsim: enrichment analysis of chromosome conformation capture with fast empirical distribution simulation","display_name":"Loopsim: enrichment analysis of chromosome conformation capture with fast empirical distribution simulation","publication_year":2025,"publication_date":"2025-07-04","ids":{"openalex":"https://openalex.org/W4412556089","doi":"https://doi.org/10.1093/nargab/lqaf098","pmid":"https://pubmed.ncbi.nlm.nih.gov/40686570"},"language":"en","primary_location":{"id":"doi:10.1093/nargab/lqaf098","doi":"https://doi.org/10.1093/nargab/lqaf098","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nargab/lqaf098","pdf_url":"https://academic.oup.com/nargab/article-pdf/7/3/lqaf098/63802557/lqaf098.pdf","source":{"id":"https://openalex.org/S4210241000","display_name":"NAR Genomics and Bioinformatics","issn_l":"2631-9268","issn":["2631-9268"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-20","russia-white-list-2","vabb-shw"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"NAR Genomics and Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nargab/article-pdf/7/3/lqaf098/63802557/lqaf098.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Gideon Shaked","orcid":"https://orcid.org/0000-0001-5822-3010","observed_orcids":["https://orcid.org/0000-0001-5822-3010"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gideon Shaked","raw_affiliation_strings":["Michigan Medicine Department of Computational Medicine and Bioinformatics, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","Department of Computational Medicine and Bioinformatics, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States"],"raw_orcid":"https://orcid.org/0000-0001-5822-3010","affiliations":[{"raw_affiliation_string":"Michigan Medicine Department of Computational Medicine and Bioinformatics, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101980280","display_name":"Haihan Zhang","orcid":"https://orcid.org/0000-0002-5902-7289","observed_orcids":["https://orcid.org/0000-0002-5902-7289"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haihan Zhang","raw_affiliation_strings":["University of Michigan Department of Biostatistics, , 1415 Washington Heights , Ann Arbor, MI 48109 ,","Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States"],"raw_orcid":"https://orcid.org/0000-0002-5902-7289","affiliations":[{"raw_affiliation_string":"University of Michigan Department of Biostatistics, , 1415 Washington Heights , Ann Arbor, MI 48109 ,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101420403","display_name":"Zhaolin Zhang","orcid":"https://orcid.org/0000-0003-1978-8160","observed_orcids":["https://orcid.org/0000-0003-1978-8160"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhaolin Zhang","raw_affiliation_strings":["Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","institution_ids":["https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047215778","display_name":"Jiayu Zhou","orcid":"https://orcid.org/0000-0003-4336-6777","observed_orcids":["https://orcid.org/0000-0003-4336-6777"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiayu Zhou","raw_affiliation_strings":["School of Information, University of Michigan , 105 S State St. , Ann Arbor , MI 48109-1285,","School of Information, University of Michigan, 105 S State St., Ann Arbor, MI 48109-1285, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information, University of Michigan , 105 S State St. , Ann Arbor , MI 48109-1285,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"School of Information, University of Michigan, 105 S State St., Ann Arbor, MI 48109-1285, United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058475475","display_name":"Johann Eli Gudjonsson","orcid":"https://orcid.org/0000-0002-0080-0812","observed_orcids":["https://orcid.org/0000-0002-0080-0812"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Johann\u00a0E Gudjonsson","raw_affiliation_strings":["Mary H. Weiser Food Allergy Center , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","Mary H. Weiser Food Allergy Center, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mary H. Weiser Food Allergy Center , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","institution_ids":[]},{"raw_affiliation_string":"Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","institution_ids":["https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Mary H. Weiser Food Allergy Center, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"James\u00a0T Elder","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James\u00a0T Elder","raw_affiliation_strings":["Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","institution_ids":["https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054852821","display_name":"Matthew T. Patrick","orcid":"https://orcid.org/0000-0002-6174-9002","observed_orcids":["https://orcid.org/0000-0002-6174-9002"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew\u00a0T Patrick","raw_affiliation_strings":["Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States"],"raw_orcid":"https://orcid.org/0000-0002-6174-9002","affiliations":[{"raw_affiliation_string":"Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","institution_ids":["https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057653412","display_name":"Lam C. Tsoi","orcid":"https://orcid.org/0000-0003-1627-5722","observed_orcids":["https://orcid.org/0000-0003-1627-5722"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lam\u00a0C Tsoi","raw_affiliation_strings":["Mary H. Weiser Food Allergy Center , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","Michigan Medicine Department of Computational Medicine and Bioinformatics, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","University of Michigan Department of Biostatistics, , 1415 Washington Heights , Ann Arbor, MI 48109 ,","Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States","Department of Computational Medicine and Bioinformatics, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","Mary H. Weiser Food Allergy Center, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mary H. Weiser Food Allergy Center , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","institution_ids":[]},{"raw_affiliation_string":"Michigan Medicine Department of Computational Medicine and Bioinformatics, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Michigan Medicine Department of Dermatology, , 1500 E Medical Center Dr , Ann Arbor, MI 48109 ,","institution_ids":["https://openalex.org/I4210114445"]},{"raw_affiliation_string":"University of Michigan Department of Biostatistics, , 1415 Washington Heights , Ann Arbor, MI 48109 ,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Department of Dermatology, Michigan Medicine, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Mary H. Weiser Food Allergy Center, 1500 E Medical Center Dr, Ann Arbor, MI 48109, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5057653412"],"corresponding_institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"],"apc_list":{"value":2766,"currency":"USD","value_usd":2766},"apc_paid":{"value":2766,"currency":"USD","value_usd":2766},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1048015,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":"3","first_page":"lqaf098","last_page":"lqaf098"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9922000169754028,"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":0.9922000169754028,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0007999999797903001,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hi-c","display_name":"Hi-C","score":0.8289999961853027},{"id":"https://openalex.org/keywords/chromosome-conformation-capture","display_name":"chromosome conformation capture","score":0.921999990940094},{"id":"https://openalex.org/keywords/empirical-null-distribution","display_name":"empirical null distribution","score":0.8180000185966492},{"id":"https://openalex.org/keywords/3d-genome-organization","display_name":"3D genome organization","score":0.8069999814033508},{"id":"https://openalex.org/keywords/chromatin-looping","display_name":"chromatin looping","score":0.8519999980926514}],"concepts":[{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.4432043135166168},{"id":"https://openalex.org/C2992684800","wikidata":"https://www.wikidata.org/wiki/Q246128","display_name":"Chromosome analysis","level":5,"score":0.4331488609313965},{"id":"https://openalex.org/C110121322","wikidata":"https://www.wikidata.org/wiki/Q865811","display_name":"Distribution (mathematics)","level":2,"score":0.41876932978630066},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35238611698150635},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3520340621471405},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33037498593330383},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2051520049571991},{"id":"https://openalex.org/C53226629","wikidata":"https://www.wikidata.org/wiki/Q189967","display_name":"Karyotype","level":4,"score":0.17344877123832703},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08206263184547424},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/nargab/lqaf098","doi":"https://doi.org/10.1093/nargab/lqaf098","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nargab/lqaf098","pdf_url":"https://academic.oup.com/nargab/article-pdf/7/3/lqaf098/63802557/lqaf098.pdf","source":{"id":"https://openalex.org/S4210241000","display_name":"NAR Genomics and Bioinformatics","issn_l":"2631-9268","issn":["2631-9268"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-20","russia-white-list-2","vabb-shw"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"NAR Genomics and Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/2024.06.03.595407","doi":"https://doi.org/10.1101/2024.06.03.595407","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2024.06.03.595407","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2024/06/04/2024.06.03.595407.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:40686570","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40686570","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,"listed_in":[],"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":"NAR genomics and bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12276010","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12276010","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,"listed_in":[],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"NAR Genom Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nargab/lqaf098","doi":"https://doi.org/10.1093/nargab/lqaf098","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nargab/lqaf098","pdf_url":"https://academic.oup.com/nargab/article-pdf/7/3/lqaf098/63802557/lqaf098.pdf","source":{"id":"https://openalex.org/S4210241000","display_name":"NAR Genomics and Bioinformatics","issn_l":"2631-9268","issn":["2631-9268"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-20","russia-white-list-2","vabb-shw"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"NAR Genomics and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1589877395","display_name":"Integrative Biology Approach to Identify and Characterize Roles of lncRNAs Associated with Psoriasis Pathology","funder_award_id":"K01AR072129","funder_id":"https://openalex.org/F4320337362","funder_display_name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases"},{"id":"https://openalex.org/G9000026626","display_name":null,"funder_award_id":"UC2-AR081033","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000033955","display_name":null,"funder_award_id":"1P30AR075043","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000272258","display_name":null,"funder_award_id":"R01AR080662","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306673","display_name":"Dermatology Foundation","ror":"https://ror.org/04xy3z086"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337362","display_name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","ror":"https://ror.org/006zn3t30"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412556089.pdf","grobid_xml":"https://content.openalex.org/works/W4412556089.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1505536714","https://openalex.org/W1544691147","https://openalex.org/W1973062929","https://openalex.org/W1977855308","https://openalex.org/W2013223495","https://openalex.org/W2021779654","https://openalex.org/W2118503070","https://openalex.org/W2124894542","https://openalex.org/W2133465414","https://openalex.org/W2145174846","https://openalex.org/W2481029670","https://openalex.org/W2616052794","https://openalex.org/W2741709539","https://openalex.org/W2906147404","https://openalex.org/W2969310280","https://openalex.org/W2973702082","https://openalex.org/W3002964216","https://openalex.org/W3041895828","https://openalex.org/W3091034669","https://openalex.org/W3092925261","https://openalex.org/W3133478475","https://openalex.org/W3136813783","https://openalex.org/W4206413332","https://openalex.org/W4212925316","https://openalex.org/W4220688679","https://openalex.org/W4284990903","https://openalex.org/W4393038887","https://openalex.org/W4408033278","https://openalex.org/W6858960729"],"related_works":["https://openalex.org/W1994964841","https://openalex.org/W2355275854","https://openalex.org/W2076779047","https://openalex.org/W2268560080","https://openalex.org/W2135054030","https://openalex.org/W2363997922","https://openalex.org/W2373101669","https://openalex.org/W2392771483","https://openalex.org/W2414648009","https://openalex.org/W2369214710"],"abstract_inverted_index":{"Gene":[0],"regulation":[1],"is":[2,52],"intricately":[3],"influenced":[4],"by":[5],"the":[6,10,37,128],"three-dimensional":[7],"organization":[8,38],"of":[9,39],"genome.":[11],"In":[12],"particular,":[13],"chromatin":[14],"can":[15,46],"exist":[16],"in":[17,43],"loop":[18,41,92,115],"structures":[19,42],"that":[20,72,86,113],"enable":[21],"long-range":[22],"regulatory":[23],"interactions.":[24],"By":[25],"utilizing":[26],"chromosome":[27,74],"conformation":[28,75],"capture":[29,73],"techniques":[30],"such":[31],"as":[32],"Hi-C,":[33],"valuable":[34],"information":[35],"regarding":[36],"these":[40],"3D":[44],"space":[45],"be":[47],"obtained.":[48],"Although":[49],"functional/feature":[50],"enrichment":[51,88],"now":[53],"a":[54,83,105,109],"common":[55],"downstream":[56],"analysis":[57,89],"for":[58,69],"various":[59],"genomic":[60],"platforms":[61],"to":[62],"provide":[63],"biological":[64],"context,":[65],"tools":[66],"specifically":[67],"designed":[68],"high-throughput":[70],"assays":[71],"remain":[76],"relatively":[77],"limited.":[78],"Here,":[79],"we":[80],"present":[81],"Loopsim,":[82],"command-line":[84],"application":[85],"performs":[87],"on":[90,98,127],"Hi-C":[91],"profiles":[93],"against":[94],"user-defined":[95],"regions":[96],"(available":[97],"GitHub":[99],"at":[100],"https://github.com/CutaneousBioinf/Loopsim).":[101],"Loopsim":[102],"efficiently":[103],"simulates":[104],"background":[106],"distribution":[107],"using":[108],"distinctive":[110],"sampling":[111],"approach":[112],"considers":[114],"size,":[116],"intervals,":[117],"loop-loop":[118],"distances,":[119],"and":[120],"structure;":[121],"it":[122],"then":[123],"computes":[124],"statistics":[125],"based":[126],"empirical":[129],"null":[130],"distribution.":[131]},"counts_by_year":[],"updated_date":"2026-10-15T10:00:46.086208","created_date":"2025-10-10T00:00:00"}