{"id":"https://openalex.org/W4206808376","doi":"https://doi.org/10.1093/bioinformatics/btab870","title":"Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs","display_name":"Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs","publication_year":2021,"publication_date":"2021-12-28","ids":{"openalex":"https://openalex.org/W4206808376","doi":"https://doi.org/10.1093/bioinformatics/btab870","pmid":"https://pubmed.ncbi.nlm.nih.gov/34978573"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab870","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab870","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/6/1729/49692948/btab870.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/38/6/1729/49692948/btab870.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100443294","display_name":"Soohyun Lee","orcid":"https://orcid.org/0000-0002-3594-6213"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Soohyun Lee","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085609895","display_name":"Clara Bakker","orcid":"https://orcid.org/0000-0001-9600-4628"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Clara R Bakker","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051116389","display_name":"Carl Vitzthum","orcid":"https://orcid.org/0000-0002-3075-2305"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carl Vitzthum","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084957565","display_name":"B. Alver","orcid":"https://orcid.org/0000-0002-5019-7652"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Burak H Alver","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022028438","display_name":"Peter J. Park","orcid":"https://orcid.org/0000-0001-9378-960X"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter J Park","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022028438","https://openalex.org/A5084957565"],"corresponding_institution_ids":["https://openalex.org/I136199984"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.5197,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.91292917,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"38","issue":"6","first_page":"1729","last_page":"1731"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9902999997138977,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9902999997138977,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13650","display_name":"Computational Physics and Python Applications","score":0.9660999774932861,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11439","display_name":"Video Analysis and Summarization","score":0.9520000219345093,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.734528660774231},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.5215139985084534},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4728719890117645},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3698294758796692},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.32578110694885254}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.734528660774231},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.5215139985084534},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4728719890117645},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3698294758796692},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.32578110694885254}],"mesh":[{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","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},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","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/btab870","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab870","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/6/1729/49692948/btab870.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:34978573","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34978573","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:10060703","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10060703","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10060703/pdf/btab870.pdf","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/btab870","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab870","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/6/1729/49692948/btab870.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":[],"awards":[{"id":"https://openalex.org/G1091973690","display_name":null,"funder_award_id":"U01 CA200059","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320338403","display_name":"Common Fund","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4206808376.pdf","grobid_xml":"https://content.openalex.org/works/W4206808376.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1973062929","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2122532582","https://openalex.org/W2131478115","https://openalex.org/W2135415614","https://openalex.org/W2142386149","https://openalex.org/W2481029670","https://openalex.org/W2582023661","https://openalex.org/W2584394140","https://openalex.org/W2960979937","https://openalex.org/W3013371767"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"The":[0],"format":[1],"specification":[2],"and":[3,11],"source":[4],"code":[5],"are":[6],"available":[7],"at":[8],"https://github.com/4dn-dcic/pairix,":[9],"https://github.com/4dn-dcic/Rpairix":[10],"https://github.com/4dn-dcic/pairsqc.":[12]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3}],"updated_date":"2026-04-12T07:58:50.170612","created_date":"2025-10-10T00:00:00"}
