{"id":"https://openalex.org/W2960979937","doi":"https://doi.org/10.1093/bioinformatics/btz540","title":"Cooler: scalable storage for Hi-C data and other genomically labeled arrays","display_name":"Cooler: scalable storage for Hi-C data and other genomically labeled arrays","publication_year":2019,"publication_date":"2019-07-09","ids":{"openalex":"https://openalex.org/W2960979937","doi":"https://doi.org/10.1093/bioinformatics/btz540","mag":"2960979937","pmid":"https://pubmed.ncbi.nlm.nih.gov/31290943"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz540","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz540","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":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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8205516","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056094388","display_name":"Nezar Abdennur","orcid":"https://orcid.org/0000-0001-5814-0864"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Nezar Abdennur","raw_affiliation_strings":["Institute for Medical Engineering and Science, Cambridge, MA 02139, USA"],"raw_orcid":"https://orcid.org/0000-0001-5814-0864","affiliations":[{"raw_affiliation_string":"Institute for Medical Engineering and Science, Cambridge, MA 02139, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017406892","display_name":"Leonid A. Mirny","orcid":"https://orcid.org/0000-0002-0785-5410"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Leonid A Mirny","raw_affiliation_strings":["Department of Physics, Massachusetts Institute of Technology , Cambridge, MA 02139, USA","Institute for Medical Engineering and Science, Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Massachusetts Institute of Technology , Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Institute for Medical Engineering and Science, Cambridge, MA 02139, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5017406892","https://openalex.org/A5056094388"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":44.0642,"has_fulltext":false,"cited_by_count":1867,"citation_normalized_percentile":{"value":0.99843372,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"36","issue":"1","first_page":"311","last_page":"316"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9987000226974487,"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":0.9987000226974487,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9968000054359436,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/scalability","display_name":"Scalability","score":0.7699835300445557},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7220854759216309},{"id":"https://openalex.org/keywords/computer-data-storage","display_name":"Computer data storage","score":0.4633494019508362},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3532499670982361},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.32426154613494873}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7699835300445557},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7220854759216309},{"id":"https://openalex.org/C194739806","wikidata":"https://www.wikidata.org/wiki/Q66221","display_name":"Computer data storage","level":2,"score":0.4633494019508362},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3532499670982361},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.32426154613494873}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz540","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz540","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31290943","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31290943","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:8205516","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8205516","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8205516","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8205516","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3875489406","display_name":null,"funder_award_id":"U54-DK107980","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G8875863982","display_name":null,"funder_award_id":"U01 CA200059","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"},{"id":"https://openalex.org/F4320338403","display_name":"Common Fund","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1587482075","https://openalex.org/W1840664805","https://openalex.org/W1915573037","https://openalex.org/W2005112390","https://openalex.org/W2020912279","https://openalex.org/W2070291575","https://openalex.org/W2072336782","https://openalex.org/W2073026107","https://openalex.org/W2090037139","https://openalex.org/W2097798909","https://openalex.org/W2109464129","https://openalex.org/W2142386149","https://openalex.org/W2185693210","https://openalex.org/W2248992661","https://openalex.org/W2461460074","https://openalex.org/W2493763501","https://openalex.org/W2584141685","https://openalex.org/W2604622795","https://openalex.org/W2741662224","https://openalex.org/W2765745983","https://openalex.org/W2803559294","https://openalex.org/W2807993805","https://openalex.org/W2888425844","https://openalex.org/W2951856336","https://openalex.org/W3083247814","https://openalex.org/W4292081093"],"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/W2389214306"],"abstract_inverted_index":{"MOTIVATION:":[0],"Most":[1],"existing":[2],"coverage-based":[3],"(epi)genomic":[4],"datasets":[5,63],"are":[6,36,208],"one-dimensional,":[7],"but":[8],"newer":[9],"technologies":[10],"probing":[11],"interactions":[12],"(physical,":[13],"genetic,":[14],"etc.)":[15],"produce":[16],"quantitative":[17],"maps":[18,35],"with":[19,30],"two-dimensional":[20],"genomic":[21,62],"coordinate":[22],"systems.":[23],"Storage":[24],"and":[25,75,127,134,141,148,156,182],"computational":[26],"costs":[27],"mount":[28],"sharply":[29],"data":[31,49,87,101,122,131,159,207],"resolution":[32],"when":[33],"such":[34],"stored":[37],"in":[38,60],"dense":[39],"form.":[40],"Hence,":[41],"there":[42],"is":[43,137,142,179,198],"a":[44,92,99,145,167],"pressing":[45],"need":[46],"to":[47,80,116,152],"develop":[48],"storage":[50],"strategies":[51],"that":[52,103],"handle":[53],"the":[54,114,121,170,187,192],"full":[55],"range":[56],"of":[57,67,83,120],"useful":[58],"resolutions":[59],"multidimensional":[61],"by":[64,144,169],"taking":[65],"advantage":[66],"their":[68],"sparse":[69,100],"nature,":[70],"while":[71],"supporting":[72],"efficient":[73],"compression":[74],"providing":[76],"fast":[77],"random":[78],"access":[79],"facilitate":[81],"development":[82],"scalable":[84],"algorithms":[85],"for":[86],"analysis.":[88],"RESULTS:":[89],"We":[90],"developed":[91],"file":[93],"format":[94,162],"called":[95],"cooler,":[96],"based":[97,138],"on":[98,139,200],"model,":[102],"can":[104,183],"support":[105],"genomically":[106],"labeled":[107],"matrices":[108],"at":[109,202,210],"any":[110],"resolution.":[111],"It":[112],"has":[113,163],"flexibility":[115],"accommodate":[117],"various":[118],"descriptions":[119],"axes":[123],"(genomic":[124],"coordinates,":[125],"tracks":[126],"bin":[128],"annotations),":[129],"resolutions,":[130],"density":[132],"patterns":[133],"metadata.":[135],"Cooler":[136,178],"HDF5":[140],"supported":[143],"Python":[146,188],"library":[147],"command":[149],"line":[150],"suite":[151],"create,":[153],"read,":[154],"inspect":[155],"manipulate":[157],"cooler":[158],"collections.":[160],"The":[161,195],"been":[164],"adopted":[165],"as":[166],"standard":[168],"NIH":[171],"4D":[172],"Nucleome":[173],"Consortium.":[174],"AVAILABILITY":[175],"AND":[176],"IMPLEMENTATION:":[177],"cross-platform,":[180],"BSD-licensed":[181],"be":[184],"installed":[185],"from":[186],"package":[189],"index":[190],"or":[191],"bioconda":[193],"repository.":[194],"source":[196],"code":[197],"maintained":[199],"Github":[201],"https://github.com/mirnylab/cooler.":[203],"SUPPLEMENTARY":[204],"INFORMATION:":[205],"Supplementary":[206],"available":[209],"Bioinformatics":[211],"online.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":119},{"year":2025,"cited_by_count":407},{"year":2024,"cited_by_count":685},{"year":2023,"cited_by_count":392},{"year":2022,"cited_by_count":119},{"year":2021,"cited_by_count":81},{"year":2020,"cited_by_count":45},{"year":2019,"cited_by_count":18},{"year":2017,"cited_by_count":1}],"updated_date":"2026-08-14T07:06:38.338062","created_date":"2019-07-23T00:00:00"}
