{"id":"https://openalex.org/W2604944932","doi":"https://doi.org/10.1186/s12859-017-1621-0","title":"Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data","display_name":"Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data","publication_year":2017,"publication_date":"2017-04-07","ids":{"openalex":"https://openalex.org/W2604944932","doi":"https://doi.org/10.1186/s12859-017-1621-0","mag":"2604944932","pmid":"https://pubmed.ncbi.nlm.nih.gov/28388874"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1621-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1621-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1621-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1621-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031697008","display_name":"William W. Greenwald","orcid":"https://orcid.org/0000-0002-6274-1571"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William W. Greenwald","raw_affiliation_strings":["Bioinformatics and Systems Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107094785","display_name":"He Li","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210087384","display_name":"Rady Children's Hospital-San Diego","ror":"https://ror.org/00414dg76","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"He Li","raw_affiliation_strings":["Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I4210087384","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034360743","display_name":"Erin N. Smith","orcid":"https://orcid.org/0000-0001-9632-4760"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210087384","display_name":"Rady Children's Hospital-San Diego","ror":"https://ror.org/00414dg76","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erin N. Smith","raw_affiliation_strings":["Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I4210087384","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015813357","display_name":"Paola Benaglio","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210087384","display_name":"Rady Children's Hospital-San Diego","ror":"https://ror.org/00414dg76","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paola Benaglio","raw_affiliation_strings":["Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I4210087384","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082629535","display_name":"Naoki Nariai","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210087384","display_name":"Rady Children's Hospital-San Diego","ror":"https://ror.org/00414dg76","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Naoki Nariai","raw_affiliation_strings":["Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I4210087384","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083421459","display_name":"Kelly A. Frazer","orcid":"https://orcid.org/0000-0002-6060-8902"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210087384","display_name":"Rady Children's Hospital-San Diego","ror":"https://ror.org/00414dg76","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kelly A. Frazer","raw_affiliation_strings":["Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. kafrazer@ucsd.edu","Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. kafrazer@ucsd.edu","Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. kafrazer@ucsd.edu","institution_ids":["https://openalex.org/I4210087384","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. kafrazer@ucsd.edu","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I4210087384","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.9069,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.85924286,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"18","issue":"1","first_page":"207","last_page":"207"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.4625000059604645,"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":0.4625000059604645,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.38190001249313354,"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"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.05079999938607216,"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/python","display_name":"Python (programming language)","score":0.7868961095809937},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7222399711608887},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6856311559677124},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.6170232892036438},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5356248021125793},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.5317208766937256},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.48322877287864685},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.46696358919143677},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.45307469367980957},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4454972743988037},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38071757555007935},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3502327799797058},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3264261484146118},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.31646108627319336},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2747635841369629},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19468370079994202}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7868961095809937},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7222399711608887},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6856311559677124},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.6170232892036438},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5356248021125793},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.5317208766937256},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.48322877287864685},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.46696358919143677},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.45307469367980957},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4454972743988037},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38071757555007935},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3502327799797058},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3264261484146118},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.31646108627319336},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2747635841369629},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19468370079994202},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-017-1621-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1621-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1621-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28388874","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28388874","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:ark:/13030/qt5dp72331","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:2875d9d2c1e943b89db17a505d6b784f","is_oa":true,"landing_page_url":"https://doaj.org/article/2875d9d2c1e943b89db17a505d6b784f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 18, Iss 1, Pp 1-6 (2017)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt5dp72331","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/5dp72331","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC bioinformatics, vol 18, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5384132","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5384132","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1621-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1621-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1621-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1413867369","display_name":null,"funder_award_id":"HG008118","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G2564695853","display_name":null,"funder_award_id":"GC1R-06673","funder_id":"https://openalex.org/F4320306171","funder_display_name":"California Institute for Regenerative Medicine"},{"id":"https://openalex.org/G321282449","display_name":null,"funder_award_id":"CG1R-06673","funder_id":"https://openalex.org/F4320306171","funder_display_name":"California Institute for Regenerative Medicine"},{"id":"https://openalex.org/G3331080861","display_name":null,"funder_award_id":"DK112155","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4568296995","display_name":null,"funder_award_id":"HL107442","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4806452686","display_name":null,"funder_award_id":"HG008118","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4906009726","display_name":null,"funder_award_id":"DK105541","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G786265456","display_name":null,"funder_award_id":"EY021237","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8463002031","display_name":null,"funder_award_id":"DK105541","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8514233497","display_name":null,"funder_award_id":"HL107442","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320306171","display_name":"California Institute for Regenerative Medicine","ror":"https://ror.org/033m8b439"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2604944932.pdf","grobid_xml":"https://content.openalex.org/works/W2604944932.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1840664805","https://openalex.org/W1973062929","https://openalex.org/W2031057223","https://openalex.org/W2080477348","https://openalex.org/W2090037139","https://openalex.org/W2102619694","https://openalex.org/W2128016314","https://openalex.org/W2142270559","https://openalex.org/W2175063164","https://openalex.org/W2185693210","https://openalex.org/W2481029670","https://openalex.org/W2493763501"],"related_works":["https://openalex.org/W47352601","https://openalex.org/W2981957539","https://openalex.org/W4287378204","https://openalex.org/W2461489085","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W2099352317","https://openalex.org/W2893042097","https://openalex.org/W2308359027"],"abstract_inverted_index":{"BACKGROUND:":[0],"Genomic":[1],"interaction":[2,74],"studies":[3],"use":[4],"next-generation":[5],"sequencing":[6,75],"(NGS)":[7],"to":[8],"examine":[9],"the":[10,16,64,115,124,189,197],"interactions":[11],"between":[12],"two":[13],"loci":[14],"on":[15],"genome,":[17],"with":[18,88,110],"subsequent":[19],"bioinformatics":[20],"analyses":[21],"typically":[22],"including":[23],"annotation,":[24],"intersection,":[25],"and":[26,37,43,61,84,92,103,123,144,175,184],"merging":[27],"of":[28,153,188],"data":[29,65,76,90],"from":[30,68,194],"multiple":[31],"experiments.":[32],"While":[33],"many":[34],"file":[35,53,82,101,118],"types":[36],"analysis":[38,56,126],"tools":[39,85],"exist":[40],"for":[41,59,86,108,120,149,166],"storing":[42,62],"manipulating":[44,60,167],"single":[45],"locus":[46],"NGS":[47],"data,":[48,122],"there":[49],"is":[50,158],"currently":[51],"no":[52],"standard":[54,81,102,119],"or":[55],"tool":[57,106,127,164],"suite":[58,107,128,165],"paired-genomic-loci:":[63],"type":[66],"resulting":[67],"\"genomic":[69],"interaction\"":[70],"studies.":[71],"As":[72],"genomic":[73],"are":[77,94,178],"becoming":[78],"prevalent,":[79],"a":[80,100,130,146,159,176,185],"format":[83],"working":[87,109],"these":[89],"conveniently":[91],"efficiently":[93],"needed.":[95],"RESULTS:":[96],"This":[97],"article":[98],"details":[99],"novel":[104],"software":[105],"paired-genomic-loci":[111,116,154,168],"data.":[112,169],"We":[113],"present":[114],"(PGL)":[117],"genomic-interactions":[121],"accompanying":[125],"\"pgltools\":":[129],"cross":[131],"platform,":[132],"pypy":[133],"compatible":[134],"python":[135,147,186],"package":[136],"available":[137,179],"both":[138],"as":[139,145],"an":[140,172],"easy-to-use":[141],"UNIX":[142],"package,":[143],"module,":[148],"integration":[150],"into":[151],"pipelines":[152],"analyses.":[155],"CONCLUSIONS:":[156],"Pgltools":[157],"freely":[160],"available,":[161],"open":[162],"source":[163],"Source":[170],"code,":[171],"in-depth":[173],"manual,":[174],"tutorial":[177],"publicly":[180],"at":[181],"www.github.com/billgreenwald/pgltools":[182],",":[183],"module":[187],"operations":[190],"can":[191],"be":[192],"installed":[193],"PyPI":[195],"via":[196],"PyGLtools":[198],"module.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}