{"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/I36258959","https://openalex.org/I4210087384"]},{"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/I36258959","https://openalex.org/I4210087384"]}]},{"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/I36258959","https://openalex.org/I4210087384"]}]},{"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/I36258959","https://openalex.org/I4210087384"]},{"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":true,"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/I36258959","https://openalex.org/I4210087384"]},{"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/I36258959","https://openalex.org/I4210087384"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5083421459"],"corresponding_institution_ids":["https://openalex.org/I36258959","https://openalex.org/I4210087384"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.7228,"has_fulltext":true,"cited_by_count":55,"citation_normalized_percentile":{"value":0.84357844,"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: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"},{"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"}],"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/G1212299991","display_name":"REGULATORY GENOMIC STUDIES IN A COHORT OF IPS CELL DERIVED CARDIOMYOCYTES","funder_award_id":"3u01hl107442-05s1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"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/G1548374827","display_name":"Commercialization of HaploSeq as a Service (HaaS) for generating chromosome-span phased genome and exome sequence information","funder_award_id":"2r44hg008118-04a1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2071219093","display_name":null,"funder_award_id":"R41 HG008118","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G2222516796","display_name":null,"funder_award_id":"U01 HL107442","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood 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/G323419876","display_name":"Functional Analysis of T2D Associated Non-coding SNPs","funder_award_id":"5u01dk105541-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4112673505","display_name":null,"funder_award_id":"DP3DK112155","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G4747812582","display_name":null,"funder_award_id":"U01DK105541","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"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/G5253705891","display_name":"Fine-mapping and functional analysis of T1D-associated variants","funder_award_id":"1dp3dk112155-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6594052649","display_name":null,"funder_award_id":"R01 EY021237","funder_id":"https://openalex.org/F4320337350","funder_display_name":"National Eye Institute"},{"id":"https://openalex.org/G7982620075","display_name":"Molecular Basis of Hereditary Retinal Degenerations","funder_award_id":"5r01ey021237-09","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/F4320337350","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":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":3},{"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":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
