{"id":"https://openalex.org/W3186780789","doi":"https://doi.org/10.1016/j.gpb.2020.11.007","title":"CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-Seq Analysis","display_name":"CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-Seq Analysis","publication_year":2021,"publication_date":"2021-07-18","ids":{"openalex":"https://openalex.org/W3186780789","doi":"https://doi.org/10.1016/j.gpb.2020.11.007","mag":"3186780789","pmid":"https://pubmed.ncbi.nlm.nih.gov/34284136"},"language":"en","primary_location":{"id":"doi:10.1016/j.gpb.2020.11.007","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.gpb.2020.11.007","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.gpb.2020.11.007","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041427080","display_name":"Xintao Qiu","orcid":"https://orcid.org/0000-0002-8560-7017"},"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"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xintao Qiu","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0002-8560-7017","affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083901548","display_name":"Avery Feit","orcid":"https://orcid.org/0000-0002-6586-9052"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Avery S. Feit","raw_affiliation_strings":["Albert Einstein College of Medicine , Bronx, NY 10461 , USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0002-6586-9052","affiliations":[{"raw_affiliation_string":"Albert Einstein College of Medicine , Bronx, NY 10461 , USA","institution_ids":["https://openalex.org/I129975664"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078181199","display_name":"Ariel Feiglin","orcid":"https://orcid.org/0000-0003-2862-7668"},"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":"Ariel Feiglin","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02215 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059400884","display_name":"Yingtian Xie","orcid":"https://orcid.org/0000-0003-0206-457X"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yingtian Xie","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0003-0206-457X","affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061194798","display_name":"Nikolas Kesten","orcid":"https://orcid.org/0000-0002-9183-8778"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nikolas Kesten","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055277353","display_name":"Len Taing","orcid":"https://orcid.org/0000-0001-7453-5372"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Len Taing","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","Department of Data Sciences, Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0001-7453-5372","affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Data Sciences, Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014349769","display_name":"Joseph Perkins","orcid":"https://orcid.org/0000-0001-9436-7660"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Perkins","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0001-9436-7660","affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022553634","display_name":"Shengqing Gu","orcid":"https://orcid.org/0000-0002-4200-0864"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shengqing Gu","raw_affiliation_strings":["Department of Data Sciences, Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health , Boston, MA 02215 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Data Sciences, Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100630217","display_name":"Yihao Li","orcid":"https://orcid.org/0000-0003-1900-8099"},"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"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yihao Li","raw_affiliation_strings":["Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0003-1900-8099","affiliations":[{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102746198","display_name":"Paloma Cejas","orcid":"https://orcid.org/0000-0002-8417-4811"},"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"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paloma Cejas","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0002-8417-4811","affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070797070","display_name":"Ningxuan Zhou","orcid":"https://orcid.org/0000-0002-7623-2276"},"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"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ningxuan Zhou","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051714606","display_name":"Rinath Jeselsohn","orcid":"https://orcid.org/0000-0001-7996-7529"},"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"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rinath Jeselsohn","raw_affiliation_strings":["Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0001-7996-7529","affiliations":[{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033532061","display_name":"Myles Brown","orcid":"https://orcid.org/0000-0002-8213-1658"},"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"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Myles Brown","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0002-8213-1658","affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010101749","display_name":"X. Shirley Liu","orcid":"https://orcid.org/0000-0001-8588-1182"},"institutions":[{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"X. Shirley Liu","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","Department of Data Sciences, Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0001-8588-1182","affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Data Sciences, Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066070097","display_name":"Henry W. Long","orcid":"https://orcid.org/0000-0001-6849-6629"},"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"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Henry W. Long","raw_affiliation_strings":["Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA"],"raw_orcid":"https://orcid.org/0000-0001-6849-6629","affiliations":[{"raw_affiliation_string":"Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215 , USA","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5066070097"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210117453"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":2.359,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.89735326,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"19","issue":"4","first_page":"652","last_page":"661"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9984999895095825,"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":0.9983999729156494,"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/workflow","display_name":"Workflow","score":0.7054916620254517},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6754569411277771},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5747225284576416},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4773585796356201},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.47639790177345276},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.45722806453704834},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3575252294540405},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2696042060852051},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.18021920323371887},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13284960389137268},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1299610137939453}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7054916620254517},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6754569411277771},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5747225284576416},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4773585796356201},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.47639790177345276},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.45722806453704834},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3575252294540405},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2696042060852051},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.18021920323371887},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13284960389137268},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1299610137939453}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","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":3,"locations":[{"id":"doi:10.1016/j.gpb.2020.11.007","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.gpb.2020.11.007","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34284136","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34284136","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9039557","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9039557","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":"Genomics Proteomics Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1016/j.gpb.2020.11.007","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.gpb.2020.11.007","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G5948587532","display_name":null,"funder_award_id":"2PO1CA163227","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6558407288","display_name":null,"funder_award_id":"P01CA080111","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1699926620","https://openalex.org/W2013287009","https://openalex.org/W2014677321","https://openalex.org/W2085184586","https://openalex.org/W2089708180","https://openalex.org/W2110417468","https://openalex.org/W2125636389","https://openalex.org/W2131610374","https://openalex.org/W2155826575","https://openalex.org/W2162557359","https://openalex.org/W2167967077","https://openalex.org/W2170200272","https://openalex.org/W2231478755","https://openalex.org/W2235841654","https://openalex.org/W2341539131","https://openalex.org/W2528138045","https://openalex.org/W2534292219","https://openalex.org/W2544405043","https://openalex.org/W2561114892","https://openalex.org/W2592743985","https://openalex.org/W2602581211","https://openalex.org/W2782687824","https://openalex.org/W2792006949","https://openalex.org/W2799170276","https://openalex.org/W2883217678","https://openalex.org/W2901027836","https://openalex.org/W2935669718","https://openalex.org/W3161977519","https://openalex.org/W4231356616","https://openalex.org/W4250385029","https://openalex.org/W6671693362"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W4286930115","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W3004891660","https://openalex.org/W2029380707","https://openalex.org/W188202134","https://openalex.org/W2969540308"],"abstract_inverted_index":{"Chromatin":[0,9],"immunoprecipitation":[1],"sequencing":[2,12],"(ChIP-seq)":[3],"and":[4,23,34,48,73,77,80,89,113,131],"the":[5],"Assay":[6],"for":[7,31,61],"Transposase-Accessible":[8],"with":[10,99],"high-throughput":[11],"(ATAC-seq)":[13],"have":[14],"become":[15],"essential":[16],"technologies":[17],"to":[18,106,127],"effectively":[19],"measure":[20],"protein-DNA":[21,111],"interactions":[22,112],"chromatin":[24,114],"accessibility.":[25],"However,":[26],"there":[27],"is":[28,135],"a":[29,32,66,85,128],"need":[30],"scalable":[33],"reproducible":[35],"pipeline":[36,92],"that":[37,93],"incorporates":[38],"proper":[39],"normalization":[40],"between":[41],"samples,":[42],"correction":[43],"of":[44,50,125],"copy":[45],"number":[46],"variations,":[47],"integration":[49],"new":[51],"downstream":[52],"analysis":[53,91],"tools.":[54],"Here":[55],"we":[56],"present":[57],"Containerized":[58],"Bioinformatics":[59],"workflow":[60,69],"Reproducible":[62],"ChIP/ATAC-seq":[63],"Analysis":[64],"(CoBRA),":[65],"modularized":[67],"computational":[68,101],"which":[70],"quantifies":[71],"ChIP-seq":[72,88],"ATAC-seq":[74,90],"peak":[75,120],"regions":[76],"performs":[78],"unsupervised":[79],"supervised":[81],"analyses.":[82],"CoBRA":[83,134],"provides":[84],"comprehensive":[86],"state-of-the-art":[87],"can":[94],"be":[95],"used":[96],"by":[97],"scientists":[98],"limited":[100],"experience.":[102],"This":[103],"enables":[104],"researchers":[105],"gain":[107],"rapid":[108],"insight":[109],"into":[110],"accessibility":[115],"through":[116],"sample":[117],"clustering,":[118],"differential":[119],"calling,":[121],"motif":[122],"enrichment,":[123],"comparison":[124],"sites":[126],"reference":[129],"database,":[130],"pathway":[132],"analysis.":[133],"publicly":[136],"available":[137],"online":[138],"at":[139],"https://bitbucket.org/cfce/cobra.":[140]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
