{"id":"https://openalex.org/W3044139896","doi":"https://doi.org/10.1145/3311790.3396621","title":"PEGR: a management platform for ChIP-based next generation sequencing pipelines","display_name":"PEGR: a management platform for ChIP-based next generation sequencing pipelines","publication_year":2020,"publication_date":"2020-07-22","ids":{"openalex":"https://openalex.org/W3044139896","doi":"https://doi.org/10.1145/3311790.3396621","mag":"3044139896","pmid":"https://pubmed.ncbi.nlm.nih.gov/35662897"},"language":"en","primary_location":{"id":"doi:10.1145/3311790.3396621","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3311790.3396621","pdf_url":null,"source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9161112","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075672658","display_name":"Danying Shao","orcid":"https://orcid.org/0000-0002-1920-3081"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Danying Shao","raw_affiliation_strings":["Pennsylvania State University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048958401","display_name":"Gretta D. Kellogg","orcid":"https://orcid.org/0000-0002-9171-8696"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gretta Kellogg","raw_affiliation_strings":["Pennsylvania State University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077269033","display_name":"Shaun Mahony","orcid":"https://orcid.org/0000-0002-2641-1807"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shaun Mahony","raw_affiliation_strings":["Pennsylvania State University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000405432","display_name":"William Lai","orcid":"https://orcid.org/0000-0003-4351-7037"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Lai","raw_affiliation_strings":["Pennsylvania State University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046527896","display_name":"B. Franklin Pugh","orcid":"https://orcid.org/0000-0001-8341-4476"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. Franklin Pugh","raw_affiliation_strings":["Pennsylvania State University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":null,"apc_paid":null,"fwci":2.2054,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.87183869,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"2020","issue":null,"first_page":"285","last_page":"292"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9825000166893005,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.98089998960495,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/computer-science","display_name":"Computer science","score":0.6470295190811157},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6359096169471741},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5940497517585754},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5500078797340393},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5450454354286194},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.49755290150642395},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4383009970188141},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41998618841171265},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.36989080905914307},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.26512300968170166},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.22947314381599426},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.17880627512931824},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17525142431259155},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12093663215637207}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6470295190811157},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6359096169471741},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5940497517585754},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5500078797340393},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5450454354286194},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.49755290150642395},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4383009970188141},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41998618841171265},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.36989080905914307},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.26512300968170166},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.22947314381599426},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.17880627512931824},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17525142431259155},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12093663215637207},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/3311790.3396621","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3311790.3396621","pdf_url":null,"source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"},{"id":"pmid:35662897","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35662897","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":"PEARC20 : Practice and Experience in Advanced Research Computing 2020 : Catch the wave : July 27-31, 2020, Portland, Or Virtual Conference. Practice and Experience in Advanced Research Computing (Conference) (2020 : Online)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9161112","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9161112","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PEARC20 (2020)","raw_type":"Text"},{"id":"pmh:oai:scholarsphere.psu.edu:5056b41e-5271-4247-9f9b-2a064d3a2961","is_oa":false,"landing_page_url":"https://scholarsphere.psu.edu/resources/5056b41e-5271-4247-9f9b-2a064d3a2961","pdf_url":null,"source":{"id":"https://openalex.org/S4306401507","display_name":"ScholarSphere (Penn State Libraries)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I3130638595","host_organization_name":"Pangasinan State University","host_organization_lineage":["https://openalex.org/I3130638595"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9161112","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9161112","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PEARC20 (2020)","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1789587885","display_name":null,"funder_award_id":"R01-ES013768","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G3475994037","display_name":"Promoter Regulation in Response to Environmental Stress","funder_award_id":"5r01es013768-12","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G70541718","display_name":null,"funder_award_id":"R01ES013768","funder_id":"https://openalex.org/F4320306080","funder_display_name":"Foundation for the National Institutes of Health"},{"id":"https://openalex.org/G8916755756","display_name":null,"funder_award_id":"R01 GM125722","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1577822803","https://openalex.org/W1973854565","https://openalex.org/W1974595249","https://openalex.org/W1986700282","https://openalex.org/W1989419347","https://openalex.org/W2030498876","https://openalex.org/W2049869291","https://openalex.org/W2063679723","https://openalex.org/W2129795133","https://openalex.org/W2618569629","https://openalex.org/W2802889540","https://openalex.org/W2883594174","https://openalex.org/W2917207851","https://openalex.org/W4404634217"],"related_works":["https://openalex.org/W2392768766","https://openalex.org/W2058118494","https://openalex.org/W2382021449","https://openalex.org/W2095118173","https://openalex.org/W2104269053","https://openalex.org/W2106424170","https://openalex.org/W1985426483","https://openalex.org/W2501188010","https://openalex.org/W4299935056","https://openalex.org/W2010935248"],"abstract_inverted_index":{"There":[0],"has":[1],"been":[2],"a":[3,57,84,101,142],"rapid":[4],"development":[5],"in":[6,17,49,177],"genome":[7,51],"sequencing,":[8],"including":[9],"high-throughput":[10],"next":[11],"generation":[12],"sequencing":[13,65,111,148],"(NGS)":[14],"technologies,":[15,33],"automation":[16],"biological":[18],"experiments,":[19,112],"new":[20],"bioinformatics":[21,132],"tools":[22],"and":[23,28,36,52,110,118,121,131,150,166,181],"utilization":[24],"of":[25,46,61,137,146,156,170],"high-performance":[26],"computing":[27],"cloud":[29],"computing.":[30],"ChIP-based":[31,75],"NGS":[32,76],"e.g.":[34],"ChIP-seq":[35],"ChIP-exo,":[37],"are":[38],"widely":[39],"used":[40],"to":[41,55],"detect":[42],"the":[43,50,74,94,114,135,147,153,164,167,183],"binding":[44],"sites":[45],"DNA-interacting":[47],"proteins":[48],"help":[53,136],"us":[54],"have":[56,141],"deeper":[58],"mechanistic":[59],"understanding":[60,145],"genomic":[62,157],"regulation.":[63,158],"As":[64],"data":[66,115,149],"is":[67,79],"generated":[68],"at":[69],"an":[70,80],"unprecedented":[71],"pace":[72],"from":[73],"pipelines,":[77],"there":[78],"urgent":[81],"need":[82],"for":[83,96,108],"metadata":[85,107],"management":[86],"system.":[87],"To":[88],"meet":[89],"this":[90,160,179],"need,":[91],"we":[92,162],"developed":[93],"Platform":[95],"Eukaryotic":[97],"Genomic":[98],"Regulation":[99],"(PEGR),":[100],"web":[102],"service":[103],"platform":[104],"that":[105],"logs":[106],"samples":[109],"manages":[113],"processing":[116],"workflows,":[117],"provides":[119],"reporting":[120],"visualization.":[122],"PEGR":[123],"links":[124],"together":[125],"people,":[126],"samples,":[127],"protocols,":[128],"DNA":[129],"sequencers":[130],"computation.":[133],"With":[134],"PEGR,":[138],"scientists":[139],"can":[140],"more":[143],"integrated":[144],"better":[151],"understand":[152],"scientific":[154],"mechanisms":[155],"In":[159],"paper,":[161],"present":[163],"architecture":[165],"major":[168],"functionalities":[169],"PEGR.":[171],"We":[172],"also":[173],"share":[174],"our":[175],"experience":[176],"developing":[178],"application":[180],"discuss":[182],"future":[184],"directions.":[185]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
