{"id":"https://openalex.org/W2016202595","doi":"https://doi.org/10.1186/1471-2105-11-369","title":"HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data","display_name":"HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data","publication_year":2010,"publication_date":"2010-07-02","ids":{"openalex":"https://openalex.org/W2016202595","doi":"https://doi.org/10.1186/1471-2105-11-369","mag":"2016202595","pmid":"https://pubmed.ncbi.nlm.nih.gov/20598134"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-369","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-369","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-369","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/counter/pdf/10.1186/1471-2105-11-369","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042399779","display_name":"Zhaohui Qin","orcid":"https://orcid.org/0000-0002-1583-146X"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhaohui S Qin","raw_affiliation_strings":["Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, 48109-2029, USA. qin@umich.edu","Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA"],"affiliations":[{"raw_affiliation_string":"Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, 48109-2029, USA. qin@umich.edu","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100639000","display_name":"Jianjun Yu","orcid":"https://orcid.org/0000-0001-9434-088X"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]},{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianjun Yu","raw_affiliation_strings":["Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 North St. Clair, Suite 1200, Chicago, IL, 60611, USA","Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 North St. Clair, Suite 1200, Chicago, IL, 60611, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA","institution_ids":["https://openalex.org/I4210117557","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016257520","display_name":"Jincheng Shen","orcid":"https://orcid.org/0000-0002-6551-3558"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jincheng Shen","raw_affiliation_strings":["Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA"],"affiliations":[{"raw_affiliation_string":"Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028616783","display_name":"Christopher A. Maher","orcid":"https://orcid.org/0000-0002-9035-603X"},"institutions":[{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I199037182","display_name":"Washtenaw Community College","ror":"https://ror.org/03k77wm53","country_code":"US","type":"education","lineage":["https://openalex.org/I199037182"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher A Maher","raw_affiliation_strings":["Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA","Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA","institution_ids":["https://openalex.org/I199037182","https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA","institution_ids":["https://openalex.org/I4210117557","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102022832","display_name":"Ming Hu","orcid":"https://orcid.org/0000-0002-6062-8794"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ming Hu","raw_affiliation_strings":["Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA"],"affiliations":[{"raw_affiliation_string":"Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089714684","display_name":"Shanker Kalyana\u2010Sundaram","orcid":"https://orcid.org/0000-0002-7309-3848"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shanker Kalyana-Sundaram","raw_affiliation_strings":["Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA","institution_ids":["https://openalex.org/I4210117557","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026756753","display_name":"Jindan Yu","orcid":"https://orcid.org/0000-0002-2326-0409"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]},{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jindan Yu","raw_affiliation_strings":["Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 North St. Clair, Suite 1200, Chicago, IL, 60611, USA","Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 North St. Clair, Suite 1200, Chicago, IL, 60611, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA","institution_ids":["https://openalex.org/I4210117557","https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108833506","display_name":"Arul M. Chinnaiyan","orcid":null},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]},{"id":"https://openalex.org/I199037182","display_name":"Washtenaw Community College","ror":"https://ror.org/03k77wm53","country_code":"US","type":"education","lineage":["https://openalex.org/I199037182"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210122509","display_name":"Ann Arbor VA Medical Center","ror":"https://ror.org/039n0s143","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1322918889","https://openalex.org/I2799886695","https://openalex.org/I4210102099","https://openalex.org/I4210122509","https://openalex.org/I4210127612"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arul M Chinnaiyan","raw_affiliation_strings":["Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA","Comprehensive Cancer Center, University of Michigan Medical School, 1500 E. Medical Center Drive, Ann Arbor, MI, 48109-0944, USA","Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","Department of Urology, University of Michigan Medical School, 1500 E. Medical Center Drive, Ann Arbor, MI, 48109-0330, USA","Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, 20815-6789, USA","Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA","institution_ids":["https://openalex.org/I199037182","https://openalex.org/I27837315"]},{"raw_affiliation_string":"Comprehensive Cancer Center, University of Michigan Medical School, 1500 E. Medical Center Drive, Ann Arbor, MI, 48109-0944, USA","institution_ids":["https://openalex.org/I4210117557"]},{"raw_affiliation_string":"Department of Pathology, University of Michigan Medical School, 1301 Catherine, Ann Arbor, Michigan, 48109-0602, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Urology, University of Michigan Medical School, 1500 E. Medical Center Drive, Ann Arbor, MI, 48109-0330, USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210122509","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD, 20815-6789, USA","institution_ids":["https://openalex.org/I1344073410"]},{"raw_affiliation_string":"Michigan Center for Translational Pathology, University of Michigan Medical School, 1400 E. Medical Center Drive, Ann Arbor, MI, 48109-0940, USA","institution_ids":["https://openalex.org/I4210117557","https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5042399779"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":6.8938,"has_fulltext":true,"cited_by_count":103,"citation_normalized_percentile":{"value":0.97742521,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"11","issue":"1","first_page":"369","last_page":"369"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":1.0,"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":1.0,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9965999722480774,"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/T10604","display_name":"RNA Research and Splicing","score":0.9965000152587891,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6849064826965332},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5828993916511536},{"id":"https://openalex.org/keywords/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.5540371537208557},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5414159297943115},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5395269989967346},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.46602344512939453},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4659512937068939},{"id":"https://openalex.org/keywords/chip","display_name":"Chip","score":0.4533327519893646},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.44600972533226013},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4296841025352478},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4215320646762848},{"id":"https://openalex.org/keywords/chip-sequencing","display_name":"ChIP-sequencing","score":0.4188951551914215},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.407239705324173},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.37867000699043274},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2574867606163025},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24599751830101013},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.22259268164634705},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20132866501808167},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18215569853782654},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.11517199873924255},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11142909526824951},{"id":"https://openalex.org/keywords/chromatin-remodeling","display_name":"Chromatin remodeling","score":0.09860920906066895}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6849064826965332},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5828993916511536},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.5540371537208557},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5414159297943115},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5395269989967346},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46602344512939453},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4659512937068939},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.4533327519893646},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.44600972533226013},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4296841025352478},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4215320646762848},{"id":"https://openalex.org/C176619506","wikidata":"https://www.wikidata.org/wiki/Q5065899","display_name":"ChIP-sequencing","level":5,"score":0.4188951551914215},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.407239705324173},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.37867000699043274},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2574867606163025},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24599751830101013},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.22259268164634705},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20132866501808167},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18215569853782654},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.11517199873924255},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11142909526824951},{"id":"https://openalex.org/C167227067","wikidata":"https://www.wikidata.org/wiki/Q5113739","display_name":"Chromatin remodeling","level":4,"score":0.09860920906066895},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000099229","descriptor_name":"RE1-Silencing Transcription Factor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006657","descriptor_name":"Histones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012097","descriptor_name":"Repressor Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050794","descriptor_name":"STAT1 Transcription Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050794","descriptor_name":"STAT1 Transcription Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050794","descriptor_name":"STAT1 Transcription Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050794","descriptor_name":"STAT1 Transcription Factor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-11-369","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-369","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-369","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:20598134","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20598134","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:deepblue.lib.umich.edu:2027.42/112381","is_oa":true,"landing_page_url":"https://hdl.handle.net/2027.42/112381","pdf_url":"https://hdl.handle.net/2027.42/112381","source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"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"},{"id":"pmh:oai:doaj.org/article:a2efa777b9f64eff81285ef229d543a5","is_oa":true,"landing_page_url":"https://doaj.org/article/a2efa777b9f64eff81285ef229d543a5","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 369 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2912305","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2912305","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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:10.1186/1471-2105-11-369","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-369","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-369","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/G1320088940","display_name":null,"funder_award_id":"K99/R00","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1883011536","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320306133","funder_display_name":"Burroughs Wellcome Fund"},{"id":"https://openalex.org/G2596904628","display_name":null,"funder_award_id":"K99/R00","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2835068597","display_name":null,"funder_award_id":"CA69568","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3219898623","display_name":null,"funder_award_id":"P50 CA69568","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4119534169","display_name":null,"funder_award_id":"W81XWH","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"},{"id":"https://openalex.org/G5617340142","display_name":null,"funder_award_id":"BC075023","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"},{"id":"https://openalex.org/G5850682332","display_name":null,"funder_award_id":"W81XWH","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7799733506","display_name":null,"funder_award_id":"HG005119","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8809597287","display_name":null,"funder_award_id":"P50 CA69568","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320306133","display_name":"Burroughs Wellcome Fund","ror":"https://ror.org/01d35cw23"},{"id":"https://openalex.org/F4320306163","display_name":"Prostate Cancer Foundation","ror":"https://ror.org/01npwtv09"},{"id":"https://openalex.org/F4320307105","display_name":"Amgen","ror":"https://ror.org/03g03ge92"},{"id":"https://openalex.org/F4320309830","display_name":"Canary Foundation","ror":"https://ror.org/04zqh4p27"},{"id":"https://openalex.org/F4320310145","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332513","display_name":"Weill Cornell Medical College","ror":"https://ror.org/02r109517"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2016202595.pdf","grobid_xml":"https://content.openalex.org/works/W2016202595.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1707745162","https://openalex.org/W1876857396","https://openalex.org/W1967656072","https://openalex.org/W1979674827","https://openalex.org/W1988294855","https://openalex.org/W1993316002","https://openalex.org/W1996212302","https://openalex.org/W2005281324","https://openalex.org/W2008535448","https://openalex.org/W2013336813","https://openalex.org/W2015416439","https://openalex.org/W2017840637","https://openalex.org/W2022148802","https://openalex.org/W2036490654","https://openalex.org/W2057267524","https://openalex.org/W2059699217","https://openalex.org/W2065579185","https://openalex.org/W2068193616","https://openalex.org/W2072152932","https://openalex.org/W2079298594","https://openalex.org/W2087401860","https://openalex.org/W2092387193","https://openalex.org/W2096286842","https://openalex.org/W2097220641","https://openalex.org/W2102904139","https://openalex.org/W2104865962","https://openalex.org/W2110065044","https://openalex.org/W2117089877","https://openalex.org/W2118628540","https://openalex.org/W2120858259","https://openalex.org/W2121967239","https://openalex.org/W2125114453","https://openalex.org/W2125838338","https://openalex.org/W2128016314","https://openalex.org/W2129795133","https://openalex.org/W2132508108","https://openalex.org/W2140022443","https://openalex.org/W2141222038","https://openalex.org/W2142808828","https://openalex.org/W2145191876","https://openalex.org/W2151754128","https://openalex.org/W2153550523","https://openalex.org/W2154431984","https://openalex.org/W2157750836","https://openalex.org/W2164813466","https://openalex.org/W2167465414","https://openalex.org/W2168148516","https://openalex.org/W2168390964","https://openalex.org/W2170386697","https://openalex.org/W2171808845","https://openalex.org/W2399991609","https://openalex.org/W2912369858","https://openalex.org/W4248318091","https://openalex.org/W4300907844"],"related_works":["https://openalex.org/W1984632551","https://openalex.org/W169483493","https://openalex.org/W307582","https://openalex.org/W4239070450","https://openalex.org/W2467475648","https://openalex.org/W2365390141","https://openalex.org/W2769829611","https://openalex.org/W1523535450","https://openalex.org/W2411645972","https://openalex.org/W4200221795"],"abstract_inverted_index":{"Using":[0],"biologically":[1],"relevant":[2],"data":[3],"collections,":[4],"we":[5],"found":[6],"that":[7],"HPeak":[8,62],"showed":[9],"a":[10],"higher":[11,46],"prevalence":[12],"of":[13,54],"the":[14,25,41,61],"expected":[15],"transcription":[16],"factor":[17],"binding":[18,55],"motifs":[19],"in":[20,38],"ChIP-enriched":[21],"sequences":[22,27],"relative":[23],"to":[24,30,40],"control":[26],"when":[28],"compared":[29],"other":[31],"currently":[32],"available":[33,66],"ChIP-Seq":[34,44],"analysis":[35],"approaches.":[36],"Additionally,":[37],"comparison":[39],"ChIP-chip":[42],"assay,":[43],"provides":[45],"resolution":[47],"along":[48],"with":[49],"improved":[50],"sensitivity":[51],"and":[52,60],"specificity":[53],"site":[56],"detection.":[57],"Additional":[58],"file":[59],"program":[63],"are":[64],"freely":[65],"at":[67],"http://www.sph.umich.edu/csg/qin/HPeak.":[68]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":13},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":17},{"year":2012,"cited_by_count":10}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
