{"id":"https://openalex.org/W2167465414","doi":"https://doi.org/10.1093/bioinformatics/btp312","title":"Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data","display_name":"Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data","publication_year":2009,"publication_date":"2009-05-14","ids":{"openalex":"https://openalex.org/W2167465414","doi":"https://doi.org/10.1093/bioinformatics/btp312","mag":"2167465414","pmid":"https://pubmed.ncbi.nlm.nih.gov/19447789"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp312","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp312","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/14/1715/48992473/bioinformatics_25_14_1715.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/14/1715/48992473/bioinformatics_25_14_1715.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081303849","display_name":"Hyungwon Choi","orcid":"https://orcid.org/0000-0002-6687-3088"},"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"]},{"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":"Hyungwon Choi","raw_affiliation_strings":["1 Department of Pathology, 2 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, 3 Departments of Statistics and Public Health Sciences, Penn State University, University Park, PA 16802 and 4 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Pathology, 2 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, 3 Departments of Statistics and Public Health Sciences, Penn State University, University Park, PA 16802 and 4 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085497637","display_name":"Alexey I. Nesvizhskii","orcid":"https://orcid.org/0000-0002-2806-7819"},"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/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":"Alexey I. Nesvizhskii","raw_affiliation_strings":["1 Department of Pathology, 2 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, 3 Departments of Statistics and Public Health Sciences, Penn State University, University Park, PA 16802 and 4 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Pathology, 2 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, 3 Departments of Statistics and Public Health Sciences, Penn State University, University Park, PA 16802 and 4 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100625254","display_name":"Debashis Ghosh","orcid":"https://orcid.org/0000-0001-9214-2249"},"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"]},{"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":"Debashis Ghosh","raw_affiliation_strings":["1 Department of Pathology, 2 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, 3 Departments of Statistics and Public Health Sciences, Penn State University, University Park, PA 16802 and 4 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Pathology, 2 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, 3 Departments of Statistics and Public Health Sciences, Penn State University, University Park, PA 16802 and 4 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I130769515"]}]},{"author_position":"last","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"]},{"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":"Zhaohui S. Qin","raw_affiliation_strings":["1 Department of Pathology, 2 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, 3 Departments of Statistics and Public Health Sciences, Penn State University, University Park, PA 16802 and 4 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Pathology, 2 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, 3 Departments of Statistics and Public Health Sciences, Penn State University, University Park, PA 16802 and 4 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5081303849"],"corresponding_institution_ids":["https://openalex.org/I130769515","https://openalex.org/I27837315"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2309,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.88061264,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"14","first_page":"1715","last_page":"1721"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.996999979019165,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9958999752998352,"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":0.7155672311782837},{"id":"https://openalex.org/keywords/chip","display_name":"Chip","score":0.6990761160850525},{"id":"https://openalex.org/keywords/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.4829115569591522},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.46998822689056396},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.44479745626449585},{"id":"https://openalex.org/keywords/tiling-array","display_name":"Tiling array","score":0.41304105520248413},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.28581929206848145},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13385820388793945},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12600421905517578},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09692355990409851},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.09108731150627136}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7155672311782837},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.6990761160850525},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.4829115569591522},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.46998822689056396},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.44479745626449585},{"id":"https://openalex.org/C119401833","wikidata":"https://www.wikidata.org/wiki/Q7802158","display_name":"Tiling array","level":5,"score":0.41304105520248413},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.28581929206848145},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13385820388793945},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12600421905517578},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09692355990409851},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.09108731150627136},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp312","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp312","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/14/1715/48992473/bioinformatics_25_14_1715.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19447789","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19447789","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2732365","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2732365","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp312","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp312","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/14/1715/48992473/bioinformatics_25_14_1715.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"},{"id":"https://openalex.org/F4320310419","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167465414.pdf","grobid_xml":"https://content.openalex.org/works/W2167465414.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1539673959","https://openalex.org/W1554672230","https://openalex.org/W1636244751","https://openalex.org/W1876857396","https://openalex.org/W1967656072","https://openalex.org/W1985038830","https://openalex.org/W1988294855","https://openalex.org/W1993316002","https://openalex.org/W2000490360","https://openalex.org/W2005281324","https://openalex.org/W2012016911","https://openalex.org/W2014119967","https://openalex.org/W2015416439","https://openalex.org/W2017840637","https://openalex.org/W2024495278","https://openalex.org/W2026882865","https://openalex.org/W2029722028","https://openalex.org/W2036490654","https://openalex.org/W2059699217","https://openalex.org/W2068193616","https://openalex.org/W2072152932","https://openalex.org/W2087401860","https://openalex.org/W2097139904","https://openalex.org/W2110015307","https://openalex.org/W2118628540","https://openalex.org/W2123490534","https://openalex.org/W2125838338","https://openalex.org/W2129795133","https://openalex.org/W2132508108","https://openalex.org/W2136932227","https://openalex.org/W2140022443","https://openalex.org/W2148133654","https://openalex.org/W2153550523","https://openalex.org/W2168148516","https://openalex.org/W2168390964","https://openalex.org/W2171407623","https://openalex.org/W2399991609","https://openalex.org/W2797111759","https://openalex.org/W2912369858","https://openalex.org/W4248318091","https://openalex.org/W6632850819"],"related_works":["https://openalex.org/W1975694968","https://openalex.org/W2141222206","https://openalex.org/W2164235180","https://openalex.org/W1996212302","https://openalex.org/W196124755","https://openalex.org/W2410864125","https://openalex.org/W2138006094","https://openalex.org/W2049726768","https://openalex.org/W1535515588","https://openalex.org/W1766557613"],"abstract_inverted_index":{"Source":[0],"code":[1],"for":[2,9],"the":[3],"software":[4],"ChIPmeta":[5],"is":[6],"freely":[7],"available":[8],"download":[10],"at":[11],"http://www.umich.edu/~hwchoi/HHMMsoftware.zip,":[12],"implemented":[13],"in":[14],"C":[15],"and":[16],"supported":[17],"on":[18],"linux.":[19]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
