{"id":"https://openalex.org/W2168487324","doi":"https://doi.org/10.1007/978-3-642-20036-6_26","title":"AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization","display_name":"AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization","publication_year":2011,"publication_date":"2011-01-01","ids":{"openalex":"https://openalex.org/W2168487324","doi":"https://doi.org/10.1007/978-3-642-20036-6_26","mag":"2168487324"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-642-20036-6_26","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-20036-6_26","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045622820","display_name":"Daniel A. Newkirk","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel Newkirk","raw_affiliation_strings":["Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA","The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033348360","display_name":"Jacob Biesinger","orcid":"https://orcid.org/0000-0003-0172-525X"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob Biesinger","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, CA, 92697, USA","The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, CA, 92697, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069691200","display_name":"Alvin Chon","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alvin Chon","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, CA, 92697, USA","The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, CA, 92697, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065671943","display_name":"Kyoko Yokomori","orcid":"https://orcid.org/0000-0002-2785-4589"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyoko Yokomori","raw_affiliation_strings":["Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084618257","display_name":"Xiaohui Xie","orcid":"https://orcid.org/0000-0002-5479-6345"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaohui Xie","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, CA, 92697, USA","The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, CA, 92697, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"The Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697, USA","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5045622820"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":0.5298,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.69782958,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"283","last_page":"297"},"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":0.9993000030517578,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.7294272184371948},{"id":"https://openalex.org/keywords/chip-sequencing","display_name":"ChIP-sequencing","score":0.721452534198761},{"id":"https://openalex.org/keywords/expectation\u2013maximization-algorithm","display_name":"Expectation\u2013maximization algorithm","score":0.5821941494941711},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5545321702957153},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5350035429000854},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5244755148887634},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.4903748035430908},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4458007216453552},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4318111538887024},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39681845903396606},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3803383409976959},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2333763837814331},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22669684886932373},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15357980132102966},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.1359117329120636},{"id":"https://openalex.org/keywords/nucleosome","display_name":"Nucleosome","score":0.11058446764945984},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.10376128554344177},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08003729581832886}],"concepts":[{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.7294272184371948},{"id":"https://openalex.org/C176619506","wikidata":"https://www.wikidata.org/wiki/Q5065899","display_name":"ChIP-sequencing","level":5,"score":0.721452534198761},{"id":"https://openalex.org/C182081679","wikidata":"https://www.wikidata.org/wiki/Q1275153","display_name":"Expectation\u2013maximization algorithm","level":3,"score":0.5821941494941711},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5545321702957153},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5350035429000854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5244755148887634},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.4903748035430908},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4458007216453552},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4318111538887024},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39681845903396606},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3803383409976959},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2333763837814331},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22669684886932373},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15357980132102966},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.1359117329120636},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.11058446764945984},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.10376128554344177},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08003729581832886},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/978-3-642-20036-6_26","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-20036-6_26","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.44999998807907104,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1214546200","https://openalex.org/W1967656072","https://openalex.org/W1968475238","https://openalex.org/W1983230603","https://openalex.org/W2016202595","https://openalex.org/W2017840637","https://openalex.org/W2024736438","https://openalex.org/W2027352426","https://openalex.org/W2040641918","https://openalex.org/W2041835455","https://openalex.org/W2044164623","https://openalex.org/W2044937161","https://openalex.org/W2047005748","https://openalex.org/W2053806756","https://openalex.org/W2055303035","https://openalex.org/W2081705896","https://openalex.org/W2085315537","https://openalex.org/W2102904139","https://openalex.org/W2105924780","https://openalex.org/W2112113834","https://openalex.org/W2115137176","https://openalex.org/W2124985265","https://openalex.org/W2125114453","https://openalex.org/W2139760555","https://openalex.org/W2141222038","https://openalex.org/W2146648681","https://openalex.org/W2154431984","https://openalex.org/W2157131586","https://openalex.org/W2157214001","https://openalex.org/W2166496717","https://openalex.org/W2171111703","https://openalex.org/W2171808845","https://openalex.org/W2172244392","https://openalex.org/W2175853567","https://openalex.org/W2918025614"],"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/W4200221795","https://openalex.org/W2045366448","https://openalex.org/W4318476585","https://openalex.org/W2769829611"],"abstract_inverted_index":null,"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}