{"id":"https://openalex.org/W2026074998","doi":"https://doi.org/10.1371/journal.pcbi.1000299","title":"Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution","display_name":"Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution","publication_year":2009,"publication_date":"2009-03-12","ids":{"openalex":"https://openalex.org/W2026074998","doi":"https://doi.org/10.1371/journal.pcbi.1000299","mag":"2026074998","pmid":"https://pubmed.ncbi.nlm.nih.gov/19293946"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000299","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000299","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000299&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000299&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100749954","display_name":"Xin He","orcid":"https://orcid.org/0000-0002-8602-5166"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xin He","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL, USA","Department of Computer Science, University of Illinois, Urbana-Champaign Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Computer Science, University of Illinois, Urbana-Champaign Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103583048","display_name":"Xu Ling","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xu Ling","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101657008","display_name":"Saurabh Sinha","orcid":"https://orcid.org/0000-0001-6033-7746"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Saurabh Sinha","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101657008"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.4197,"has_fulltext":true,"cited_by_count":44,"citation_normalized_percentile":{"value":0.92830063,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5","issue":"3","first_page":"e1000299","last_page":"e1000299"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9990000128746033,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.6887969970703125},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6193395256996155},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.553203821182251},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.547334611415863},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5179883241653442},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.49146759510040283},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.46553340554237366},{"id":"https://openalex.org/keywords/blastoderm","display_name":"Blastoderm","score":0.4508332312107086},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.45014503598213196},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.434174507856369},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4244837462902069},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4204564392566681},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.372593492269516},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3426406979560852},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32883960008621216},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2798416018486023},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26720571517944336},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.1454896330833435},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.11056339740753174},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.09289312362670898}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.6887969970703125},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6193395256996155},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.553203821182251},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.547334611415863},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5179883241653442},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.49146759510040283},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.46553340554237366},{"id":"https://openalex.org/C98535976","wikidata":"https://www.wikidata.org/wiki/Q4088022","display_name":"Blastoderm","level":4,"score":0.4508332312107086},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.45014503598213196},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.434174507856369},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4244837462902069},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4204564392566681},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.372593492269516},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3426406979560852},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32883960008621216},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2798416018486023},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26720571517944336},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.1454896330833435},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.11056339740753174},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.09289312362670898},{"id":"https://openalex.org/C87073359","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryogenesis","level":3,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1000299","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000299","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000299&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:19293946","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19293946","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1000299","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000299","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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:63182d98b8204ab5b4805978838cd284","is_oa":true,"landing_page_url":"https://doaj.org/article/63182d98b8204ab5b4805978838cd284","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 5, Iss 3, p e1000299 (2009)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/148208","is_oa":true,"landing_page_url":"https://figshare.com/articles/Alignment_and_Prediction_of_cis_Regulatory_Modules_Based_on_a_Probabilistic_Model_of_Evolution/148208","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2657044","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2657044","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000299","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000299","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000299&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7300000190734863,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332222","display_name":"University of Illinois at Urbana-Champaign","ror":"https://ror.org/047426m28"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2026074998.pdf","grobid_xml":"https://content.openalex.org/works/W2026074998.grobid-xml"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W10219220","https://openalex.org/W614012683","https://openalex.org/W1753000577","https://openalex.org/W1963590211","https://openalex.org/W1969770714","https://openalex.org/W1984053739","https://openalex.org/W1987229243","https://openalex.org/W1994190548","https://openalex.org/W2001706442","https://openalex.org/W2008900336","https://openalex.org/W2009596137","https://openalex.org/W2012354488","https://openalex.org/W2013034014","https://openalex.org/W2019136439","https://openalex.org/W2021839440","https://openalex.org/W2023635398","https://openalex.org/W2024665422","https://openalex.org/W2026398852","https://openalex.org/W2030816054","https://openalex.org/W2046233233","https://openalex.org/W2046374070","https://openalex.org/W2058552632","https://openalex.org/W2059823654","https://openalex.org/W2061149284","https://openalex.org/W2067579500","https://openalex.org/W2077941487","https://openalex.org/W2080901145","https://openalex.org/W2092979861","https://openalex.org/W2095901576","https://openalex.org/W2097311877","https://openalex.org/W2102159699","https://openalex.org/W2102231586","https://openalex.org/W2102304447","https://openalex.org/W2103465619","https://openalex.org/W2109314645","https://openalex.org/W2114122189","https://openalex.org/W2116015974","https://openalex.org/W2117017773","https://openalex.org/W2120248467","https://openalex.org/W2127164334","https://openalex.org/W2127688908","https://openalex.org/W2128482297","https://openalex.org/W2128713736","https://openalex.org/W2133147430","https://openalex.org/W2139659560","https://openalex.org/W2140538490","https://openalex.org/W2142418747","https://openalex.org/W2142946358","https://openalex.org/W2143255831","https://openalex.org/W2145958666","https://openalex.org/W2147847662","https://openalex.org/W2148441137","https://openalex.org/W2148450265","https://openalex.org/W2149769193","https://openalex.org/W2150612336","https://openalex.org/W2151464048","https://openalex.org/W2151907070","https://openalex.org/W2155237411","https://openalex.org/W2155717510","https://openalex.org/W2155940790","https://openalex.org/W2160659074","https://openalex.org/W2161387979","https://openalex.org/W2165890696","https://openalex.org/W2166444569","https://openalex.org/W2166894044","https://openalex.org/W2167055123","https://openalex.org/W2168735550","https://openalex.org/W2169056802","https://openalex.org/W2170628952","https://openalex.org/W2740984310","https://openalex.org/W3099586128"],"related_works":["https://openalex.org/W2113617499","https://openalex.org/W2110472417","https://openalex.org/W2061232824","https://openalex.org/W2109830628","https://openalex.org/W2145929420","https://openalex.org/W1983122635","https://openalex.org/W2159154305","https://openalex.org/W2032600042","https://openalex.org/W2169472710","https://openalex.org/W2026074998"],"abstract_inverted_index":{"Cross-species":[0],"comparison":[1,18],"has":[2],"emerged":[3],"as":[4,101,169,171,270],"a":[5,25,58,88,97,111,164,283],"powerful":[6],"paradigm":[7],"for":[8,28],"predicting":[9],"cis-regulatory":[10,275],"modules":[11],"(CRMs)":[12],"and":[13,76,93,125,160,185,243],"understanding":[14],"their":[15,234],"evolution.":[16,108],"The":[17],"requires":[19],"reliable":[20],"sequence":[21,39,107,161],"alignment,":[22],"which":[23],"remains":[24],"challenging":[26],"task":[27],"less":[29],"conserved":[30,141,260],"noncoding":[31],"sequences.":[32,51,79],"Furthermore,":[33],"the":[34,46,77,120,140,153,216,224,241],"existing":[35,133],"models":[36],"of":[37,49,60,67,69,84,91,95,105,122,135,156,187,211],"DNA":[38],"evolution":[40,62,68],"generally":[41],"do":[42],"not":[43,238],"explicitly":[44],"treat":[45],"special":[47],"properties":[48],"CRM":[50,61,123,148,188],"To":[52],"address":[53],"these":[54],"limitations,":[55],"we":[56,174,195],"propose":[57],"model":[59,90,117],"that":[63,114,176],"captures":[64],"different":[65],"modes":[66],"functional":[70],"transcription":[71,213,253],"factor":[72],"binding":[73,142,157,204,209,245],"sites":[74,143,246],"(TFBSs)":[75],"background":[78],"A":[80],"particularly":[81],"novel":[82],"aspect":[83],"our":[85,177,200],"work":[86],"is":[87,130,179,268],"probabilistic":[89,165],"gains":[92],"losses":[94],"TFBSs,":[96],"process":[98],"being":[99],"recognized":[100],"an":[102],"important":[103],"part":[104],"regulatory":[106],"We":[109],"present":[110],"computational":[112],"framework":[113],"uses":[115,139],"this":[116],"to":[118,132,144,181,202,252,257,279],"solve":[119],"problems":[121],"alignment":[124,128,137,162,184],"prediction.":[126],"Our":[127,147,266],"method":[129,150],"similar":[131],"methods":[134],"statistical":[136],"but":[138],"improve":[145,182],"alignment.":[146],"prediction":[149,186],"deals":[151],"with":[152,219],"inherent":[154],"uncertainties":[155],"site":[158,205],"annotations":[159],"in":[163,207,215,240,247,263,282],"framework.":[166],"In":[167],"simulated":[168],"well":[170],"real":[172],"data,":[173],"demonstrate":[175],"program":[178,201],"able":[180],"both":[183],"sequences":[189,226,250],"over":[190],"several":[191],"state-of-the-art":[192],"methods.":[193],"Finally,":[194],"used":[196],"alignments":[197],"produced":[198],"by":[199],"study":[203],"conservation":[206],"genome-wide":[208],"data":[210],"key":[212],"factors":[214],"Drosophila":[217],"blastoderm,":[218],"two":[220],"intriguing":[221],"results:":[222],"(i)":[223],"factor-bound":[225],"are":[227,237],"under":[228],"strong":[229],"evolutionary":[230],"constraints":[231],"even":[232],"if":[233],"neighboring":[235],"genes":[236],"expressed":[239],"blastoderm":[242],"(ii)":[244],"distal":[248],"bound":[249],"(relative":[251],"start":[254],"sites)":[255],"tend":[256],"be":[258,280],"more":[259],"than":[261],"those":[262],"proximal":[264],"regions.":[265],"approach":[267],"implemented":[269],"software,":[271],"EMMA":[272],"(Evolutionary":[273],"Model-based":[274],"Module":[276],"Analysis),":[277],"ready":[278],"applied":[281],"broad":[284],"biological":[285],"context.":[286]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
