{"id":"https://openalex.org/W2024665422","doi":"https://doi.org/10.1371/journal.pcbi.0030216","title":"MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules","display_name":"MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules","publication_year":2007,"publication_date":"2007-11-07","ids":{"openalex":"https://openalex.org/W2024665422","doi":"https://doi.org/10.1371/journal.pcbi.0030216","mag":"2024665422","pmid":"https://pubmed.ncbi.nlm.nih.gov/17997594"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0030216","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030216","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.0030216","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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 at Urbana-Champaign, Urbana, Illinois, United States of America. sinhas@cs.uiuc.edu","Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America. sinhas@cs.uiuc.edu","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101820232","display_name":"Xin He","orcid":"https://orcid.org/0000-0003-3094-9850"},"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 at Urbana-Champaign, Urbana, Illinois, United States of America","Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"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":2.1529,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.86893677,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"3","issue":"11","first_page":"e216","last_page":"e216"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10222","display_name":"Genomics and Chromatin Dynamics","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/T10184","display_name":"Plant Molecular Biology Research","score":0.9947999715805054,"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/probabilistic-logic","display_name":"Probabilistic logic","score":0.6599213480949402},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5320613980293274},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5311214923858643},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5244265198707581},{"id":"https://openalex.org/keywords/cis-regulatory-module","display_name":"Cis-regulatory module","score":0.5203599333763123},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.48792049288749695},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.474936306476593},{"id":"https://openalex.org/keywords/drosophila-melanogaster","display_name":"Drosophila melanogaster","score":0.457535058259964},{"id":"https://openalex.org/keywords/melanogaster","display_name":"Melanogaster","score":0.4540087878704071},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4251408874988556},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.41901516914367676},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3608752191066742},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22110900282859802},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20632097125053406},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17538437247276306},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.14667314291000366},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.09273266792297363}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6599213480949402},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5320613980293274},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5311214923858643},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5244265198707581},{"id":"https://openalex.org/C190796033","wikidata":"https://www.wikidata.org/wiki/Q1093165","display_name":"Cis-regulatory module","level":5,"score":0.5203599333763123},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.48792049288749695},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.474936306476593},{"id":"https://openalex.org/C2780104201","wikidata":"https://www.wikidata.org/wiki/Q130888","display_name":"Drosophila melanogaster","level":3,"score":0.457535058259964},{"id":"https://openalex.org/C2776998849","wikidata":"https://www.wikidata.org/wiki/Q3766082","display_name":"Melanogaster","level":4,"score":0.4540087878704071},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4251408874988556},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41901516914367676},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3608752191066742},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22110900282859802},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20632097125053406},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17538437247276306},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.14667314291000366},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.09273266792297363},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.0030216","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030216","pdf_url":null,"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:17997594","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17997594","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:CiteSeerX.psu:10.1.1.283.9905","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.283.9905","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/71/5f/PLoS_Comput_Biol_2007_Nov_9_3(11)_e216.tar.gz","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:0030216","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030216","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:8a922d01d81a4cc38af6a0e57f3df673","is_oa":true,"landing_page_url":"https://doaj.org/article/8a922d01d81a4cc38af6a0e57f3df673","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 3, Iss 11, p e216 (2007)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2622467","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC2065892","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2065892","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2065892","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.0030216","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030216","pdf_url":null,"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":[{"id":"https://metadata.un.org/sdg/15","score":0.7200000286102295,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1584129042","https://openalex.org/W1595688369","https://openalex.org/W1980397590","https://openalex.org/W1991770658","https://openalex.org/W2009570821","https://openalex.org/W2025289680","https://openalex.org/W2051333589","https://openalex.org/W2055043387","https://openalex.org/W2067579500","https://openalex.org/W2074231493","https://openalex.org/W2086699924","https://openalex.org/W2092979861","https://openalex.org/W2095617232","https://openalex.org/W2097311877","https://openalex.org/W2102159699","https://openalex.org/W2102424972","https://openalex.org/W2103465619","https://openalex.org/W2110335151","https://openalex.org/W2112221859","https://openalex.org/W2112814753","https://openalex.org/W2114122189","https://openalex.org/W2117017773","https://openalex.org/W2117549173","https://openalex.org/W2119104284","https://openalex.org/W2127164334","https://openalex.org/W2134591904","https://openalex.org/W2137502130","https://openalex.org/W2140115103","https://openalex.org/W2140872496","https://openalex.org/W2146696273","https://openalex.org/W2148441137","https://openalex.org/W2149769193","https://openalex.org/W2155237411","https://openalex.org/W2155717510","https://openalex.org/W2157523980","https://openalex.org/W2165228646","https://openalex.org/W2165378709","https://openalex.org/W2166444569","https://openalex.org/W2169056802","https://openalex.org/W2170628952","https://openalex.org/W2610493105"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W2141411672"],"abstract_inverted_index":{"The":[0,105,179],"discovery":[1],"and":[2,20,43,138,162,215],"analysis":[3,101,219],"of":[4,18,35,73,112,145,158,170,182,192,202,205,220],"cis-regulatory":[5,171,183],"modules":[6],"(CRMs)":[7],"in":[8,76,102,120,212],"metazoan":[9],"genomes":[10],"is":[11,186,196],"crucial":[12],"for":[13,31,37,44,51,117],"understanding":[14,45],"the":[15,71,77,90,143,146,190,200],"transcriptional":[16],"control":[17],"development":[19],"many":[21,193],"other":[22],"biological":[23],"processes.":[24],"Cross-species":[25],"sequence":[26,60],"comparison":[27],"holds":[28],"much":[29],"promise":[30],"improving":[32],"computational":[33,156],"prediction":[34],"CRMs,":[36],"elucidating":[38],"their":[39],"binding":[40,74,94],"site":[41,95],"composition,":[42],"how":[46],"they":[47],"evolve.":[48],"Current":[49],"methods":[50],"analyzing":[52],"orthologous":[53,129],"CRMs":[54,130],"from":[55,131,176],"multiple":[56],"species":[57,135],"rely":[58],"upon":[59],"alignments":[61,111,204],"produced":[62],"by":[63,189,199],"off-the-shelf":[64],"alignment":[65,91,118,160],"algorithms,":[66],"which":[67,185],"do":[68],"not":[69],"exploit":[70],"presence":[72],"sites":[75],"sequences.":[78],"We":[79,124,149],"present":[80],"here":[81],"a":[82,121,164],"unified":[83],"probabilistic":[84],"framework,":[85],"called":[86],"MORPH,":[87],"that":[88,151,174],"integrates":[89],"task":[92],"with":[93],"predictions,":[96],"allowing":[97],"more":[98,167,217],"robust":[99],"CRM":[100,221],"two":[103,113,132],"species.":[104],"framework":[106],"sums":[107],"over":[108],"all":[109],"possible":[110],"sequences,":[114],"thus":[115],"accounting":[116],"ambiguities":[119],"natural":[122],"way.":[123],"perform":[125],"extensive":[126],"tests":[127],"on":[128],"moderately":[133],"diverged":[134],"Drosophila":[136],"melanogaster":[137],"D.":[139],"mojavensis,":[140],"to":[141],"demonstrate":[142],"advantages":[144],"new":[147],"approach.":[148],"show":[150],"it":[152],"can":[153],"overcome":[154],"certain":[155],"artifacts":[157],"traditional":[159],"tools":[161],"provide":[163],"different,":[165],"likely":[166],"accurate,":[168],"picture":[169],"evolution":[172],"than":[173],"obtained":[175],"existing":[177],"methods.":[178],"burgeoning":[180],"field":[181],"evolution,":[184],"amply":[187],"supported":[188],"availability":[191],"related":[194],"genomes,":[195],"currently":[197],"thwarted":[198],"lack":[201],"accurate":[203],"regulatory":[206],"regions.":[207],"Our":[208],"work":[209],"will":[210],"fill":[211],"this":[213],"void":[214],"enable":[216],"reliable":[218],"evolution.":[222]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":5}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}