{"id":"https://openalex.org/W2112814521","doi":"https://doi.org/10.1093/bioinformatics/btt753","title":"Characterization of the SOS meta-regulon in the human gut microbiome","display_name":"Characterization of the SOS meta-regulon in the human gut microbiome","publication_year":2014,"publication_date":"2014-01-08","ids":{"openalex":"https://openalex.org/W2112814521","doi":"https://doi.org/10.1093/bioinformatics/btt753","mag":"2112814521","pmid":"https://pubmed.ncbi.nlm.nih.gov/24407225"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt753","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt753","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/9/1193/48922318/bioinformatics_30_9_1193.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/9/1193/48922318/bioinformatics_30_9_1193.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075085041","display_name":"Joseph P. Cornish","orcid":null},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph P. Cornish","raw_affiliation_strings":["Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035985616","display_name":"Neus Sanchez-Alberola","orcid":null},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Neus Sanchez-Alberola","raw_affiliation_strings":["Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005325892","display_name":"Patrick O\u2019Neill","orcid":null},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick K. O\u2019Neill","raw_affiliation_strings":["Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083690955","display_name":"Ronald O'Keefe","orcid":null},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ronald O'Keefe","raw_affiliation_strings":["Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040922338","display_name":"Jameel Gheba","orcid":null},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jameel Gheba","raw_affiliation_strings":["Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077706818","display_name":"Ivan Erill","orcid":"https://orcid.org/0000-0002-7280-7191"},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ivan Erill","raw_affiliation_strings":["Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5077706818"],"corresponding_institution_ids":["https://openalex.org/I79272384"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.6553,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.68231007,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"30","issue":"9","first_page":"1193","last_page":"1197"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9961000084877014,"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/T11482","display_name":"RNA modifications and cancer","score":0.9961000084877014,"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":0.9879999756813049,"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/T11247","display_name":"Plant nutrient uptake and metabolism","score":0.978600025177002,"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/regulon","display_name":"Regulon","score":0.9514979124069214},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7569135427474976},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7127387523651123},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7082131505012512},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6990626454353333},{"id":"https://openalex.org/keywords/biogenesis","display_name":"Biogenesis","score":0.6425687074661255},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.5414829254150391},{"id":"https://openalex.org/keywords/integrase","display_name":"Integrase","score":0.49668675661087036},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.45659977197647095},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.3363519310951233},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.311248779296875}],"concepts":[{"id":"https://openalex.org/C62361671","wikidata":"https://www.wikidata.org/wiki/Q1754612","display_name":"Regulon","level":4,"score":0.9514979124069214},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7569135427474976},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7127387523651123},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7082131505012512},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6990626454353333},{"id":"https://openalex.org/C131934819","wikidata":"https://www.wikidata.org/wiki/Q135390","display_name":"Biogenesis","level":3,"score":0.6425687074661255},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.5414829254150391},{"id":"https://openalex.org/C14430832","wikidata":"https://www.wikidata.org/wiki/Q412550","display_name":"Integrase","level":3,"score":0.49668675661087036},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45659977197647095},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.3363519310951233},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.311248779296875}],"mesh":[{"descriptor_ui":"D000099160","descriptor_name":"LexA Repressor Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012697","descriptor_name":"Serine Endopeptidases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012697","descriptor_name":"Serine Endopeptidases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012697","descriptor_name":"Serine Endopeptidases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012697","descriptor_name":"Serine Endopeptidases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012697","descriptor_name":"Serine Endopeptidases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012697","descriptor_name":"Serine Endopeptidases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013014","descriptor_name":"SOS Response, Genetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013014","descriptor_name":"SOS Response, Genetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013014","descriptor_name":"SOS Response, Genetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btt753","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt753","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/9/1193/48922318/bioinformatics_30_9_1193.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24407225","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24407225","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":"Journal Article"},{"id":"pmh:oai:ddd.uab.cat:288700","is_oa":true,"landing_page_url":"https://ddd.uab.cat/record/288700","pdf_url":"https://ddd.uab.cat/pub/artpub/2014/288700/2014_Bioinformatics.pdf","source":{"id":"https://openalex.org/S4306400380","display_name":"Dip\u00f2sit Digital de Documents de la UAB (Universitat Aut\u00f2noma de Barcelona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123044942","host_organization_name":"Universitat Aut\u00f2noma de Barcelona","host_organization_lineage":["https://openalex.org/I123044942"],"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":null,"raw_type":"Article"},{"id":"pmh:oai:europepmc.org:2975773","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3998124","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":null,"raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.799.324","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.799.324","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/26/7e/btt753.PMC3998124.pdf","raw_type":"text"},{"id":"pmh:oai:mdsoar.org:11603/11471","is_oa":true,"landing_page_url":"http://hdl.handle.net/11603/11471","pdf_url":null,"source":{"id":"https://openalex.org/S4306402556","display_name":"Maryland Shared Open Access Repository (USMAI Consortium)","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"doi:10.13016/m2q52fh36","is_oa":true,"landing_page_url":"https://doi.org/10.13016/m2q52fh36","pdf_url":null,"source":{"id":"https://openalex.org/S4306402644","display_name":"Digital Repository at the University of Maryland (University of Maryland College Park)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66946132","host_organization_name":"University of Maryland, College Park","host_organization_lineage":["https://openalex.org/I66946132"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Collection"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt753","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt753","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/9/1193/48922318/bioinformatics_30_9_1193.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1227930696","display_name":null,"funder_award_id":"DMS-0821311","funder_id":"https://openalex.org/F4320309204","funder_display_name":"University of Maryland, Baltimore County"},{"id":"https://openalex.org/G1546822563","display_name":null,"funder_award_id":"CNS-0821258","funder_id":"https://openalex.org/F4320309204","funder_display_name":"University of Maryland, Baltimore County"},{"id":"https://openalex.org/G2458018307","display_name":null,"funder_award_id":"CNS-1228778","funder_id":"https://openalex.org/F4320309204","funder_display_name":"University of Maryland, Baltimore County"},{"id":"https://openalex.org/G2529001125","display_name":"Evolution of Regulatory Sequence Motifs","funder_award_id":"1158056","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3145218617","display_name":"MRI: Acquisition of Hybrid CPU/GPU Nodes for the Interdisciplinary UMBC High Performance Computing Facility","funder_award_id":"1228778","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G376085753","display_name":"MRI:    Acquisition of an Interdisciplinary Facility for High-Performance Computing","funder_award_id":"0821258","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7129481701","display_name":"SCREMS: Parallel Computing for Interdisciplinary Research in Mathematics and Statistics","funder_award_id":"0821311","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309204","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2112814521.pdf","grobid_xml":"https://content.openalex.org/works/W2112814521.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W244629935","https://openalex.org/W1516095354","https://openalex.org/W1526653855","https://openalex.org/W1567796477","https://openalex.org/W1871175037","https://openalex.org/W1977516923","https://openalex.org/W1982690271","https://openalex.org/W1990622623","https://openalex.org/W2007416596","https://openalex.org/W2009690857","https://openalex.org/W2023046869","https://openalex.org/W2030036822","https://openalex.org/W2031893281","https://openalex.org/W2039036921","https://openalex.org/W2039724494","https://openalex.org/W2040126316","https://openalex.org/W2061017907","https://openalex.org/W2062402656","https://openalex.org/W2064442647","https://openalex.org/W2072547387","https://openalex.org/W2088894320","https://openalex.org/W2091607609","https://openalex.org/W2101366952","https://openalex.org/W2107243418","https://openalex.org/W2110415727","https://openalex.org/W2112374610","https://openalex.org/W2115026474","https://openalex.org/W2124094019","https://openalex.org/W2125826054","https://openalex.org/W2133790733","https://openalex.org/W2136970762","https://openalex.org/W2137173826","https://openalex.org/W2137285295","https://openalex.org/W2140494885","https://openalex.org/W2155516053","https://openalex.org/W2169314851","https://openalex.org/W2170196186","https://openalex.org/W2171296640"],"related_works":["https://openalex.org/W61127607","https://openalex.org/W1984136937","https://openalex.org/W1786268878","https://openalex.org/W2794893700","https://openalex.org/W4281651837","https://openalex.org/W4313622135","https://openalex.org/W4362693150","https://openalex.org/W4282031271","https://openalex.org/W2164421791","https://openalex.org/W4220701345"],"abstract_inverted_index":{"MOTIVATION:":[0],"Data":[1],"from":[2],"metagenomics":[3],"projects":[4],"remain":[5],"largely":[6],"untapped":[7],"for":[8,146,149],"the":[9,32,36,52,59,63,73,83,88,113,121,138,144],"analysis":[10,71],"of":[11,62,75,82,90,112,123,140],"transcriptional":[12,116],"regulatory":[13,28],"networks.":[14],"Here,":[15],"we":[16,109],"provide":[17],"proof-of-concept":[18],"that":[19],"metagenomic":[20],"data":[21,56],"can":[22],"be":[23],"effectively":[24],"leveraged":[25],"to":[26,50,118],"analyze":[27],"networks":[29],"by":[30],"characterizing":[31],"SOS":[33,64,84,114],"meta-regulon":[34],"in":[35,44,47,66,99,120],"human":[37,53],"gut":[38,54],"microbiome.":[39],"RESULTS:":[40],"We":[41,86,136],"combine":[42],"well-established":[43],"silico":[45],"and":[46,57,105,108,132,143],"vitro":[48],"techniques":[49],"mine":[51],"microbiome":[55],"determine":[58],"relative":[60],"composition":[61],"network":[65,92],"a":[67,79,124,129,133],"natural":[68],"setting.":[69],"Our":[70],"highlights":[72],"importance":[74],"translesion":[76],"synthesis":[77],"as":[78],"primary":[80],"function":[81],"response.":[85],"predict":[87],"association":[89],"this":[91,147],"with":[93],"three":[94],"novel":[95],"protein":[96],"clusters":[97],"involved":[98],"cell":[100,125],"wall":[101,126],"biogenesis,":[102],"chromosome":[103],"partitioning":[104],"restriction":[106],"modification,":[107],"confirm":[110],"binding":[111],"response":[115],"repressor":[117],"sites":[119],"promoter":[122],"biogenesis":[127],"enzyme,":[128],"phage":[130],"integrase":[131],"death-on-curing":[134],"protein.":[135],"discuss":[137],"implications":[139],"these":[141],"findings":[142],"potential":[145],"approach":[148],"metagenome":[150],"analysis.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-29T07:29:34.045763","created_date":"2025-10-10T00:00:00"}
