{"id":"https://openalex.org/W2951734692","doi":"https://doi.org/10.1186/s12859-018-2038-0","title":"xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria","display_name":"xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria","publication_year":2018,"publication_date":"2018-02-05","ids":{"openalex":"https://openalex.org/W2951734692","doi":"https://doi.org/10.1186/s12859-018-2038-0","mag":"2951734692","pmid":"https://pubmed.ncbi.nlm.nih.gov/29402213"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2038-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2038-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2038-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2038-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010020076","display_name":"Eliot Bush","orcid":"https://orcid.org/0000-0001-5476-8005"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eliot C. Bush","raw_affiliation_strings":["Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA. bush@hmc.edu","Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5476-8005","affiliations":[{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA. bush@hmc.edu","institution_ids":["https://openalex.org/I133543626"]},{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029408265","display_name":"Anne E. Clark","orcid":"https://orcid.org/0000-0003-2105-3032"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anne E. Clark","raw_affiliation_strings":["Current address: Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, 98195-5065, WA, USA","Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Current address: Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, 98195-5065, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022245184","display_name":"Carissa A. DeRanek","orcid":"https://orcid.org/0009-0002-3462-9694"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carissa A. DeRanek","raw_affiliation_strings":["Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112439747","display_name":"Alexander Eng","orcid":"https://orcid.org/0000-0003-0158-7547"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Eng","raw_affiliation_strings":["Current address: Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, 98195-5065, WA, USA","Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Current address: Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, 98195-5065, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112667063","display_name":"Juliet Forman","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Juliet Forman","raw_affiliation_strings":["Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036626449","display_name":"Kevin N. Heath","orcid":"https://orcid.org/0000-0001-6922-6823"},"institutions":[{"id":"https://openalex.org/I107077323","display_name":"Worcester Polytechnic Institute","ror":"https://ror.org/05ejpqr48","country_code":"US","type":"education","lineage":["https://openalex.org/I107077323"]},{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin Heath","raw_affiliation_strings":["Current address: Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, 01609, MA, USA","Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Current address: Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, 01609, MA, USA","institution_ids":["https://openalex.org/I107077323"]},{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000482777","display_name":"Alexander B. Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander B. Lee","raw_affiliation_strings":["Current address: Quantitative Biosciences Program, Georgia Institute of Technology, 837 State Street, Atlanta, 30332-0430, GA, USA","Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Current address: Quantitative Biosciences Program, Georgia Institute of Technology, 837 State Street, Atlanta, 30332-0430, GA, USA","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048488682","display_name":"Daniel M. Stoebel","orcid":"https://orcid.org/0000-0002-9461-7567"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel M. Stoebel","raw_affiliation_strings":["Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065877493","display_name":"Zunyan Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zunyan Wang","raw_affiliation_strings":["Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058732811","display_name":"Matthew Wilber","orcid":null},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Wilber","raw_affiliation_strings":["Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080379145","display_name":"Helen Wu","orcid":"https://orcid.org/0000-0002-8251-5037"},"institutions":[{"id":"https://openalex.org/I133543626","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45","country_code":"US","type":"education","lineage":["https://openalex.org/I133543626"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Helen Wu","raw_affiliation_strings":["Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Harvey Mudd College, 301 Platt Blvd., Claremont, 91711, CA, USA","institution_ids":["https://openalex.org/I133543626"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5010020076"],"corresponding_institution_ids":["https://openalex.org/I133543626"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7424,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.71459731,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"19","issue":"1","first_page":"32","last_page":"32"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.362199991941452,"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":0.362199991941452,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.12759999930858612,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10943","display_name":"Escherichia coli research studies","score":0.09080000221729279,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"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/clade","display_name":"Clade","score":0.8113964200019836},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5965495109558105},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5602968335151672},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.5304673910140991},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5195631980895996},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4728151559829712},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.34177514910697937},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1654244065284729}],"concepts":[{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.8113964200019836},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5965495109558105},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5602968335151672},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5304673910140991},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5195631980895996},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4728151559829712},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.34177514910697937},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1654244065284729},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044404","descriptor_name":"Genomic Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044404","descriptor_name":"Genomic Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044404","descriptor_name":"Genomic Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-018-2038-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2038-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2038-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29402213","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29402213","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:4df4d9d46ad8439db721f4e2497715df","is_oa":true,"landing_page_url":"https://doaj.org/article/4df4d9d46ad8439db721f4e2497715df","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":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-11 (2018)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5799925","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5799925","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2038-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2038-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2038-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6600000262260437,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[{"id":"https://openalex.org/G5111189878","display_name":null,"funder_award_id":"52007544","funder_id":"https://openalex.org/F4320306082","funder_display_name":"Howard Hughes Medical Institute"},{"id":"https://openalex.org/G8745301779","display_name":null,"funder_award_id":"52007544","funder_id":"https://openalex.org/F4320309332","funder_display_name":"Harvey Mudd College"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320309332","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45"},{"id":"https://openalex.org/F4320337408","display_name":"Division of Undergraduate Education","ror":"https://ror.org/02kd4km72"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951734692.pdf","grobid_xml":"https://content.openalex.org/works/W2951734692.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1537213512","https://openalex.org/W1553112231","https://openalex.org/W1599371468","https://openalex.org/W1920132337","https://openalex.org/W1951382963","https://openalex.org/W1964752634","https://openalex.org/W1966336245","https://openalex.org/W1968146772","https://openalex.org/W1970056626","https://openalex.org/W1991330646","https://openalex.org/W1996249120","https://openalex.org/W2009320470","https://openalex.org/W2014746756","https://openalex.org/W2019209738","https://openalex.org/W2023447018","https://openalex.org/W2031487259","https://openalex.org/W2040745248","https://openalex.org/W2052426953","https://openalex.org/W2066051085","https://openalex.org/W2078980341","https://openalex.org/W2097813770","https://openalex.org/W2107109782","https://openalex.org/W2108228587","https://openalex.org/W2108473040","https://openalex.org/W2115095549","https://openalex.org/W2121695290","https://openalex.org/W2122804925","https://openalex.org/W2124574960","https://openalex.org/W2125456570","https://openalex.org/W2128055504","https://openalex.org/W2128584436","https://openalex.org/W2129978006","https://openalex.org/W2131105067","https://openalex.org/W2133683841","https://openalex.org/W2136303589","https://openalex.org/W2138676891","https://openalex.org/W2138952930","https://openalex.org/W2139627484","https://openalex.org/W2139636599","https://openalex.org/W2140320695","https://openalex.org/W2142402047","https://openalex.org/W2145753399","https://openalex.org/W2151863305","https://openalex.org/W2151906718","https://openalex.org/W2155090350","https://openalex.org/W2156103113","https://openalex.org/W2158847524","https://openalex.org/W2160219419","https://openalex.org/W2165286432","https://openalex.org/W2170484617","https://openalex.org/W2170959083","https://openalex.org/W2170982891","https://openalex.org/W2260037449","https://openalex.org/W2276690235","https://openalex.org/W2307372947","https://openalex.org/W2328284780","https://openalex.org/W2334656801","https://openalex.org/W2380785990","https://openalex.org/W2565952559","https://openalex.org/W2610656577","https://openalex.org/W2951126701"],"related_works":["https://openalex.org/W3184844573","https://openalex.org/W2074109587","https://openalex.org/W2956528092","https://openalex.org/W1985918308","https://openalex.org/W3011700674","https://openalex.org/W4307775460","https://openalex.org/W1923231248","https://openalex.org/W2383763250","https://openalex.org/W248275141","https://openalex.org/W2518331723"],"abstract_inverted_index":{"BACKGROUND:":[0],"Genomic":[1],"islands":[2,64,85,101,118,135,190,222,273,285],"play":[3],"an":[4,246,296],"important":[5],"role":[6],"in":[7,47,65,71,89,94,108,180,228,256,307],"microbial":[8],"genome":[9,230],"evolution,":[10],"providing":[11],"a":[12,128,141,157,163,181,208,229,268,290,308],"mechanism":[13],"for":[14,226,299,327],"strains":[15,107],"to":[16,18,35,45,82,187,219,277],"adapt":[17],"new":[19],"ecological":[20],"conditions.":[21],"A":[22],"variety":[23,209],"of":[24,39,54,68,143,159,172,210,236,248,251,270,303,310],"computational":[25],"methods,":[26],"both":[27],"genome-composition":[28],"based":[29],"and":[30,136,162,184,197,267,286,316],"comparative,":[31],"have":[32,126],"been":[33],"developed":[34,127],"identify":[36,63,283],"them.":[37],"Some":[38],"these":[40,117],"methods":[41,60],"are":[42,79,87,103,195],"explicitly":[43],"designed":[44],"work":[46],"single":[48],"strains,":[49],"while":[50],"others":[51],"make":[52],"use":[53,171,263],"multiple":[55,76],"strains.":[56],"In":[57,260],"general,":[58],"existing":[59],"do":[61,97],"not":[62,98],"the":[66,69,109,113,121,175,217,234,237,249,252,257,275,301,324,328,339],"context":[67],"phylogeny":[70],"which":[72,102,116,148,318],"they":[73,150,320],"evolved.":[74],"Even":[75],"strain":[77,91],"approaches":[78],"best":[80],"suited":[81],"identifying":[83],"genomic":[84,134,221,272,284,304,314],"that":[86,132,279,342],"present":[88],"one":[90],"but":[92],"absent":[93],"others.":[95],"They":[96],"automatically":[99],"recognize":[100],"shared":[104],"between":[105],"some":[106],"clade":[110,142,309],"or":[111],"determine":[112],"branch":[114,149,319],"on":[115,289,322],"inserted":[119,151,321],"within":[120,140,323],"phylogenetic":[122,167,291,325],"tree.":[123,292],"RESULTS:":[124],"We":[125,232],"software":[129],"package,":[130],"xenoGI,":[131],"identifies":[133,313],"maps":[137],"their":[138,166],"origin":[139],"closely":[144],"related":[145],"bacteria,":[146,244],"determining":[147],"on.":[152],"It":[153,312],"takes":[154],"as":[155,214,216],"input":[156],"set":[158,269],"sequenced":[160],"genomes":[161],"tree":[164,326],"specifying":[165],"relationships.":[168],"Making":[169],"heavy":[170],"synteny":[173],"information,":[174],"package":[176,206,238],"builds":[177],"gene":[178],"families":[179,192],"species-tree-aware":[182],"way,":[183],"then":[185],"attempts":[186],"combine":[188],"into":[189,223],"those":[191],"whose":[193,198],"members":[194],"adjacent":[196],"most":[199],"recent":[200],"common":[201],"ancestor":[202],"is":[203,295,332],"shared.":[204],"The":[205],"provides":[207],"text-based":[211],"analysis":[212],"functions,":[213],"well":[215],"ability":[218],"export":[220],"formats":[224],"suitable":[225],"viewing":[227],"browser.":[231],"demonstrate":[233],"capabilities":[235],"with":[239],"several":[240],"examples":[241],"from":[242,265,274],"enteric":[243],"including":[245],"examination":[247],"evolution":[250],"acid":[253],"fitness":[254],"island":[255,305],"genus":[258],"Escherichia.":[259],"addition":[261],"we":[262],"output":[264],"simulations":[266],"known":[271],"literature":[276],"show":[278],"xenoGI":[280,294],"can":[281],"accurately":[282],"place":[287],"them":[288],"CONCLUSIONS:":[293],"effective":[297],"tool":[298],"studying":[300],"history":[302],"insertions":[306],"microbes.":[311],"islands,":[315],"determines":[317],"clade.":[329],"Such":[330],"information":[331],"valuable":[333],"because":[334],"it":[335],"helps":[336],"us":[337],"understand":[338],"adaptive":[340],"path":[341],"has":[343],"produced":[344],"living":[345],"species.":[346]},"counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}