{"id":"https://openalex.org/W1967173988","doi":"https://doi.org/10.1186/1471-2105-13-s18-a12","title":"Detecting structural variants involving repetitive elements: capturing transposition events of IS elements in the genome of Escherichia coli","display_name":"Detecting structural variants involving repetitive elements: capturing transposition events of IS elements in the genome of Escherichia coli","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W1967173988","doi":"https://doi.org/10.1186/1471-2105-13-s18-a12","mag":"1967173988"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s18-a12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s18-a12","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S18-A12","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S18-A12","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017723224","display_name":"Heewook Lee","orcid":"https://orcid.org/0000-0002-3528-6833"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Heewook Lee","raw_affiliation_strings":["School of Informatics and Computing, Indiana University, Bloomington, IN, USA","School of Informatics and Computing, Indiana University Bloomington, USA"],"affiliations":[{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"School of Informatics and Computing, Indiana University Bloomington, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077796584","display_name":"Ellen Popodi","orcid":"https://orcid.org/0000-0002-0267-9577"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ellen Popodi","raw_affiliation_strings":["Department of Biology, Indiana University, Bloomington, IN, USA","Department of Biology, Indiana University, Bloomington, #N#USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"Department of Biology, Indiana University, Bloomington, #N#USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020453712","display_name":"Patricia L. Foster","orcid":"https://orcid.org/0000-0002-7236-4378"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patricia L Foster","raw_affiliation_strings":["Department of Biology, Indiana University, Bloomington, IN, USA","Department of Biology, Indiana University, Bloomington, #N#USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"Department of Biology, Indiana University, Bloomington, #N#USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078007096","display_name":"Haixu Tang","orcid":"https://orcid.org/0000-0001-8963-8155"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haixu Tang","raw_affiliation_strings":["School of Informatics and Computing, Indiana University, Bloomington, IN, USA","School of Informatics and Computing, Indiana University Bloomington, USA"],"affiliations":[{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"School of Informatics and Computing, Indiana University Bloomington, USA","institution_ids":["https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5017723224"],"corresponding_institution_ids":["https://openalex.org/I4210119109"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4034,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.60756171,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"13","issue":"S18","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9987999796867371,"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"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.8080006837844849},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7492219805717468},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.661264181137085},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6467426419258118},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6305904984474182},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5638341903686523},{"id":"https://openalex.org/keywords/transposition","display_name":"Transposition (logic)","score":0.5145246386528015},{"id":"https://openalex.org/keywords/insert","display_name":"Insert (composites)","score":0.5061134696006775},{"id":"https://openalex.org/keywords/insertion-sequence","display_name":"Insertion sequence","score":0.4352354407310486},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2919660210609436},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18123561143875122},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09819886088371277}],"concepts":[{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.8080006837844849},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7492219805717468},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.661264181137085},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6467426419258118},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6305904984474182},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5638341903686523},{"id":"https://openalex.org/C12455157","wikidata":"https://www.wikidata.org/wiki/Q7835331","display_name":"Transposition (logic)","level":2,"score":0.5145246386528015},{"id":"https://openalex.org/C2780098074","wikidata":"https://www.wikidata.org/wiki/Q6037362","display_name":"Insert (composites)","level":2,"score":0.5061134696006775},{"id":"https://openalex.org/C157887575","wikidata":"https://www.wikidata.org/wiki/Q417216","display_name":"Insertion sequence","level":5,"score":0.4352354407310486},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2919660210609436},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18123561143875122},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09819886088371277},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1471-2105-13-s18-a12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s18-a12","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S18-A12","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":"pmh:oai:europepmc.org:2521758","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3522030","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s18-a12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s18-a12","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S18-A12","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":[],"awards":[{"id":"https://openalex.org/G781304374","display_name":null,"funder_award_id":"W911NF-09-1-0444","funder_id":"https://openalex.org/F4320333591","funder_display_name":"Multidisciplinary University Research Initiative"}],"funders":[{"id":"https://openalex.org/F4320333591","display_name":"Multidisciplinary University Research Initiative","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1967173988.pdf","grobid_xml":"https://content.openalex.org/works/W1967173988.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2013221974","https://openalex.org/W2019385975","https://openalex.org/W2099809434","https://openalex.org/W2105588144"],"related_works":["https://openalex.org/W2063677980","https://openalex.org/W2135134199","https://openalex.org/W2363061577","https://openalex.org/W2026307780","https://openalex.org/W2142244856","https://openalex.org/W2034211960","https://openalex.org/W2078042340","https://openalex.org/W2171277850","https://openalex.org/W2065978184","https://openalex.org/W1501118784"],"abstract_inverted_index":{"Background":[0],"Discordant":[1],"read":[2,33,68,98],"pairs":[3,34,69],"[1,2]":[4],"\u2013":[5,18,75],"those":[6],"deviating":[7],"either":[8],"from":[9],"expected":[10],"insert":[11],"size":[12],"range":[13],"or":[14],"correct":[15],"relative":[16],"orientation":[17],"have":[19,71],"served":[20],"as":[21,55],"vital":[22],"clues":[23],"to":[24,80],"identifying":[25],"structural":[26],"variants":[27],"(SV)":[28],"in":[29,39,64],"genomes.":[30],"Collecting":[31],"discordant":[32,67],"is":[35,43],"the":[36],"first":[37],"step":[38],"SV":[40],"detection":[41],"and":[42,83],"often":[44],"done":[45],"by":[46],"sequence":[47,57],"alignment.":[48],"When":[49],"there":[50],"are":[51],"repetitive":[52,104],"elements,":[53],"such":[54,88],"insertion":[56],"(IS),":[58],"a":[59],"class":[60],"of":[61,86],"transposable":[62],"elements":[63],"bacterial":[65],"genomes,":[66],"can":[70],"multiple":[72],"mapping":[73,90],"loci":[74],"making":[76],"them":[77],"more":[78],"challenging":[79],"be":[81],"placed":[82],"interpreted.":[84],"Instead":[85],"resolving":[87],"tangled":[89],"results,":[91],"many":[92],"tools":[93],"simply":[94],"ignore":[95],"these":[96],"mapped":[97],"pairs,":[99],"potentially":[100],"missing":[101],"SVs":[102],"involving":[103],"elements.":[105]},"counts_by_year":[{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
