{"id":"https://openalex.org/W4416640352","doi":"https://doi.org/10.5256/f1000research.22447.r54557","title":"Peer Review Report For: Large scale enterohemorrhagic E coli population genomic analysis using whole genome typing reveals recombination clusters and potential drug target [version 2; peer review: 1 approved, 1 approved with reservations]","display_name":"Peer Review Report For: Large scale enterohemorrhagic E coli population genomic analysis using whole genome typing reveals recombination clusters and potential drug target [version 2; peer review: 1 approved, 1 approved with reservations]","publication_year":2019,"publication_date":"2019-11-06","ids":{"openalex":"https://openalex.org/W4416640352","doi":"https://doi.org/10.5256/f1000research.22447.r54557"},"language":"en","primary_location":{"id":"doi:10.5256/f1000research.22447.r54557","doi":"https://doi.org/10.5256/f1000research.22447.r54557","is_oa":true,"landing_page_url":"https://doi.org/10.5256/f1000research.22447.r54557","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"University of Arizona","raw_type":"peer-review"},"volume":null,"type":"peer-review","indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.5256/f1000research.22447.r54557","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068159548","display_name":"DJ Darwin R. Bandoy","orcid":"https://orcid.org/0000-0003-1852-2256","observed_orcids":["https://orcid.org/0000-0003-1852-2256"]},"institutions":[{"id":"https://openalex.org/I120108168","display_name":"University of the Philippines Los Ba\u00f1os","ror":"https://ror.org/030s54078","country_code":"PH","type":"education","lineage":["https://openalex.org/I103911934","https://openalex.org/I120108168"]}],"countries":["PH"],"is_corresponding":true,"raw_author_name":"DJ Darwin Bandoy","raw_affiliation_strings":["Department of Veterinary Paraclinical Sciences, University of the Philippines Los Ba\u00f1os, Los Ba\u00f1os, Laguna, 4031"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Paraclinical Sciences, University of the Philippines Los Ba\u00f1os, Los Ba\u00f1os, Laguna, 4031","institution_ids":["https://openalex.org/I120108168"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5068159548"],"corresponding_institution_ids":["https://openalex.org/I120108168"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10943","display_name":"Escherichia coli research studies","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10943","display_name":"Escherichia coli research studies","score":0.9994999766349792,"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"}},{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/enterohemorrhagic-escherichia-coli","display_name":"enterohemorrhagic Escherichia coli","score":0.9959999918937683},{"id":"https://openalex.org/keywords/population-genomics","display_name":"population genomics","score":0.8669999837875366},{"id":"https://openalex.org/keywords/pan-genome","display_name":"pan-genome","score":0.8119999766349792},{"id":"https://openalex.org/keywords/core-genome","display_name":"core genome","score":0.6729999780654907},{"id":"https://openalex.org/keywords/sdia","display_name":"SdiA","score":0.9739999771118164},{"id":"https://openalex.org/keywords/quorum-sensing","display_name":"quorum sensing","score":0.8830000162124634},{"id":"https://openalex.org/keywords/therapeutic-target","display_name":"therapeutic target","score":0.6809999942779541},{"id":"https://openalex.org/keywords/ligand-binding-site","display_name":"ligand binding sites","score":0.7289999723434448},{"id":"https://openalex.org/keywords/nonsynonymous-mutations","display_name":"non-synonymous mutations","score":0.8080000281333923},{"id":"https://openalex.org/keywords/pathotype-evolution","display_name":"pathotype evolution","score":0.5910000205039978},{"id":"https://openalex.org/keywords/prophylaxis","display_name":"prophylaxis","score":0.5580000281333923}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5770000219345093},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5759999752044678},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5400999784469604},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5109999775886536},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.5051000118255615},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4668999910354614},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4650000035762787},{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.4505999982357025},{"id":"https://openalex.org/C2781209916","wikidata":"https://www.wikidata.org/wiki/Q3215756","display_name":"Typing","level":2,"score":0.384799987077713},{"id":"https://openalex.org/C2909960733","wikidata":"https://www.wikidata.org/wiki/Q68541106","display_name":"Antimicrobial drug","level":3,"score":0.3727000057697296},{"id":"https://openalex.org/C102744134","wikidata":"https://www.wikidata.org/wiki/Q22280388","display_name":"Homologous recombination","level":3,"score":0.36160001158714294},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.3580000102519989},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.35190001130104065},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.31949999928474426},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.30550000071525574},{"id":"https://openalex.org/C85721925","wikidata":"https://www.wikidata.org/wiki/Q31151","display_name":"Population genetics","level":3,"score":0.2754000127315521},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.26649999618530273},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.25049999356269836}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5256/f1000research.22447.r54557","doi":"https://doi.org/10.5256/f1000research.22447.r54557","is_oa":true,"landing_page_url":"https://doi.org/10.5256/f1000research.22447.r54557","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"University of Arizona","raw_type":"peer-review"},{"id":"doi:10.5256/f1000research.22447.r54557","doi":"https://doi.org/10.5256/f1000research.22447.r54557","is_oa":true,"landing_page_url":"https://doi.org/10.5256/f1000research.22447.r54557","pdf_url":null,"source":{"id":"https://openalex.org/S7407050752","display_name":"Faculty of 1000 Research Ltd","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.5256/f1000research.22447.r54557","doi":"https://doi.org/10.5256/f1000research.22447.r54557","is_oa":true,"landing_page_url":"https://doi.org/10.5256/f1000research.22447.r54557","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"University of Arizona","raw_type":"peer-review"},"sustainable_development_goals":[{"score":0.9537000060081482,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Enterohemorrhagic":[0],"Escherichia":[1],"coli":[2],"continues":[3],"to":[4,41,67],"be":[5,106],"a":[6,22,116,125],"significant":[7],"public":[8],"health":[9],"risk.":[10],"With":[11],"the":[12,69,88,101],"onset":[13],"of":[14,25,44,73,100,121],"next":[15],"generation":[16],"sequencing,":[17],"whole":[18],"genome":[19,63],"sequences":[20],"require":[21],"new":[23],"paradigm":[24],"analysis":[26,38,64],"relevant":[27],"for":[28,92,108,118],"epidemiology":[29],"and":[30],"drug":[31,77,129],"discovery.":[32,130],"A":[33],"large-scale":[34],"bacterial":[35],"population":[36,70,97],"genomic":[37],"was":[39,65],"applied":[40],"702":[42],"isolates":[43],"serotypes":[45],"associated":[46],"with":[47,56],"EHEC":[48],"resulting":[49],"in":[50,87,128],"five":[51],"pangenome":[52,57],"clusters.":[53,61],"Serotype":[54],"incongruence":[55],"types":[58],"suggests":[59],"recombination":[60],"Core":[62],"performed":[66],"determine":[68],"wide":[71,98],"distribution":[72],"sdiA":[74,102],"as":[75,115],"potential":[76,109,126],"target.":[78],"Protein":[79],"modelling":[80],"revealed":[81],"nonsynonymous":[82],"variants":[83],"are":[84],"notably":[85],"absent":[86],"ligand":[89,103],"binding":[90],"site":[91,104],"quorum":[93],"sensing,":[94],"indicating":[95],"that":[96],"conservation":[99],"can":[105],"targeted":[107],"prophylactic":[110],"purposes.":[111],"Applying":[112],"pathotype-wide":[113],"pangenomics":[114],"guide":[117],"determining":[119],"evolution":[120],"pharmacophore":[122],"sites":[123],"is":[124],"approach":[127]},"counts_by_year":[],"updated_date":"2026-10-12T09:40:04.860316","created_date":"2025-10-10T00:00:00"}
