{"id":"https://openalex.org/W4404976894","doi":"https://doi.org/10.1186/s12859-024-05952-x","title":"Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets","display_name":"Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4404976894","doi":"https://doi.org/10.1186/s12859-024-05952-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/39627685"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05952-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05952-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05952-x","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/counter/pdf/10.1186/s12859-024-05952-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026384256","display_name":"Lauren Bradford","orcid":"https://orcid.org/0000-0003-0686-1648"},"institutions":[{"id":"https://openalex.org/I67031392","display_name":"Carleton University","ror":"https://ror.org/02qtvee93","country_code":"CA","type":"education","lineage":["https://openalex.org/I67031392"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Lauren M. Bradford","raw_affiliation_strings":["Department of Biology, Carleton University, Ottawa, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Carleton University, Ottawa, Canada","institution_ids":["https://openalex.org/I67031392"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015660108","display_name":"Catherine D. Carrillo","orcid":"https://orcid.org/0000-0002-2334-8718"},"institutions":[{"id":"https://openalex.org/I1307613440","display_name":"Canadian Food Inspection Agency","ror":"https://ror.org/00qxr8t08","country_code":"CA","type":"government","lineage":["https://openalex.org/I1307613440"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Catherine Carrillo","raw_affiliation_strings":["Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Canada","institution_ids":["https://openalex.org/I1307613440"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049171921","display_name":"Alex Wong","orcid":"https://orcid.org/0000-0001-6249-3013"},"institutions":[{"id":"https://openalex.org/I173268674","display_name":"Texas A&M University System","ror":"https://ror.org/0034eay46","country_code":"US","type":"education","lineage":["https://openalex.org/I173268674"]},{"id":"https://openalex.org/I67031392","display_name":"Carleton University","ror":"https://ror.org/02qtvee93","country_code":"CA","type":"education","lineage":["https://openalex.org/I67031392"]}],"countries":["CA","US"],"is_corresponding":true,"raw_author_name":"Alex Wong","raw_affiliation_strings":["Department of Biology, Carleton University, Ottawa, Canada. alexwong@cunet.carleton.ca","Institute for Advancing Health Through Agriculture, Texas A & M University, College Station, USA. alexwong@cunet.carleton.ca"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Carleton University, Ottawa, Canada. alexwong@cunet.carleton.ca","institution_ids":["https://openalex.org/I67031392"]},{"raw_affiliation_string":"Institute for Advancing Health Through Agriculture, Texas A & M University, College Station, USA. alexwong@cunet.carleton.ca","institution_ids":["https://openalex.org/I173268674"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5049171921"],"corresponding_institution_ids":["https://openalex.org/I173268674","https://openalex.org/I67031392"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.3493,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.95730341,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"25","issue":"1","first_page":"372","last_page":"372"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":0.6552000045776367,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food 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"}},"topics":[{"id":"https://openalex.org/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":0.6552000045776367,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food 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/T11684","display_name":"Vibrio bacteria research studies","score":0.06120000034570694,"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/T10900","display_name":"Listeria monocytogenes in Food Safety","score":0.0575999990105629,"subfield":{"id":"https://openalex.org/subfields/1305","display_name":"Biotechnology"},"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/false-positive-paradox","display_name":"False positive paradox","score":0.8554492592811584},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.8487619161605835},{"id":"https://openalex.org/keywords/shotgun","display_name":"Shotgun","score":0.8273077011108398},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6856800317764282},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.6666631698608398},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5736895799636841},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5494776964187622},{"id":"https://openalex.org/keywords/true-positive-rate","display_name":"True positive rate","score":0.4555233418941498},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38110417127609253},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.34608858823776245},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28979116678237915},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.23943045735359192},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2047877311706543},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.175896555185318},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07584834098815918}],"concepts":[{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.8554492592811584},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8487619161605835},{"id":"https://openalex.org/C2781434637","wikidata":"https://www.wikidata.org/wiki/Q486396","display_name":"Shotgun","level":3,"score":0.8273077011108398},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6856800317764282},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.6666631698608398},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5736895799636841},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5494776964187622},{"id":"https://openalex.org/C2989486834","wikidata":"https://www.wikidata.org/wiki/Q3808900","display_name":"True positive rate","level":2,"score":0.4555233418941498},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38110417127609253},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34608858823776245},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28979116678237915},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.23943045735359192},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2047877311706543},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.175896555185318},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07584834098815918}],"mesh":[{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005189","descriptor_name":"False Positive Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005516","descriptor_name":"Food Microbiology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005516","descriptor_name":"Food Microbiology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005516","descriptor_name":"Food Microbiology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005516","descriptor_name":"Food Microbiology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012475","descriptor_name":"Salmonella","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012475","descriptor_name":"Salmonella","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012475","descriptor_name":"Salmonella","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012475","descriptor_name":"Salmonella","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05952-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05952-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05952-x","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39627685","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39627685","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:pubmedcentral.nih.gov:11613480","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11613480","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11613480/pdf/12859_2024_Article_5952.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:b0df87ad884c49e4a529657c73ca0244","is_oa":false,"landing_page_url":"https://doaj.org/article/b0df87ad884c49e4a529657c73ca0244","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-14 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05952-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05952-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05952-x","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/G5016654360","display_name":null,"funder_award_id":"OAF-2020-101088","funder_id":"https://openalex.org/F4320319908","funder_display_name":"Ontario Ministry of Agriculture, Food and Rural Affairs"}],"funders":[{"id":"https://openalex.org/F4320311580","display_name":"Canadian Food Inspection Agency","ror":"https://ror.org/00qxr8t08"},{"id":"https://openalex.org/F4320319908","display_name":"Ontario Ministry of Agriculture, Food and Rural Affairs","ror":"https://ror.org/033w59g46"},{"id":"https://openalex.org/F4320331257","display_name":"Alliance de recherche num\u00e9rique du Canada","ror":"https://ror.org/010r6td27"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404976894.pdf","grobid_xml":"https://content.openalex.org/works/W4404976894.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W42763705","https://openalex.org/W1577762533","https://openalex.org/W1986908904","https://openalex.org/W1995853873","https://openalex.org/W2003347102","https://openalex.org/W2026084043","https://openalex.org/W2064683530","https://openalex.org/W2099239174","https://openalex.org/W2108234281","https://openalex.org/W2131271579","https://openalex.org/W2138271600","https://openalex.org/W2157539385","https://openalex.org/W2159954944","https://openalex.org/W2164868452","https://openalex.org/W2207819727","https://openalex.org/W2260365656","https://openalex.org/W2337645646","https://openalex.org/W2337747100","https://openalex.org/W2465681871","https://openalex.org/W2730233141","https://openalex.org/W2739666533","https://openalex.org/W2765274345","https://openalex.org/W2769270984","https://openalex.org/W2773939681","https://openalex.org/W2896881594","https://openalex.org/W2897603717","https://openalex.org/W2901550377","https://openalex.org/W2950150251","https://openalex.org/W2956133711","https://openalex.org/W2972695893","https://openalex.org/W2988567318","https://openalex.org/W2990618091","https://openalex.org/W2993621518","https://openalex.org/W3014666387","https://openalex.org/W3081604815","https://openalex.org/W3092955234","https://openalex.org/W3093073085","https://openalex.org/W3114215764","https://openalex.org/W3121495243","https://openalex.org/W3122109253","https://openalex.org/W3143063265","https://openalex.org/W3144913167","https://openalex.org/W3176012848","https://openalex.org/W3207392230","https://openalex.org/W4225081585","https://openalex.org/W4225258284","https://openalex.org/W4283695012","https://openalex.org/W4321611856","https://openalex.org/W4387440002"],"related_works":["https://openalex.org/W4210312276","https://openalex.org/W2417514914","https://openalex.org/W1641084016","https://openalex.org/W2018832993","https://openalex.org/W4255415692","https://openalex.org/W2994945316","https://openalex.org/W3128701120","https://openalex.org/W4253705341","https://openalex.org/W4386668515","https://openalex.org/W2081065512"],"abstract_inverted_index":{"BACKGROUND:":[0],"Culture-independent":[1],"diagnostic":[2],"tests":[3],"are":[4],"gaining":[5],"popularity":[6],"as":[7,22,54,147],"tools":[8],"for":[9,19,140],"detecting":[10],"pathogens":[11,57,188],"in":[12,34,71],"food.":[13],"Shotgun":[14],"sequencing":[15,39,52,86],"holds":[16],"substantial":[17],"promise":[18],"food":[20,62],"testing":[21],"it":[23,183],"provides":[24],"abundant":[25],"information":[26],"on":[27],"microbial":[28],"communities,":[29],"but":[30,116,126],"the":[31,93,102,178],"challenge":[32],"is":[33,114,123,162,184],"analyzing":[35],"large":[36],"and":[37,48,83,95,108,142,159,193],"complex":[38],"datasets":[40,87],"with":[41,189],"a":[42,137],"high":[43,153,191],"degree":[44],"of":[45,97,181],"both":[46],"sensitivity":[47,69],"specificity.":[49],"Falsely":[50],"classifying":[51],"reads":[53,90,144],"originating":[55],"from":[56],"can":[58],"lead":[59,75],"to":[60,76,91,118,128,164,176,186],"unnecessary":[61],"recalls":[63],"or":[64],"production":[65],"shutdowns,":[66],"while":[67,121,151],"low":[68,132],"resulting":[70],"false":[72,98,119,166],"negatives":[73],"could":[74],"preventable":[77],"illness.":[78],"RESULTS:":[79],"We":[80,134],"used":[81],"simulated":[82],"published":[84],"shotgun":[85],"containing":[88],"Salmonella-derived":[89],"explore":[92],"appearance":[94],"mitigation":[96],"positive":[99,167],"results":[100],"using":[101],"popular":[103],"taxonomic":[104,179],"annotation":[105],"softwares":[106],"Kraken2":[107,113,150],"Metaphlan4.":[109],"Using":[110],"default":[111],"parameters,":[112],"sensitive":[115],"prone":[117],"positives,":[120],"Metaphlan4":[122],"more":[124],"specific":[125],"unable":[127],"detect":[129,187],"Salmonella":[130,148],"at":[131],"abundance.":[133],"then":[135],"developed":[136],"bioinformatic":[138],"pipeline":[139],"identifying":[141],"removing":[143],"falsely":[145],"identified":[146],"by":[149],"retaining":[152],"sensitivity.":[154,194],"Carefully":[155],"considering":[156],"software":[157],"parameters":[158,172],"database":[160],"choices":[161],"essential":[163],"avoiding":[165],"sample":[168],"calls.":[169],"With":[170],"well-chosen":[171],"plus":[173],"additional":[174],"steps":[175],"confirm":[177],"origin":[180],"reads,":[182],"possible":[185],"very":[190],"specificity":[192]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}