{"id":"https://openalex.org/W4292608675","doi":"https://doi.org/10.1128/msystems.00491-22","title":"Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples","display_name":"Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples","publication_year":2022,"publication_date":"2022-08-22","ids":{"openalex":"https://openalex.org/W4292608675","doi":"https://doi.org/10.1128/msystems.00491-22","pmid":"https://pubmed.ncbi.nlm.nih.gov/35993719","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/9600527"},"language":"en","primary_location":{"id":"doi:10.1128/msystems.00491-22","doi":"https://doi.org/10.1128/msystems.00491-22","is_oa":true,"landing_page_url":"https://doi.org/10.1128/msystems.00491-22","pdf_url":null,"source":{"id":"https://openalex.org/S4210181942","display_name":"mSystems","issn_l":"2379-5077","issn":["2379-5077"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320263","host_organization_name":"American Society for Microbiology","host_organization_lineage":["https://openalex.org/P4310320263"],"host_organization_lineage_names":["American Society for Microbiology"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"mSystems","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1128/msystems.00491-22","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024502187","display_name":"Jonathon L. Baker","orcid":"https://orcid.org/0000-0001-5378-322X","observed_orcids":["https://orcid.org/0000-0001-5378-322X"]},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jonathon L. Baker","raw_affiliation_strings":["Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA","Genomic Medicine Group, J. Craig Venter Institute, 4120 Capricorn Lan, La Jolla, CA 92037","Department of Pediatrics, UC San Diego School of Medicine, La Jolla, California, USA","Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA"],"raw_orcid":"https://orcid.org/0000-0001-5378-322X","affiliations":[{"raw_affiliation_string":"Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Genomic Medicine Group, J. Craig Venter Institute, 4120 Capricorn Lan, La Jolla, CA 92037","institution_ids":["https://openalex.org/I1301553790"]},{"raw_affiliation_string":"Department of Pediatrics, UC San Diego School of Medicine, La Jolla, California, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA","institution_ids":["https://openalex.org/I1301553790"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5024502187"],"corresponding_institution_ids":["https://openalex.org/I1301553790","https://openalex.org/I36258959"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":1.4706,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.82205404,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"7","issue":"5","first_page":"e0049122","last_page":"e0049122"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9911999702453613,"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":0.9911999702453613,"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/T10257","display_name":"Oral microbiology and periodontitis research","score":0.002199999988079071,"subfield":{"id":"https://openalex.org/subfields/3506","display_name":"Periodontics"},"field":{"id":"https://openalex.org/fields/35","display_name":"Dentistry"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"nanopore sequencing","score":0.9819999933242798},{"id":"https://openalex.org/keywords/bacterial-genome-assembly","display_name":"bacterial genome assembly","score":0.7710000276565552},{"id":"https://openalex.org/keywords/saliva","display_name":"saliva","score":0.5989999771118164},{"id":"https://openalex.org/keywords/human-microbiome","display_name":"human microbiome","score":0.9089999794960022},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"whole genome sequencing","score":0.6029999852180481},{"id":"https://openalex.org/keywords/repetitive-regions","display_name":"repetitive regions","score":0.4959999918937683},{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.5239999890327454}],"concepts":[{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.8429272770881653},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.7146744728088379},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5343676209449768},{"id":"https://openalex.org/C504460877","wikidata":"https://www.wikidata.org/wiki/Q155925","display_name":"Saliva","level":2,"score":0.5340942740440369},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.517166793346405},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.5016260147094727},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4799623489379883},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3364541232585907},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30565744638442993},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.23242634534835815},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.20702442526817322},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13506922125816345},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012463","descriptor_name":"Saliva","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1128/msystems.00491-22","doi":"https://doi.org/10.1128/msystems.00491-22","is_oa":true,"landing_page_url":"https://doi.org/10.1128/msystems.00491-22","pdf_url":null,"source":{"id":"https://openalex.org/S4210181942","display_name":"mSystems","issn_l":"2379-5077","issn":["2379-5077"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320263","host_organization_name":"American Society for Microbiology","host_organization_lineage":["https://openalex.org/P4310320263"],"host_organization_lineage_names":["American Society for Microbiology"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"mSystems","raw_type":"journal-article"},{"id":"doi:10.1101/2022.05.19.492709","doi":"https://doi.org/10.1101/2022.05.19.492709","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2022.05.19.492709","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/05/19/2022.05.19.492709.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:35993719","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35993719","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,"listed_in":[],"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":"mSystems","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9600527","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9600527/","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"mSystems","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:85d997502bf24be99febbfc3b10b5125","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/85d997502bf24be99febbfc3b10b5125","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,"listed_in":[],"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":"mSystems, Vol 7, Iss 5 (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1128/msystems.00491-22","doi":"https://doi.org/10.1128/msystems.00491-22","is_oa":true,"landing_page_url":"https://doi.org/10.1128/msystems.00491-22","pdf_url":null,"source":{"id":"https://openalex.org/S4210181942","display_name":"mSystems","issn_l":"2379-5077","issn":["2379-5077"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320263","host_organization_name":"American Society for Microbiology","host_organization_lineage":["https://openalex.org/P4310320263"],"host_organization_lineage_names":["American Society for Microbiology"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"mSystems","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G8583194314","display_name":"Investigating Membrane Alterations as a Mechanism of Acid Tolerance in Cariogenic Bacteria","funder_award_id":"K99DE029228","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337365","display_name":"National Institute of Dental and Craniofacial Research","ror":"https://ror.org/004a2wv92"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4292608675.pdf","grobid_xml":"https://content.openalex.org/works/W4292608675.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1519765314","https://openalex.org/W1878521557","https://openalex.org/W1933623310","https://openalex.org/W1958058086","https://openalex.org/W1971403296","https://openalex.org/W1974427319","https://openalex.org/W1978650924","https://openalex.org/W1980873478","https://openalex.org/W1982855075","https://openalex.org/W2007772656","https://openalex.org/W2012016911","https://openalex.org/W2055666215","https://openalex.org/W2096093282","https://openalex.org/W2103441770","https://openalex.org/W2103901746","https://openalex.org/W2104291141","https://openalex.org/W2110417468","https://openalex.org/W2113601822","https://openalex.org/W2128769815","https://openalex.org/W2145336165","https://openalex.org/W2149125985","https://openalex.org/W2196319067","https://openalex.org/W2200571950","https://openalex.org/W2202810729","https://openalex.org/W2549871051","https://openalex.org/W2737142452","https://openalex.org/W2784407026","https://openalex.org/W2789843538","https://openalex.org/W2938868597","https://openalex.org/W2948263509","https://openalex.org/W2949004447","https://openalex.org/W2952167528","https://openalex.org/W2976566477","https://openalex.org/W2984207160","https://openalex.org/W3005528502","https://openalex.org/W3007172120","https://openalex.org/W3011678041","https://openalex.org/W3028280407","https://openalex.org/W3045328792","https://openalex.org/W3090409446","https://openalex.org/W3091506611","https://openalex.org/W3091821172","https://openalex.org/W3103886580","https://openalex.org/W3107284391","https://openalex.org/W3112234114","https://openalex.org/W3116000462","https://openalex.org/W3119314116","https://openalex.org/W3124271747","https://openalex.org/W3125609739","https://openalex.org/W3127571602","https://openalex.org/W3129459161","https://openalex.org/W3157514565","https://openalex.org/W3166213992","https://openalex.org/W3192547606","https://openalex.org/W3199385470","https://openalex.org/W4200305737","https://openalex.org/W4210738868","https://openalex.org/W4220999759","https://openalex.org/W4223452608","https://openalex.org/W4226049735","https://openalex.org/W4226092504","https://openalex.org/W4243977291"],"related_works":["https://openalex.org/W4280509459","https://openalex.org/W1537604141","https://openalex.org/W4283809266","https://openalex.org/W6910608929","https://openalex.org/W6941333292","https://openalex.org/W6892926737","https://openalex.org/W2026273138","https://openalex.org/W2086018751","https://openalex.org/W3177878208","https://openalex.org/W3194252622"],"abstract_inverted_index":{"Obtaining":[0],"complete":[1,15],"and":[2],"accurate":[3],"genomes":[4,16],"is":[5],"crucial":[6],"to":[7,38],"the":[8,22,29],"study":[9],"of":[10,17,21,28],"any":[11],"organism.":[12],"Previously,":[13],"obtaining":[14],"bacteria,":[18],"including":[19],"those":[20],"human":[23],"microbiome,":[24],"frequently":[25],"required":[26],"isolation":[27],"organism,":[30],"as":[31,33],"well":[32],"low-throughput,":[34],"manual":[35],"sequencing":[36],"methods":[37],"resolve":[39],"repeat":[40],"regions.":[41]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":12}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2022-08-22T00:00:00"}