{"id":"https://openalex.org/W4387520008","doi":"https://doi.org/10.1186/s12859-023-05512-9","title":"cgMSI: pathogen detection within species from nanopore metagenomic sequencing data","display_name":"cgMSI: pathogen detection within species from nanopore metagenomic sequencing data","publication_year":2023,"publication_date":"2023-10-12","ids":{"openalex":"https://openalex.org/W4387520008","doi":"https://doi.org/10.1186/s12859-023-05512-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/37821827"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05512-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05512-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05512-9","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/counter/pdf/10.1186/s12859-023-05512-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101468223","display_name":"Xu Zhu","orcid":"https://orcid.org/0000-0001-8581-8247"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xu Zhu","raw_affiliation_strings":["School of Informatics, Xiamen University, Xiamen, Fujian, China"],"affiliations":[{"raw_affiliation_string":"School of Informatics, Xiamen University, Xiamen, Fujian, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101949537","display_name":"Lili Zhao","orcid":"https://orcid.org/0000-0001-5735-7666"},"institutions":[{"id":"https://openalex.org/I4210162545","display_name":"Children\u2019s Hospital of Fudan University Xiamen Branch","ror":"https://ror.org/05wg75z42","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210162545"]},{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lili Zhao","raw_affiliation_strings":["Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China"],"affiliations":[{"raw_affiliation_string":"Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China","institution_ids":["https://openalex.org/I4210162545","https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030935823","display_name":"Lihong Huang","orcid":"https://orcid.org/0000-0002-5179-474X"},"institutions":[{"id":"https://openalex.org/I4210087327","display_name":"First Affiliated Hospital of Xiamen University","ror":"https://ror.org/0006swh35","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210087327"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lihong Huang","raw_affiliation_strings":["Computer Management Center, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China"],"affiliations":[{"raw_affiliation_string":"Computer Management Center, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China","institution_ids":["https://openalex.org/I4210087327"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062411566","display_name":"Wenxian Yang","orcid":"https://orcid.org/0000-0002-5349-9680"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wenxian Yang","raw_affiliation_strings":["Aginome Scientific, Xiamen, Fujian, China"],"affiliations":[{"raw_affiliation_string":"Aginome Scientific, Xiamen, Fujian, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100613491","display_name":"Liansheng Wang","orcid":"https://orcid.org/0000-0002-2096-454X"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liansheng Wang","raw_affiliation_strings":["National Institute for Data Science in Health and Medicine, Informatics, Xiamen University, Xiamen, Fujian, China. lswang@xmu.edu.cn","School of Informatics, Xiamen University, Xiamen, Fujian, China. lswang@xmu.edu.cn","National Institute for Data Science in Health and Medicine, Informatics, Xiamen University, Xiamen, Fujian, China"],"affiliations":[{"raw_affiliation_string":"National Institute for Data Science in Health and Medicine, Informatics, Xiamen University, Xiamen, Fujian, China. lswang@xmu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"School of Informatics, Xiamen University, Xiamen, Fujian, China. lswang@xmu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"National Institute for Data Science in Health and Medicine, Informatics, Xiamen University, Xiamen, Fujian, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068270780","display_name":"Rongshan Yu","orcid":"https://orcid.org/0000-0003-2179-173X"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rongshan Yu","raw_affiliation_strings":["National Institute for Data Science in Health and Medicine, Informatics, Xiamen University, Xiamen, Fujian, China. rsyu@xmu.edu.cn","School of Informatics, Xiamen University, Xiamen, Fujian, China. rsyu@xmu.edu.cn","National Institute for Data Science in Health and Medicine, Informatics, Xiamen University, Xiamen, Fujian, China"],"affiliations":[{"raw_affiliation_string":"National Institute for Data Science in Health and Medicine, Informatics, Xiamen University, Xiamen, Fujian, China. rsyu@xmu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"School of Informatics, Xiamen University, Xiamen, Fujian, China. rsyu@xmu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"National Institute for Data Science in Health and Medicine, Informatics, Xiamen University, Xiamen, Fujian, China","institution_ids":["https://openalex.org/I191208505"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101468223"],"corresponding_institution_ids":["https://openalex.org/I191208505"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6226,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.70918219,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"24","issue":"1","first_page":"387","last_page":"387"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.9902999997138977,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9861000180244446,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.9045932292938232},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6968883872032166},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.6569805145263672},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6222176551818848},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5812634229660034},{"id":"https://openalex.org/keywords/pathogen","display_name":"Pathogen","score":0.47454676032066345},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4320662021636963},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.42187464237213135},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3590603470802307},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27834051847457886},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20618435740470886},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07846814393997192}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9045932292938232},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6968883872032166},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.6569805145263672},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6222176551818848},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5812634229660034},{"id":"https://openalex.org/C2776460866","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogen","level":2,"score":0.47454676032066345},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4320662021636963},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.42187464237213135},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3590603470802307},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27834051847457886},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20618435740470886},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07846814393997192}],"mesh":[{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081414","descriptor_name":"Nanopore Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","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":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05512-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05512-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05512-9","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:37821827","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37821827","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:10568937","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10568937","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10568937/pdf/12859_2023_Article_5512.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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"},{"id":"pmh:oai:doaj.org/article:90558b8f9b364cc7b37fe86d6096fa84","is_oa":true,"landing_page_url":"https://doaj.org/article/90558b8f9b364cc7b37fe86d6096fa84","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-15 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05512-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05512-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05512-9","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":0.6000000238418579,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4387520008.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W2032142842","https://openalex.org/W2106533426","https://openalex.org/W2119888547","https://openalex.org/W2127036970","https://openalex.org/W2159954944","https://openalex.org/W2173732482","https://openalex.org/W2259815689","https://openalex.org/W2345658906","https://openalex.org/W2521268641","https://openalex.org/W2592811885","https://openalex.org/W2729314544","https://openalex.org/W2789843538","https://openalex.org/W2889178232","https://openalex.org/W2898604559","https://openalex.org/W2907712446","https://openalex.org/W2950266744","https://openalex.org/W2950671516","https://openalex.org/W2951160681","https://openalex.org/W2951254987","https://openalex.org/W2951278111","https://openalex.org/W2953173925","https://openalex.org/W2958388979","https://openalex.org/W2987444673","https://openalex.org/W2990618091","https://openalex.org/W3034087136","https://openalex.org/W3099584446","https://openalex.org/W3122118092","https://openalex.org/W3144913167","https://openalex.org/W3186559574","https://openalex.org/W3216719515","https://openalex.org/W4210521982","https://openalex.org/W4211037082","https://openalex.org/W4221044588","https://openalex.org/W4283812770"],"related_works":["https://openalex.org/W4280653686","https://openalex.org/W4386105821","https://openalex.org/W3088570659","https://openalex.org/W2494580947","https://openalex.org/W3129972012","https://openalex.org/W1969665739","https://openalex.org/W9519152","https://openalex.org/W2088375436","https://openalex.org/W4320709878","https://openalex.org/W3196354870"],"abstract_inverted_index":{"We":[0],"developed":[1],"cgMSI":[2,10],"for":[3],"nanopore":[4],"metagenomic":[5],"pathogen":[6],"detection":[7],"within":[8],"species.":[9],"is":[11],"available":[12],"at":[13],"https://github.com/ZHU-XU-xmu/cgMSI":[14],".":[15]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
