{"id":"https://openalex.org/W4402147396","doi":"https://doi.org/10.1093/bib/bbae424","title":"CAIM: coverage-based analysis for identification of microbiome","display_name":"CAIM: coverage-based analysis for identification of microbiome","publication_year":2024,"publication_date":"2024-07-25","ids":{"openalex":"https://openalex.org/W4402147396","doi":"https://doi.org/10.1093/bib/bbae424","pmid":"https://pubmed.ncbi.nlm.nih.gov/39222062"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae424","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae424","pdf_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae424/58994655/bbae424.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae424/58994655/bbae424.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104730164","display_name":"Daniel A. Acheampong","orcid":"https://orcid.org/0000-0002-4976-7945"},"institutions":[{"id":"https://openalex.org/I114131015","display_name":"Stowers Institute for Medical Research","ror":"https://ror.org/04bgfm609","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I114131015"]},{"id":"https://openalex.org/I79620101","display_name":"University of Arkansas for Medical Sciences","ror":"https://ror.org/00xcryt71","country_code":"US","type":"education","lineage":["https://openalex.org/I79620101"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel A Acheampong","raw_affiliation_strings":["Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","Stowers Institute for Medical Research , 1000 E 50 St, Kansas City, MO 64110, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","institution_ids":["https://openalex.org/I79620101"]},{"raw_affiliation_string":"Stowers Institute for Medical Research , 1000 E 50 St, Kansas City, MO 64110, United States","institution_ids":["https://openalex.org/I114131015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007314004","display_name":"Piroon Jenjaroenpun","orcid":"https://orcid.org/0000-0002-1555-401X"},"institutions":[{"id":"https://openalex.org/I1332387789","display_name":"Siriraj Hospital","ror":"https://ror.org/0331zs648","country_code":"TH","type":"healthcare","lineage":["https://openalex.org/I1332387789"]},{"id":"https://openalex.org/I25399158","display_name":"Mahidol University","ror":"https://ror.org/01znkr924","country_code":"TH","type":"education","lineage":["https://openalex.org/I25399158"]},{"id":"https://openalex.org/I79620101","display_name":"University of Arkansas for Medical Sciences","ror":"https://ror.org/00xcryt71","country_code":"US","type":"education","lineage":["https://openalex.org/I79620101"]}],"countries":["TH","US"],"is_corresponding":false,"raw_author_name":"Piroon Jenjaroenpun","raw_affiliation_strings":["Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","Division of Medical Bioinformatics , Department of Research, Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","Mahidol University , Department of Research, Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","institution_ids":["https://openalex.org/I79620101"]},{"raw_affiliation_string":"Division of Medical Bioinformatics , Department of Research, Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","institution_ids":["https://openalex.org/I1332387789"]},{"raw_affiliation_string":"Mahidol University , Department of Research, Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","institution_ids":["https://openalex.org/I1332387789","https://openalex.org/I25399158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022928039","display_name":"Thidathip Wongsurawat","orcid":"https://orcid.org/0000-0002-3659-2074"},"institutions":[{"id":"https://openalex.org/I1332387789","display_name":"Siriraj Hospital","ror":"https://ror.org/0331zs648","country_code":"TH","type":"healthcare","lineage":["https://openalex.org/I1332387789"]},{"id":"https://openalex.org/I25399158","display_name":"Mahidol University","ror":"https://ror.org/01znkr924","country_code":"TH","type":"education","lineage":["https://openalex.org/I25399158"]},{"id":"https://openalex.org/I79620101","display_name":"University of Arkansas for Medical Sciences","ror":"https://ror.org/00xcryt71","country_code":"US","type":"education","lineage":["https://openalex.org/I79620101"]}],"countries":["TH","US"],"is_corresponding":false,"raw_author_name":"Thidathip Wongsurawat","raw_affiliation_strings":["Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","Division of Medical Bioinformatics , Department of Research, Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","Mahidol University , Department of Research, Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","institution_ids":["https://openalex.org/I79620101"]},{"raw_affiliation_string":"Division of Medical Bioinformatics , Department of Research, Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","institution_ids":["https://openalex.org/I1332387789"]},{"raw_affiliation_string":"Mahidol University , Department of Research, Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","institution_ids":["https://openalex.org/I1332387789","https://openalex.org/I25399158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037921470","display_name":"Alongkorn Kurilung","orcid":"https://orcid.org/0000-0003-0839-4967"},"institutions":[{"id":"https://openalex.org/I79620101","display_name":"University of Arkansas for Medical Sciences","ror":"https://ror.org/00xcryt71","country_code":"US","type":"education","lineage":["https://openalex.org/I79620101"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alongkorn Kurilung","raw_affiliation_strings":["Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","institution_ids":["https://openalex.org/I79620101"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033110455","display_name":"Yotsawat Pomyen","orcid":"https://orcid.org/0000-0002-1070-3047"},"institutions":[{"id":"https://openalex.org/I39737112","display_name":"Chulabhorn Research Institute","ror":"https://ror.org/00nb6mq69","country_code":"TH","type":"facility","lineage":["https://openalex.org/I39737112"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Yotsawat Pomyen","raw_affiliation_strings":["Translational Research Unit, Chulabhorn Research Institute , 54 Kamphaeng Phet Rd., Laksi, Bangkok 10210, Thailand"],"raw_orcid":"https://orcid.org/0000-0002-1070-3047","affiliations":[{"raw_affiliation_string":"Translational Research Unit, Chulabhorn Research Institute , 54 Kamphaeng Phet Rd., Laksi, Bangkok 10210, Thailand","institution_ids":["https://openalex.org/I39737112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043574544","display_name":"Sangam Kandel","orcid":"https://orcid.org/0000-0002-2875-6462"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I79620101","display_name":"University of Arkansas for Medical Sciences","ror":"https://ror.org/00xcryt71","country_code":"US","type":"education","lineage":["https://openalex.org/I79620101"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sangam Kandel","raw_affiliation_strings":["Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","Influenza Research Institute , Department of Pathobiological Sciences, School of Veterinary Medicine, , 575 Science Drive, Madison, WI 53711, United States","University of Wisconsin-Madison , Department of Pathobiological Sciences, School of Veterinary Medicine, , 575 Science Drive, Madison, WI 53711, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","institution_ids":["https://openalex.org/I79620101"]},{"raw_affiliation_string":"Influenza Research Institute , Department of Pathobiological Sciences, School of Veterinary Medicine, , 575 Science Drive, Madison, WI 53711, United States","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin-Madison , Department of Pathobiological Sciences, School of Veterinary Medicine, , 575 Science Drive, Madison, WI 53711, United States","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104730232","display_name":"Pattapon Kunadirek","orcid":null},"institutions":[{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Pattapon Kunadirek","raw_affiliation_strings":["Center of Excellence in Hepatitis and Liver Cancer , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand","Chulalongkorn University , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence in Hepatitis and Liver Cancer , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand","institution_ids":[]},{"raw_affiliation_string":"Chulalongkorn University , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand","institution_ids":["https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075056137","display_name":"Natthaya Chuaypen","orcid":"https://orcid.org/0000-0002-5415-510X"},"institutions":[{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Natthaya Chuaypen","raw_affiliation_strings":["Center of Excellence in Hepatitis and Liver Cancer , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand","Chulalongkorn University , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence in Hepatitis and Liver Cancer , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand","institution_ids":[]},{"raw_affiliation_string":"Chulalongkorn University , Department of Biochemistry, Faculty of Medicine, , Rama 4 road, Pathumwan, Bangkok 10330, Thailand","institution_ids":["https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027621397","display_name":"Kanthida Kusonmano","orcid":"https://orcid.org/0000-0002-6532-9144"},"institutions":[{"id":"https://openalex.org/I108108428","display_name":"Thammasat University","ror":"https://ror.org/002yp7f20","country_code":"TH","type":"education","lineage":["https://openalex.org/I108108428"]},{"id":"https://openalex.org/I60837268","display_name":"King Mongkut's University of Technology Thonburi","ror":"https://ror.org/0057ax056","country_code":"TH","type":"education","lineage":["https://openalex.org/I60837268"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Kanthida Kusonmano","raw_affiliation_strings":["Bioinformatics and Systems Biology Program , School of Bioresources and Technology, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand","King Mongkut\u2019s University of Technology Thonburi , Pilot Plant Development and Training Institute, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand","King Mongkut\u2019s University of Technology Thonburi , School of Bioresources and Technology, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand","Systems Biology and Bioinformatics Research Laboratory , Pilot Plant Development and Training Institute, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program , School of Bioresources and Technology, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand","institution_ids":["https://openalex.org/I108108428"]},{"raw_affiliation_string":"King Mongkut\u2019s University of Technology Thonburi , Pilot Plant Development and Training Institute, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand","institution_ids":["https://openalex.org/I60837268"]},{"raw_affiliation_string":"King Mongkut\u2019s University of Technology Thonburi , School of Bioresources and Technology, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand","institution_ids":["https://openalex.org/I60837268"]},{"raw_affiliation_string":"Systems Biology and Bioinformatics Research Laboratory , Pilot Plant Development and Training Institute, , 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Road, Tha Kham, Bang Khun Thian, Bangkok 10150, Thailand","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008739880","display_name":"Intawat Nookaew","orcid":"https://orcid.org/0000-0001-8901-1088"},"institutions":[{"id":"https://openalex.org/I1332387789","display_name":"Siriraj Hospital","ror":"https://ror.org/0331zs648","country_code":"TH","type":"healthcare","lineage":["https://openalex.org/I1332387789"]},{"id":"https://openalex.org/I25399158","display_name":"Mahidol University","ror":"https://ror.org/01znkr924","country_code":"TH","type":"education","lineage":["https://openalex.org/I25399158"]},{"id":"https://openalex.org/I79620101","display_name":"University of Arkansas for Medical Sciences","ror":"https://ror.org/00xcryt71","country_code":"US","type":"education","lineage":["https://openalex.org/I79620101"]}],"countries":["TH","US"],"is_corresponding":false,"raw_author_name":"Intawat Nookaew","raw_affiliation_strings":["Department of Biochemistry , Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","Division of Endocrinology , Department of Medicine, , 4301 W Markham St, Little Rock, AR 72205, United States","Mahidol University , Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","University of Arkansas for Medical Sciences , Department of Medicine, , 4301 W Markham St, Little Rock, AR 72205, United States"],"raw_orcid":"https://orcid.org/0000-0001-8901-1088","affiliations":[{"raw_affiliation_string":"Department of Biochemistry , Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","institution_ids":["https://openalex.org/I1332387789"]},{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","institution_ids":["https://openalex.org/I79620101"]},{"raw_affiliation_string":"Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences , 4301 W Markham St, Little Rock, AR 72205, United States","institution_ids":["https://openalex.org/I79620101"]},{"raw_affiliation_string":"Division of Endocrinology , Department of Medicine, , 4301 W Markham St, Little Rock, AR 72205, United States","institution_ids":[]},{"raw_affiliation_string":"Mahidol University , Faculty of Medicine Siriraj Hospital, , 2 Wang Lang Road, Siriraj, Bangkok Noi, Bangkok 10700, Thailand","institution_ids":["https://openalex.org/I1332387789","https://openalex.org/I25399158"]},{"raw_affiliation_string":"University of Arkansas for Medical Sciences , Department of Medicine, , 4301 W Markham St, Little Rock, AR 72205, United States","institution_ids":["https://openalex.org/I79620101"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.2247,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.78915464,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"25","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9983000159263611,"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/T10066","display_name":"Gut microbiota and health","score":0.9983000159263611,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9958999752998352,"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/T10552","display_name":"Colorectal Cancer Screening and Detection","score":0.9118000268936157,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.946345865726471},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.7139908075332642},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.6411575675010681},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6335539817810059},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5757836699485779},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.559895932674408},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5506972670555115},{"id":"https://openalex.org/keywords/shotgun","display_name":"Shotgun","score":0.5286106467247009},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.506763756275177},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41943058371543884},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26967930793762207},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24638229608535767},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.19511693716049194},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18144571781158447},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17716026306152344}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.946345865726471},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.7139908075332642},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6411575675010681},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6335539817810059},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5757836699485779},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.559895932674408},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5506972670555115},{"id":"https://openalex.org/C2781434637","wikidata":"https://www.wikidata.org/wiki/Q486396","display_name":"Shotgun","level":3,"score":0.5286106467247009},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.506763756275177},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41943058371543884},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26967930793762207},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24638229608535767},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.19511693716049194},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18144571781158447},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17716026306152344}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":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},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"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":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae424","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae424","pdf_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae424/58994655/bbae424.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39222062","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39222062","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11367759","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11367759","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11367759/pdf/bbae424.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","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae424","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae424","pdf_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae424/58994655/bbae424.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5400000214576721,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"},{"score":0.4300000071525574,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G3572205594","display_name":null,"funder_award_id":"P20GM125503","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6819921390","display_name":null,"funder_award_id":"P20GM125503","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7267555437","display_name":null,"funder_award_id":"R01CA143130","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402147396.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W46659105","https://openalex.org/W1556060949","https://openalex.org/W1966809619","https://openalex.org/W2039531605","https://openalex.org/W2096525273","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2129690444","https://openalex.org/W2134751812","https://openalex.org/W2141637710","https://openalex.org/W2154003902","https://openalex.org/W2509730012","https://openalex.org/W2560014131","https://openalex.org/W2568184332","https://openalex.org/W2605897695","https://openalex.org/W2789843538","https://openalex.org/W2897603717","https://openalex.org/W2927453907","https://openalex.org/W2932049125","https://openalex.org/W2949098970","https://openalex.org/W2950150251","https://openalex.org/W2951176108","https://openalex.org/W2952152744","https://openalex.org/W2958388979","https://openalex.org/W2968450569","https://openalex.org/W2981079979","https://openalex.org/W2986925300","https://openalex.org/W2990618091","https://openalex.org/W2991113705","https://openalex.org/W3079060667","https://openalex.org/W3083852019","https://openalex.org/W3089125281","https://openalex.org/W3137871957","https://openalex.org/W3142515935","https://openalex.org/W3144050603","https://openalex.org/W4210320669","https://openalex.org/W4231041617","https://openalex.org/W4298124890","https://openalex.org/W4313261720","https://openalex.org/W4384338853","https://openalex.org/W4394666350"],"related_works":["https://openalex.org/W3139084279","https://openalex.org/W4210312276","https://openalex.org/W4394334725","https://openalex.org/W4394325869","https://openalex.org/W3043668926","https://openalex.org/W4394383033","https://openalex.org/W4394278351","https://openalex.org/W4394378620","https://openalex.org/W4394291587","https://openalex.org/W4321764688"],"abstract_inverted_index":{"Accurate":[0],"taxonomic":[1,57,190],"profiling":[2],"of":[3,52,100,127,189,205,230],"microbial":[4,16,155],"taxa":[5,156],"in":[6,20,82,153,158,244],"a":[7,34,44,107,147,170,257],"metagenomic":[8,37,66,83,131,203],"sample":[9],"is":[10],"vital":[11],"to":[12,79,90,169,200],"gain":[13],"insights":[14],"into":[15],"ecology.":[17],"Recent":[18],"advancements":[19],"sequencing":[21,183,194],"technologies":[22],"have":[23],"contributed":[24],"tremendously":[25],"toward":[26],"understanding":[27],"these":[28],"microbes":[29],"at":[30],"species":[31,81,260],"resolution":[32],"through":[33],"whole":[35],"shotgun":[36,202],"approach.":[38,122],"In":[39,103],"this":[40],"study,":[41],"we":[42,105],"developed":[43],"new":[45],"bioinformatics":[46],"tool,":[47],"coverage-based":[48],"analysis":[49],"for":[50,55],"identification":[51],"microbiome":[53],"(CAIM),":[54],"accurate":[56],"classification":[58],"and":[59,64,134,157,178,181,185,210,218,224,248],"quantification":[60],"within":[61],"both":[62,175],"long-":[63],"short-read":[65],"samples":[67,84],"using":[68,85,232,240],"an":[69],"alignment-based":[70],"method.":[71],"CAIM":[72,128,145,165,197],"depends":[73],"on":[74,129,174],"two":[75],"different":[76,216],"containment":[77],"techniques":[78],"identify":[80],"their":[86],"genome":[87],"coverage":[88],"information":[89],"filter":[91],"out":[92],"false":[93],"positives":[94],"rather":[95],"than":[96,118,162,238],"the":[97,119,125,193,233,241],"traditional":[98,120],"approach":[99],"relative":[101,160],"abundance.":[102],"addition,":[104],"propose":[106],"nucleotide-count-based":[108],"abundance":[109],"estimation,":[110],"which":[111],"yield":[112],"lesser":[113],"root":[114],"mean":[115],"square":[116],"error":[117],"read-count":[121],"We":[123],"evaluated":[124],"performance":[126,150,229],"28":[130],"mock":[132],"communities":[133],"2":[135],"synthetic":[136],"datasets":[137,152,204],"by":[138],"comparing":[139],"it":[140],"with":[141,256],"other":[142,163],"top-performing":[143],"tools.":[144,164],"maintained":[146],"consistently":[148],"good":[149],"across":[151],"identifying":[154],"estimating":[159],"abundances":[161],"was":[166,198,236],"then":[167],"applied":[168,199],"real":[171],"dataset":[172],"sequenced":[173],"Nanopore":[176],"(with":[177],"without":[179],"amplification)":[180],"Illumina":[182],"platforms":[184],"found":[186],"high":[187],"similarity":[188],"profiles":[191],"between":[192],"platforms.":[195],"Lastly,":[196],"fecal":[201],"232":[206],"colorectal":[207,246],"cancer":[208,222,247,251],"patients":[209,223,252],"229":[211],"controls":[212,255],"obtained":[213],"from":[214,253],"4":[215],"countries":[217],"44":[219],"primary":[220,249],"liver":[221,250],"76":[225],"controls.":[226],"The":[227],"predictive":[228],"models":[231],"genome-coverage":[234],"cutoff":[235],"better":[237],"those":[239],"relative-abundance":[242],"cutoffs":[243],"discriminating":[245],"healthy":[254],"highly":[258],"confident":[259],"markers.":[261]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
