{"id":"https://openalex.org/W2118734291","doi":"https://doi.org/10.1186/preaccept-1218610333125217","title":"Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing","display_name":"Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2118734291","doi":"https://doi.org/10.1186/preaccept-1218610333125217","mag":"2118734291","pmid":"https://pubmed.ncbi.nlm.nih.gov/25344286","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4232682"},"language":"en","primary_location":{"id":"doi:10.1186/preaccept-1218610333125217","doi":"https://doi.org/10.1186/preaccept-1218610333125217","is_oa":true,"landing_page_url":"https://doi.org/10.1186/preaccept-1218610333125217","pdf_url":"https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-014-0487-y","source":{"id":"https://openalex.org/S81160022","display_name":"Genome biology","issn_l":"1465-6906","issn":["1465-6906","1465-6914","1474-7596","1474-760X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"Genome Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-014-0487-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066967353","display_name":"Kyle L. Bittinger","orcid":"https://orcid.org/0000-0003-3472-5934","observed_orcids":["https://orcid.org/0000-0003-3472-5934"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyle Bittinger","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053640758","display_name":"Emily Sarah Charlson","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily S Charlson","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Elizabeth Loy","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elizabeth Loy","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058503714","display_name":"David J. Shirley","orcid":"https://orcid.org/0000-0003-4529-0403","observed_orcids":["https://orcid.org/0000-0003-4529-0403"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David J Shirley","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110258522","display_name":"Andrew R. Haas","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew R Haas","raw_affiliation_strings":["Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044285287","display_name":"Alice L. Laughlin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alice Laughlin","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091021702","display_name":"Yanjie Yi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanjie Yi","raw_affiliation_strings":["Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032759284","display_name":"Gary D. Wu","orcid":"https://orcid.org/0000-0002-1829-8795","observed_orcids":["https://orcid.org/0000-0002-1829-8795"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gary D Wu","raw_affiliation_strings":["Gastroenterology Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gastroenterology Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041936168","display_name":"James D. Lewis","orcid":"https://orcid.org/0000-0003-3107-3862","observed_orcids":["https://orcid.org/0000-0003-3107-3862"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James D Lewis","raw_affiliation_strings":["Gastroenterology Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gastroenterology Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067519373","display_name":"Ian Frank","orcid":"https://orcid.org/0000-0002-7824-0106","observed_orcids":["https://orcid.org/0000-0002-7824-0106"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ian Frank","raw_affiliation_strings":["Infectious Diseases Division, Department of Medicine, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Infectious Diseases Division, Department of Medicine, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007268439","display_name":"Edward Cantu","orcid":"https://orcid.org/0000-0003-1105-0129","observed_orcids":["https://orcid.org/0000-0003-1105-0129"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward Cantu","raw_affiliation_strings":["Department of Cardiovascular Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cardiovascular Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026370860","display_name":"Joshua Matthew Diamond","orcid":"https://orcid.org/0000-0002-3695-4637","observed_orcids":["https://orcid.org/0000-0002-3695-4637"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua M Diamond","raw_affiliation_strings":["Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086233693","display_name":"Jason D. Christie","orcid":"https://orcid.org/0000-0003-0519-218X","observed_orcids":["https://orcid.org/0000-0003-0519-218X"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason D Christie","raw_affiliation_strings":["Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074582058","display_name":"Ronald G. Collman","orcid":"https://orcid.org/0000-0002-0508-3701","observed_orcids":["https://orcid.org/0000-0002-0508-3701"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ronald G Collman","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Pulmonary, Allergy and Critical Care Division, University of Pennsylvania School of Medicine, 522 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016535188","display_name":"Frederic D. Bushman","orcid":"https://orcid.org/0000-0003-4740-4056","observed_orcids":["https://orcid.org/0000-0003-4740-4056"]},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Frederic D Bushman","raw_affiliation_strings":["Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, University of Pennsylvania School of Medicine, 426 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, 19104, PA, USA","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5016535188","https://openalex.org/A5074582058"],"corresponding_institution_ids":["https://openalex.org/I79576946"],"apc_list":{"value":5490,"currency":"USD","value_usd":5490},"apc_paid":{"value":5490,"currency":"USD","value_usd":5490},"fwci":6.0707,"has_fulltext":true,"cited_by_count":145,"citation_normalized_percentile":{"value":0.96994285,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"15","issue":"10","first_page":"487","last_page":"487"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10150","display_name":"Antifungal resistance and susceptibility","score":0.6166999936103821,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10150","display_name":"Antifungal resistance and susceptibility","score":0.6166999936103821,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.05939999967813492,"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/T10825","display_name":"Plant Pathogens and Fungal Diseases","score":0.04899999871850014,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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"}}],"keywords":[{"id":"https://openalex.org/keywords/mycobiome","display_name":"fungal communities","score":0.5569999814033508},{"id":"https://openalex.org/keywords/respiratory-tract","display_name":"respiratory tract","score":0.9629999995231628},{"id":"https://openalex.org/keywords/dna-quantification","display_name":"DNA quantification","score":0.6240000128746033},{"id":"https://openalex.org/keywords/hiv","display_name":"HIV","score":0.6800000071525574},{"id":"https://openalex.org/keywords/lung-transplant-recipients","display_name":"lung transplant recipients","score":0.9359999895095825},{"id":"https://openalex.org/keywords/candida","display_name":"Candida","score":0.9739999771118164},{"id":"https://openalex.org/keywords/cryptococcus","display_name":"Cryptococcus","score":0.9990000128746033},{"id":"https://openalex.org/keywords/aspergillus","display_name":"Aspergillus","score":1.0},{"id":"https://openalex.org/keywords/mitis-group-streptococci","display_name":"mitis group streptococci","score":0.8920000195503235},{"id":"https://openalex.org/keywords/multispecies-biofilms","display_name":"polymicrobial biofilms","score":0.8989999890327454},{"id":"https://openalex.org/keywords/fungal-bacterial-interactions","display_name":"fungal-bacterial interactions","score":0.7570000290870667},{"id":"https://openalex.org/keywords/fungal-pathogen-detection","display_name":"fungal pathogen detection","score":0.49799999594688416}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8824928998947144},{"id":"https://openalex.org/C47042493","wikidata":"https://www.wikidata.org/wiki/Q265799","display_name":"Human genetics","level":3,"score":0.8422936201095581},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5908317565917969},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5281904935836792},{"id":"https://openalex.org/C64015301","wikidata":"https://www.wikidata.org/wiki/Q5533480","display_name":"Genome Biology","level":5,"score":0.4810178875923157},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.47538578510284424},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3932971954345703},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.343483030796051},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3346641957759857},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.217855304479599},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.21763843297958374}],"mesh":[{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012137","descriptor_name":"Respiratory System","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D044822","descriptor_name":"Biodiversity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/preaccept-1218610333125217","doi":"https://doi.org/10.1186/preaccept-1218610333125217","is_oa":true,"landing_page_url":"https://doi.org/10.1186/preaccept-1218610333125217","pdf_url":"https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-014-0487-y","source":{"id":"https://openalex.org/S81160022","display_name":"Genome biology","issn_l":"1465-6906","issn":["1465-6906","1465-6914","1474-7596","1474-760X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"Genome Biology","raw_type":"journal-article"},{"id":"doi:10.1186/s13059-014-0487-y","doi":"https://doi.org/10.1186/s13059-014-0487-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13059-014-0487-y","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13059-014-0487-y.pdf","source":{"id":"https://openalex.org/S81160022","display_name":"Genome biology","issn_l":"1465-6906","issn":["1465-6906","1465-6914","1474-7596","1474-760X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"Genome Biology","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:3201522","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4232682","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4232682","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4232682","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":"Genome Biol","raw_type":"Text"},{"id":"pmid:25344286","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25344286","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":"Genome biology","raw_type":"Comparative Study"}],"best_oa_location":{"id":"doi:10.1186/preaccept-1218610333125217","doi":"https://doi.org/10.1186/preaccept-1218610333125217","is_oa":true,"landing_page_url":"https://doi.org/10.1186/preaccept-1218610333125217","pdf_url":"https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-014-0487-y","source":{"id":"https://openalex.org/S81160022","display_name":"Genome biology","issn_l":"1465-6906","issn":["1465-6906","1465-6914","1474-7596","1474-760X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"Genome Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.9763000011444092}],"study_designs":[{"display_name":"Observational Study","id":"https://openalex.org/study-designs/observational-study"}],"awards":[{"id":"https://openalex.org/G1852790566","display_name":null,"funder_award_id":"P30 AI 045008","funder_id":"https://openalex.org/F4320309370","funder_display_name":"University of Pennsylvania"},{"id":"https://openalex.org/G226574744","display_name":null,"funder_award_id":"P30-AI-045008","funder_id":"https://openalex.org/F4320332582","funder_display_name":"Center for AIDS Research, University of Washington"},{"id":"https://openalex.org/G2451029711","display_name":null,"funder_award_id":"L32 MD008850","funder_id":"https://openalex.org/F4320337534","funder_display_name":"National Institute on Minority Health and Health Disparities"},{"id":"https://openalex.org/G5034747954","display_name":"Human Respiratory Tract Microbiome in Health, HIV Infection and HIV Lung Disease","funder_award_id":"U01HL098957","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6935180956","display_name":"Microbial Pathogenesis and Genomics","funder_award_id":"T32AI060516","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G7602213891","display_name":"Lung Transplant donor: prediction, evaluation, and mechanism","funder_award_id":"K23HL116656","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G8173708265","display_name":"Lung Transplant Microbiome and Chronic Allograft Dysfunction","funder_award_id":"R01HL113252","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G9000266210","display_name":null,"funder_award_id":"AI045008","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000887542","display_name":"Penn Center for AIDS Research","funder_award_id":"P30AI045008","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332582","display_name":"Center for AIDS Research, University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337534","display_name":"National Institute on Minority Health and Health Disparities","ror":"https://ror.org/0493hgw16"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2118734291.pdf","grobid_xml":"https://content.openalex.org/works/W2118734291.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1491668332","https://openalex.org/W1607979174","https://openalex.org/W1964948648","https://openalex.org/W1965509718","https://openalex.org/W1966974215","https://openalex.org/W1968206284","https://openalex.org/W1980476578","https://openalex.org/W2000542878","https://openalex.org/W2004397336","https://openalex.org/W2006509711","https://openalex.org/W2010841805","https://openalex.org/W2025060030","https://openalex.org/W2031611770","https://openalex.org/W2045073446","https://openalex.org/W2050745388","https://openalex.org/W2064812408","https://openalex.org/W2072970694","https://openalex.org/W2080720319","https://openalex.org/W2085068503","https://openalex.org/W2085987970","https://openalex.org/W2088369864","https://openalex.org/W2092681530","https://openalex.org/W2104318549","https://openalex.org/W2110065044","https://openalex.org/W2110345840","https://openalex.org/W2114338344","https://openalex.org/W2124351063","https://openalex.org/W2127758025","https://openalex.org/W2133211453","https://openalex.org/W2134564677","https://openalex.org/W2136527023","https://openalex.org/W2138609440","https://openalex.org/W2141980700","https://openalex.org/W2143285077","https://openalex.org/W2150180798","https://openalex.org/W2153927784","https://openalex.org/W2154026962","https://openalex.org/W2155092137","https://openalex.org/W2156800033","https://openalex.org/W2159542223","https://openalex.org/W2161163382","https://openalex.org/W2166559909","https://openalex.org/W2167783345","https://openalex.org/W2170196186","https://openalex.org/W2582743722","https://openalex.org/W2770131614","https://openalex.org/W3140139051"],"related_works":["https://openalex.org/W6958948397","https://openalex.org/W7147048341","https://openalex.org/W4410273695","https://openalex.org/W2005755022","https://openalex.org/W1931285493","https://openalex.org/W2136305645","https://openalex.org/W3207930435","https://openalex.org/W2916662629","https://openalex.org/W2949761114","https://openalex.org/W2115747388"],"abstract_inverted_index":{"BACKGROUND:":[0],"Fungi":[1],"are":[2,53,174],"important":[3],"pathogens":[4],"but":[5],"challenging":[6],"to":[7,60,102,123,195],"enumerate":[8],"using":[9,40,189],"next-generation":[10],"sequencing":[11,101],"because":[12],"of":[13,23,71,92,140,161],"low":[14],"absolute":[15],"abundance":[16],"in":[17,36,112,149,172,177,199,213],"many":[18],"samples":[19,118],"and":[20,65,69,77,85,110,119,147,155,163,166,206,215],"high":[21],"levels":[22],"fungal":[24,33,75,162,197],"DNA":[25,49,57,113],"from":[26,80,108,115],"contaminating":[27],"sources.":[28],"RESULTS:":[29],"Here,":[30],"we":[31],"analyze":[32,159],"lineages":[34],"present":[35],"the":[37,67,132,200],"human":[38,201],"airway":[39],"an":[41],"improved":[42,128],"method":[43],"for":[44,96],"contamination":[45],"filtering.":[46],"We":[47,73,98,136,158],"use":[48,99],"quantification":[50],"data,":[51,64],"which":[52],"routinely":[54],"acquired":[55],"during":[56],"library":[58],"preparation,":[59],"annotate":[61],"output":[62],"sequence":[63],"improve":[66],"identification":[68],"filtering":[70,133],"contaminants.":[72],"compare":[74],"communities":[76,79,170,198,212],"bacterial":[78,164,211],"healthy":[81],"subjects,":[82,84],"HIV+":[83],"lung":[86,94],"transplant":[87],"recipients,":[88],"providing":[89],"a":[90],"gradient":[91],"increasing":[93],"impairment":[95],"comparison.":[97],"deep":[100],"characterize":[103,196],"ribosomal":[104],"rRNA":[105],"gene":[106],"segments":[107],"fungi":[109],"bacteria":[111],"extracted":[114],"bronchiolar":[116],"lavage":[117],"oropharyngeal":[120,169],"wash.":[121],"Comparison":[122],"clinical":[124],"culture":[125],"data":[126],"documents":[127],"detection":[129],"after":[130],"applying":[131],"procedure.":[134],"CONCLUSIONS:":[135],"find":[137,167],"increased":[138],"representation":[139],"medically":[141],"relevant":[142],"organisms,":[143],"including":[144],"Candida,":[145],"Cryptococcus,":[146],"Aspergillus,":[148],"subjects":[150],"with":[151,184,210],"increasingly":[152],"severe":[153],"pulmonary":[154],"immunologic":[156],"deficits.":[157],"covariation":[160],"taxa,":[165],"that":[168],"rich":[171,176],"Candida":[173],"also":[175],"mitis":[178],"group":[179],"Streptococci,a":[180],"community":[181],"pattern":[182],"associated":[183],"pathogenic":[185],"polymicrobial":[186],"biofilms.":[187],"Thus,":[188],"this":[190],"approach,":[191],"it":[192],"is":[193],"possible":[194],"respiratory":[202],"tract":[203],"more":[204],"accurately":[205],"explore":[207],"their":[208],"interactions":[209],"health":[214],"disease.":[216]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":5}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}