{"id":"https://openalex.org/W4410661450","doi":"https://doi.org/10.1093/bib/bbaf227","title":"mKmer: an unbiased <i>K</i>-mer embedding of microbiomic single-microbe RNA sequencing data","display_name":"mKmer: an unbiased <i>K</i>-mer embedding of microbiomic single-microbe RNA sequencing data","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4410661450","doi":"https://doi.org/10.1093/bib/bbaf227","pmid":"https://pubmed.ncbi.nlm.nih.gov/40407385"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf227","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf227","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf227/63308317/bbaf227.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","license_id":"https://openalex.org/licenses/cc-by","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/26/3/bbaf227/63308317/bbaf227.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056281599","display_name":"Fangyu Mo","orcid":"https://orcid.org/0009-0003-0560-5551"},"institutions":[{"id":"https://openalex.org/I4210156466","display_name":"Institute of Crop Science","ror":"https://ror.org/053g6zg46","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1323638106","https://openalex.org/I4210156466"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","JP"],"is_corresponding":false,"raw_author_name":"Fangyu Mo","raw_affiliation_strings":["Hainan Institute, Zhejiang University , Zhenzhou Road, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan Province ,","Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hainan Institute, Zhejiang University , Zhenzhou Road, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan Province ,","institution_ids":[]},{"raw_affiliation_string":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210156466","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007530254","display_name":"Qinghong Qian","orcid":null},"institutions":[{"id":"https://openalex.org/I4210156466","display_name":"Institute of Crop Science","ror":"https://ror.org/053g6zg46","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1323638106","https://openalex.org/I4210156466"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","JP"],"is_corresponding":false,"raw_author_name":"Qinghong Qian","raw_affiliation_strings":["Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210156466","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100872631","display_name":"Xiaolin Lu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","IN"],"is_corresponding":false,"raw_author_name":"Xiaolin Lu","raw_affiliation_strings":["Institute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210148697","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087612111","display_name":"Dihuai Zheng","orcid":"https://orcid.org/0009-0001-5199-6835"},"institutions":[{"id":"https://openalex.org/I4210156466","display_name":"Institute of Crop Science","ror":"https://ror.org/053g6zg46","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1323638106","https://openalex.org/I4210156466"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","JP"],"is_corresponding":false,"raw_author_name":"Dihuai Zheng","raw_affiliation_strings":["Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210156466","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103173370","display_name":"Wenjie Cai","orcid":"https://orcid.org/0000-0002-5352-8779"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenjie Cai","raw_affiliation_strings":["Liangzhu Laboratory (Zhejiang Provincial Laboratory for Systems Medicine and Precision Diagnosis), Zhejiang University , 1369 Wenyi West Road, Yuhang District, Hangzhou 311121, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Liangzhu Laboratory (Zhejiang Provincial Laboratory for Systems Medicine and Precision Diagnosis), Zhejiang University , 1369 Wenyi West Road, Yuhang District, Hangzhou 311121, Zhejiang Province ,","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037649298","display_name":"Jie Yao","orcid":"https://orcid.org/0000-0002-7898-1799"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","IN"],"is_corresponding":false,"raw_author_name":"Jie Yao","raw_affiliation_strings":["Institute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210148697","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115601812","display_name":"Hongyu Chen","orcid":"https://orcid.org/0000-0002-5325-9249"},"institutions":[{"id":"https://openalex.org/I4210156466","display_name":"Institute of Crop Science","ror":"https://ror.org/053g6zg46","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1323638106","https://openalex.org/I4210156466"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","JP"],"is_corresponding":false,"raw_author_name":"Hongyu Chen","raw_affiliation_strings":["Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210156466","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025153042","display_name":"Yujie Huang","orcid":"https://orcid.org/0000-0001-7349-6711"},"institutions":[{"id":"https://openalex.org/I4210156466","display_name":"Institute of Crop Science","ror":"https://ror.org/053g6zg46","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1323638106","https://openalex.org/I4210156466"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","JP"],"is_corresponding":false,"raw_author_name":"Yujie Huang","raw_affiliation_strings":["Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210156466","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100368885","display_name":"Xiang Zhang","orcid":"https://orcid.org/0000-0002-7543-8352"},"institutions":[{"id":"https://openalex.org/I4210166576","display_name":"First Affiliated Hospital Zhejiang University","ror":"https://ror.org/05m1p5x56","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210166576"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiang Zhang","raw_affiliation_strings":["Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210166576","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049865185","display_name":"Sanling Wu","orcid":"https://orcid.org/0000-0001-7734-6542"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sanling Wu","raw_affiliation_strings":["Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114889635","display_name":"Yifei Shen","orcid":"https://orcid.org/0000-0001-7174-4793"},"institutions":[{"id":"https://openalex.org/I4210166576","display_name":"First Affiliated Hospital Zhejiang University","ror":"https://ror.org/05m1p5x56","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210166576"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yifei Shen","raw_affiliation_strings":["Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210166576","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027272159","display_name":"Yinqi Bai","orcid":"https://orcid.org/0000-0003-1017-5712"},"institutions":[{"id":"https://openalex.org/I4405259006","display_name":"BGI Research, Sanya","ror":"https://ror.org/01j5pk676","country_code":"CN","type":"facility","lineage":["https://openalex.org/I100135526","https://openalex.org/I4387153646","https://openalex.org/I4405259006"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yinqi Bai","raw_affiliation_strings":["BGI-Sanya, Zhenzhou Road, Yazhou Bay Science and Technology City , Yazhou District, Sanya 572025, Hainan Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Sanya, Zhenzhou Road, Yazhou Bay Science and Technology City , Yazhou District, Sanya 572025, Hainan Province ,","institution_ids":["https://openalex.org/I4405259006"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100329324","display_name":"Yongcheng Wang","orcid":"https://orcid.org/0000-0003-2820-4243"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongcheng Wang","raw_affiliation_strings":["Liangzhu Laboratory, Zhejiang University , 1369 Wenyi West Road, Yuhang District, Hangzhou 311113, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Liangzhu Laboratory, Zhejiang University , 1369 Wenyi West Road, Yuhang District, Hangzhou 311113, Zhejiang Province ,","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036059897","display_name":"Weiqin Jiang","orcid":"https://orcid.org/0000-0003-3200-8835"},"institutions":[{"id":"https://openalex.org/I4210166576","display_name":"First Affiliated Hospital Zhejiang University","ror":"https://ror.org/05m1p5x56","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210166576"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiqin Jiang","raw_affiliation_strings":["Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , 79 Qingchun Road, Shangcheng District, Hangzhou 310003, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210166576","https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007314776","display_name":"Longjiang Fan","orcid":"https://orcid.org/0000-0003-4846-0500"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]},{"id":"https://openalex.org/I4210156466","display_name":"Institute of Crop Science","ror":"https://ror.org/053g6zg46","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1323638106","https://openalex.org/I4210156466"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","IN","JP"],"is_corresponding":false,"raw_author_name":"Longjiang Fan","raw_affiliation_strings":["Hainan Institute, Zhejiang University , Zhenzhou Road, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan Province ,","Institute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hainan Institute, Zhejiang University , Zhenzhou Road, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan Province ,","institution_ids":[]},{"raw_affiliation_string":"Institute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210148697","https://openalex.org/I76130692"]},{"raw_affiliation_string":"Institute of Crop Science, Zhejiang University , 866 Yuhangtang Road, Xihu District, Hangzhou 310058, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210156466","https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"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":0.8477,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.70656648,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"26","issue":"3","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":0.9994999766349792,"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":0.9994999766349792,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9951000213623047,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9883000254631042,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6960036754608154},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.6398307681083679},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6248509883880615},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5622879862785339},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4750616252422333},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4697561264038086},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.42225381731987},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4102001190185547},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30565178394317627},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.29299795627593994},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10977789759635925}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6960036754608154},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6398307681083679},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6248509883880615},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5622879862785339},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4750616252422333},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4697561264038086},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.42225381731987},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4102001190185547},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30565178394317627},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29299795627593994},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10977789759635925}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"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/bbaf227","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf227","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf227/63308317/bbaf227.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40407385","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40407385","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:12100620","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12100620","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,"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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf227","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf227","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf227/63308317/bbaf227.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.7400000095367432,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320326677","display_name":"Education Department of Hainan Province","ror":null},{"id":"https://openalex.org/F4320330084","display_name":"Research and Innovation Foundation","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410661450.pdf","grobid_xml":"https://content.openalex.org/works/W4410661450.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1709815505","https://openalex.org/W1987971958","https://openalex.org/W1988460088","https://openalex.org/W2036057672","https://openalex.org/W2051224630","https://openalex.org/W2074299224","https://openalex.org/W2080528636","https://openalex.org/W2089859322","https://openalex.org/W2096128575","https://openalex.org/W2101289642","https://openalex.org/W2101291993","https://openalex.org/W2102212449","https://openalex.org/W2103777723","https://openalex.org/W2116846792","https://openalex.org/W2124799197","https://openalex.org/W2141661216","https://openalex.org/W2141802202","https://openalex.org/W2144440398","https://openalex.org/W2159008215","https://openalex.org/W2159954944","https://openalex.org/W2166123725","https://openalex.org/W2169456326","https://openalex.org/W2337747100","https://openalex.org/W2345658906","https://openalex.org/W2529838505","https://openalex.org/W2550084345","https://openalex.org/W2745194224","https://openalex.org/W2794542364","https://openalex.org/W2897603717","https://openalex.org/W2906742147","https://openalex.org/W2951160681","https://openalex.org/W2952109315","https://openalex.org/W2969920107","https://openalex.org/W2990618091","https://openalex.org/W3037144858","https://openalex.org/W3042305844","https://openalex.org/W3107358297","https://openalex.org/W3112600195","https://openalex.org/W3159504416","https://openalex.org/W3164692211","https://openalex.org/W3199469477","https://openalex.org/W3203848352","https://openalex.org/W4306160156","https://openalex.org/W4378716051","https://openalex.org/W4387729455","https://openalex.org/W4390673422","https://openalex.org/W4391884153","https://openalex.org/W4393995158","https://openalex.org/W4396773118","https://openalex.org/W4398140004","https://openalex.org/W4398761389","https://openalex.org/W4402226770","https://openalex.org/W4402965270","https://openalex.org/W6944127214"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W4401372636","https://openalex.org/W1969665739","https://openalex.org/W2608221519","https://openalex.org/W3094269189","https://openalex.org/W2767445485","https://openalex.org/W2112814626","https://openalex.org/W2114671460"],"abstract_inverted_index":{"The":[0],"advanced":[1],"single-microbe":[2],"RNA":[3],"sequencing":[4],"(smRNA-seq)":[5],"technique":[6],"addresses":[7],"the":[8,13,23,41,47,106],"pressing":[9],"need":[10],"to":[11,89],"understand":[12],"complexity":[14],"and":[15,96,123,133],"diversity":[16],"of":[17,35,43,55],"microbial":[18,25,56,69],"communities,":[19],"as":[20,22],"well":[21],"distinct":[24],"states":[26],"defined":[27],"by":[28],"different":[29],"gene":[30,60,85,103],"expression":[31],"profiles.":[32],"Current":[33],"analyses":[34],"smRNA-seq":[36,147],"data":[37],"heavily":[38],"rely":[39],"on":[40],"integrity":[42],"reference":[44,57,141],"genomes":[45,58],"within":[46],"queried":[48],"microbiota.":[49],"However,":[50],"establishing":[51],"a":[52,63,140],"comprehensive":[53],"collection":[54],"or":[59,86],"sets":[61],"remains":[62],"significant":[64],"challenge":[65],"for":[66,93,145],"most":[67],"real-world":[68],"ecosystems.":[70],"Here,":[71],"we":[72,114],"developed":[73],"an":[74],"unbiased":[75],"embedding":[76],"algorithm":[77],"utilizing":[78],"K-mer":[79],"signatures,":[80],"named":[81],"mKmer,":[82],"which":[83],"bypasses":[84],"genome":[87],"alignment":[88],"enable":[90],"species":[91],"identification":[92],"individual":[94],"microbes":[95],"downstream":[97],"functional":[98],"enrichment":[99],"analysis.":[100],"By":[101],"substituting":[102],"features":[104],"in":[105,121],"canonical":[107],"cell-by-gene":[108],"matrix":[109],"with":[110],"highly":[111],"conserved":[112],"K-mers,":[113],"demonstrate":[115],"that":[116],"mKmer":[117],"outperforms":[118],"gene-based":[119],"methods":[120],"clustering":[122],"motif":[124],"inference":[125],"tasks":[126],"using":[127],"benchmark":[128],"datasets":[129],"from":[130],"crop":[131],"soil":[132],"human":[134],"gut":[135],"microbiomes.":[136],"Our":[137],"method":[138],"provides":[139],"genome-free":[142],"analytical":[143],"framework":[144],"advancing":[146],"studies.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-05-24T00:00:00"}