{"id":"https://openalex.org/W2612505479","doi":"https://doi.org/10.1093/bib/bby012","title":"Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes","display_name":"Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes","publication_year":2018,"publication_date":"2018-02-22","ids":{"openalex":"https://openalex.org/W2612505479","doi":"https://doi.org/10.1093/bib/bby012","mag":"2612505479","pmid":"https://pubmed.ncbi.nlm.nih.gov/29481588"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby012","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby012","pdf_url":"https://academic.oup.com/bib/article-pdf/19/2/360/25524272/bby012.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"erratum","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/19/2/360/25524272/bby012.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083782143","display_name":"Sheng-Yong Niu","orcid":"https://orcid.org/0000-0002-7734-1191"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Sheng-Yong Niu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049718088","display_name":"Jinyu Yang","orcid":"https://orcid.org/0000-0002-7004-3570"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jinyu Yang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032867744","display_name":"Adam McDermaid","orcid":"https://orcid.org/0000-0001-8616-1574"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Adam McDermaid","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101680912","display_name":"Jing Zhao","orcid":"https://orcid.org/0000-0002-2395-4777"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jing Zhao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110921685","display_name":"Yu Kang","orcid":"https://orcid.org/0000-0001-5196-0376"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yu Kang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5022408570","display_name":"Qin Ma","orcid":"https://orcid.org/0000-0002-3264-8392"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qin Ma","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5083782143"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.2477,"has_fulltext":false,"cited_by_count":64,"citation_normalized_percentile":{"value":0.92947665,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"19","issue":"2","first_page":"360","last_page":"360"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9993000030517578,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9966999888420105,"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/metagenomics","display_name":"Metagenomics","score":0.9676913022994995},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7059444189071655},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.6605159044265747},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6189950108528137},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.48250579833984375},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.43083617091178894},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.42901909351348877},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3703094720840454},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3151455521583557},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2504783570766449},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23018062114715576}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9676913022994995},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7059444189071655},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6605159044265747},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6189950108528137},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.48250579833984375},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.43083617091178894},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.42901909351348877},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3703094720840454},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3151455521583557},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2504783570766449},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23018062114715576},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bby012","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby012","pdf_url":"https://academic.oup.com/bib/article-pdf/19/2/360/25524272/bby012.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29481588","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29481588","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}],"best_oa_location":{"id":"doi:10.1093/bib/bby012","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby012","pdf_url":"https://academic.oup.com/bib/article-pdf/19/2/360/25524272/bby012.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G367708065","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3709464396","display_name":null,"funder_award_id":"-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3730782400","display_name":null,"funder_award_id":"1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4897854425","display_name":null,"funder_award_id":"grant number ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310344","display_name":"South Dakota State University","ror":"https://ror.org/015jmes13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2612505479.pdf","grobid_xml":"https://content.openalex.org/works/W2612505479.grobid-xml"},"referenced_works_count":108,"referenced_works":["https://openalex.org/W1433995531","https://openalex.org/W1537762226","https://openalex.org/W1578104218","https://openalex.org/W1703384511","https://openalex.org/W1874993960","https://openalex.org/W1945011216","https://openalex.org/W1986708244","https://openalex.org/W1988925586","https://openalex.org/W1989348205","https://openalex.org/W1989854862","https://openalex.org/W1996719637","https://openalex.org/W2003347102","https://openalex.org/W2008274231","https://openalex.org/W2008459449","https://openalex.org/W2011084061","https://openalex.org/W2011375141","https://openalex.org/W2023046869","https://openalex.org/W2031893281","https://openalex.org/W2034285706","https://openalex.org/W2034537627","https://openalex.org/W2035396875","https://openalex.org/W2036649644","https://openalex.org/W2041117131","https://openalex.org/W2045204781","https://openalex.org/W2062535783","https://openalex.org/W2062685052","https://openalex.org/W2063158722","https://openalex.org/W2069689025","https://openalex.org/W2072970694","https://openalex.org/W2074168377","https://openalex.org/W2075716829","https://openalex.org/W2077631777","https://openalex.org/W2079520182","https://openalex.org/W2088833470","https://openalex.org/W2091922579","https://openalex.org/W2096791516","https://openalex.org/W2097205777","https://openalex.org/W2097341408","https://openalex.org/W2099837668","https://openalex.org/W2100228443","https://openalex.org/W2106197985","https://openalex.org/W2107903949","https://openalex.org/W2108234281","https://openalex.org/W2108718991","https://openalex.org/W2110491379","https://openalex.org/W2114034054","https://openalex.org/W2115026474","https://openalex.org/W2116913446","https://openalex.org/W2119497560","https://openalex.org/W2120172561","https://openalex.org/W2124351063","https://openalex.org/W2124799197","https://openalex.org/W2124985265","https://openalex.org/W2125826054","https://openalex.org/W2128601422","https://openalex.org/W2128769815","https://openalex.org/W2128964206","https://openalex.org/W2129742737","https://openalex.org/W2130253098","https://openalex.org/W2131271579","https://openalex.org/W2132801908","https://openalex.org/W2133579817","https://openalex.org/W2133790733","https://openalex.org/W2136145671","https://openalex.org/W2140452573","https://openalex.org/W2142428670","https://openalex.org/W2143280034","https://openalex.org/W2144550002","https://openalex.org/W2146341019","https://openalex.org/W2147783737","https://openalex.org/W2149573313","https://openalex.org/W2153267836","https://openalex.org/W2154364831","https://openalex.org/W2155066423","https://openalex.org/W2156296225","https://openalex.org/W2156492633","https://openalex.org/W2157107905","https://openalex.org/W2157630710","https://openalex.org/W2159008215","https://openalex.org/W2159482845","https://openalex.org/W2159954944","https://openalex.org/W2162368885","https://openalex.org/W2166706771","https://openalex.org/W2167415413","https://openalex.org/W2170146596","https://openalex.org/W2170551349","https://openalex.org/W2171051890","https://openalex.org/W2171309014","https://openalex.org/W2179438025","https://openalex.org/W2201193916","https://openalex.org/W2212407137","https://openalex.org/W2227583040","https://openalex.org/W2254199494","https://openalex.org/W2307206101","https://openalex.org/W2322763599","https://openalex.org/W2339590532","https://openalex.org/W2393255758","https://openalex.org/W2401404581","https://openalex.org/W2408489451","https://openalex.org/W2409427249","https://openalex.org/W2526219319","https://openalex.org/W2529517309","https://openalex.org/W2559588208","https://openalex.org/W2569284525","https://openalex.org/W2586360538","https://openalex.org/W2624135745","https://openalex.org/W2758005814","https://openalex.org/W3030218091"],"related_works":["https://openalex.org/W2391004329","https://openalex.org/W1968369492","https://openalex.org/W2043102924","https://openalex.org/W2995607319","https://openalex.org/W1222064643","https://openalex.org/W2761818597","https://openalex.org/W2624135745","https://openalex.org/W1543301402","https://openalex.org/W2315403509","https://openalex.org/W3139084279"],"abstract_inverted_index":{"Metagenomic":[0],"and":[1,16,28,61,84,114,148,157],"metatranscriptomic":[2,85,115,158],"sequencing":[3],"approaches":[4],"are":[5],"more":[6],"frequently":[7],"being":[8],"used":[9,23],"to":[10,13,24,54,123,143],"link":[11],"microbiota":[12,32],"important":[14,68],"diseases":[15],"ecological":[17],"changes.":[18],"Many":[19],"analyses":[20,43,53,86],"have":[21],"been":[22],"compare":[25],"the":[26,56,90,118,128],"taxonomic":[27],"functional":[29,150],"profiles":[30],"of":[31,41,72,79,94,112,120],"across":[33],"habitats":[34],"or":[35,92],"individuals.":[36],"While":[37],"a":[38,95],"large":[39],"portion":[40],"metagenomic":[42,52,83,113,156],"focus":[44],"on":[45],"species-level":[46],"profiling,":[47],"some":[48],"studies":[49],"use":[50],"strain-level":[51],"investigate":[55],"relationship":[57],"between":[58],"specific":[59],"strains":[60],"certain":[62],"circumstances.":[63],"Metatranscriptomic":[64],"analysis":[65],"provides":[66],"another":[67],"insight":[69],"into":[70],"activities":[71],"genes":[73,102],"by":[74],"examining":[75],"gene":[76,97,151],"expression":[77],"levels":[78],"microbiota.":[80],"Hence,":[81],"combining":[82],"will":[87],"help":[88],"understand":[89],"activity":[91],"enrichment":[93],"given":[96],"set,":[98],"such":[99],"as":[100],"drug-resistant":[101],"among":[103],"microbiome":[104,133],"samples.":[105],"Here,":[106],"we":[107,136],"summarize":[108],"existing":[109],"bioinformatics":[110],"tools":[111,130],"data":[116],"analysis,":[117],"purpose":[119],"which":[121],"is":[122],"assist":[124],"researchers":[125],"in":[126],"deciding":[127],"appropriate":[129],"for":[131,154],"their":[132],"studies.":[134],"Additionally,":[135],"propose":[137],"an":[138],"Integrated":[139],"Meta-Function":[140],"mapping":[141,152],"pipeline":[142],"incorporate":[144],"various":[145],"reference":[146],"databases":[147],"accelerate":[149],"procedures":[153],"both":[155],"analyses.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-13T08:25:38.343686","created_date":"2025-10-10T00:00:00"}
