{"id":"https://openalex.org/W4323046497","doi":"https://doi.org/10.1186/s12859-022-05121-y","title":"Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly","display_name":"Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly","publication_year":2023,"publication_date":"2023-03-03","ids":{"openalex":"https://openalex.org/W4323046497","doi":"https://doi.org/10.1186/s12859-022-05121-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/36869298"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-05121-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-05121-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05121-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05121-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025611353","display_name":"Arianna I. Krinos","orcid":"https://orcid.org/0000-0001-9767-8392"},"institutions":[{"id":"https://openalex.org/I1302918504","display_name":"Planetary Science Institute","ror":"https://ror.org/05vvg9554","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1302918504"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]},{"id":"https://openalex.org/I66958751","display_name":"Woods Hole Oceanographic Institution","ror":"https://ror.org/03zbnzt98","country_code":"US","type":"funder","lineage":["https://openalex.org/I66958751"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Arianna I. Krinos","raw_affiliation_strings":["Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. akrinos@mit.edu","Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA. akrinos@mit.edu","MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA. akrinos@mit.edu","MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA"],"raw_orcid":"https://orcid.org/0000-0001-9767-8392","affiliations":[{"raw_affiliation_string":"Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. akrinos@mit.edu","institution_ids":["https://openalex.org/I66958751"]},{"raw_affiliation_string":"Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA. akrinos@mit.edu","institution_ids":["https://openalex.org/I63966007","https://openalex.org/I1302918504"]},{"raw_affiliation_string":"MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA. akrinos@mit.edu","institution_ids":["https://openalex.org/I66958751"]},{"raw_affiliation_string":"MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA","institution_ids":["https://openalex.org/I66958751"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033853446","display_name":"Natalie R. Cohen","orcid":"https://orcid.org/0000-0001-6156-9186"},"institutions":[{"id":"https://openalex.org/I122690471","display_name":"Skidaway Institute of Oceanography","ror":"https://ror.org/03hjqxp26","country_code":"US","type":"education","lineage":["https://openalex.org/I122690471","https://openalex.org/I165733156"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Natalie R. Cohen","raw_affiliation_strings":["Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA"],"raw_orcid":"https://orcid.org/0000-0001-6156-9186","affiliations":[{"raw_affiliation_string":"Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA","institution_ids":["https://openalex.org/I165733156","https://openalex.org/I122690471"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081551197","display_name":"Michael J. Follows","orcid":"https://orcid.org/0000-0002-3102-0341"},"institutions":[{"id":"https://openalex.org/I1302918504","display_name":"Planetary Science Institute","ror":"https://ror.org/05vvg9554","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1302918504"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael J. Follows","raw_affiliation_strings":["Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I1302918504","https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013626144","display_name":"Harriet Alexander","orcid":"https://orcid.org/0000-0003-1308-8008"},"institutions":[{"id":"https://openalex.org/I66958751","display_name":"Woods Hole Oceanographic Institution","ror":"https://ror.org/03zbnzt98","country_code":"US","type":"funder","lineage":["https://openalex.org/I66958751"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Harriet Alexander","raw_affiliation_strings":["Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. halexander@whoi.edu","Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA"],"raw_orcid":"https://orcid.org/0000-0003-1308-8008","affiliations":[{"raw_affiliation_string":"Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. halexander@whoi.edu","institution_ids":["https://openalex.org/I66958751"]},{"raw_affiliation_string":"Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA","institution_ids":["https://openalex.org/I66958751"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025611353"],"corresponding_institution_ids":["https://openalex.org/I1302918504","https://openalex.org/I63966007","https://openalex.org/I66958751"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.3083,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.79801358,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"24","issue":"1","first_page":"74","last_page":"74"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5364000201225281,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5364000201225281,"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/T11879","display_name":"Protist diversity and phylogeny","score":0.28790000081062317,"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":0.05660000070929527,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44621333479881287},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3956674337387085},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39074644446372986}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44621333479881287},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3956674337387085},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39074644446372986}],"mesh":[{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","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":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-022-05121-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-05121-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05121-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36869298","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36869298","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9983209","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9983209","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9983209/pdf/12859_2022_Article_5121.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:dd29ee99fff2429cb05f76e035611d18","is_oa":true,"landing_page_url":"https://doaj.org/article/dd29ee99fff2429cb05f76e035611d18","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-36 (2023)","raw_type":"article"},{"id":"pmh:oai:osti.gov:1959841","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1959841","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1186/s12859-022-05121-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-05121-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05121-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/14","display_name":"Life below water","score":0.699999988079071}],"awards":[{"id":"https://openalex.org/G1120226135","display_name":null,"funder_award_id":"OCE-1948025","funder_id":"https://openalex.org/F4320332171","funder_display_name":"Directorate for Geosciences"},{"id":"https://openalex.org/G1924631527","display_name":null,"funder_award_id":"549931","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2077327224","display_name":null,"funder_award_id":"549931","funder_id":"https://openalex.org/F4320306164","funder_display_name":"Simons Foundation"},{"id":"https://openalex.org/G3265013047","display_name":null,"funder_award_id":"931886","funder_id":"https://openalex.org/F4320306164","funder_display_name":"Simons Foundation"},{"id":"https://openalex.org/G428142873","display_name":null,"funder_award_id":"DE-SC0020347","funder_id":"https://openalex.org/F4320338285","funder_display_name":"Krell Institute"},{"id":"https://openalex.org/G4980030888","display_name":"Collaborative Research: Defining the role of the pan genome in Emiliania huxleyi ecology and biogeography","funder_award_id":"1948025","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5564850799","display_name":null,"funder_award_id":"DE-SC0020347","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320332171","display_name":"Directorate for Geosciences","ror":"https://ror.org/05p847d66"},{"id":"https://openalex.org/F4320338285","display_name":"Krell Institute","ror":"https://ror.org/02pas9b60"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4323046497.pdf"},"referenced_works_count":93,"referenced_works":["https://openalex.org/W1578104218","https://openalex.org/W1650969180","https://openalex.org/W1900937478","https://openalex.org/W1966116114","https://openalex.org/W1984156791","https://openalex.org/W1986034711","https://openalex.org/W1989142927","https://openalex.org/W1993920730","https://openalex.org/W1995875735","https://openalex.org/W1996168018","https://openalex.org/W1997424630","https://openalex.org/W2011657487","https://openalex.org/W2019619926","https://openalex.org/W2020501518","https://openalex.org/W2048783574","https://openalex.org/W2050463578","https://openalex.org/W2055043387","https://openalex.org/W2062535783","https://openalex.org/W2070585151","https://openalex.org/W2074707589","https://openalex.org/W2083266238","https://openalex.org/W2101072984","https://openalex.org/W2109218242","https://openalex.org/W2109555511","https://openalex.org/W2109848222","https://openalex.org/W2112604975","https://openalex.org/W2113679889","https://openalex.org/W2114548104","https://openalex.org/W2115501618","https://openalex.org/W2126419817","https://openalex.org/W2127175247","https://openalex.org/W2131271579","https://openalex.org/W2137126604","https://openalex.org/W2142678478","https://openalex.org/W2149554155","https://openalex.org/W2153116581","https://openalex.org/W2155628349","https://openalex.org/W2158714788","https://openalex.org/W2160969485","https://openalex.org/W2226047933","https://openalex.org/W2233705203","https://openalex.org/W2239988481","https://openalex.org/W2282315506","https://openalex.org/W2341599515","https://openalex.org/W2500607307","https://openalex.org/W2519890620","https://openalex.org/W2554677631","https://openalex.org/W2560164530","https://openalex.org/W2592811885","https://openalex.org/W2599417231","https://openalex.org/W2759833325","https://openalex.org/W2766239397","https://openalex.org/W2784434641","https://openalex.org/W2800231416","https://openalex.org/W2802954574","https://openalex.org/W2898402099","https://openalex.org/W2944627925","https://openalex.org/W2949841808","https://openalex.org/W2950464315","https://openalex.org/W2950954328","https://openalex.org/W2951149542","https://openalex.org/W2951182431","https://openalex.org/W2951254987","https://openalex.org/W2952126099","https://openalex.org/W2953008890","https://openalex.org/W2963275748","https://openalex.org/W2966039341","https://openalex.org/W2970881455","https://openalex.org/W2972131171","https://openalex.org/W2983947643","https://openalex.org/W2988396470","https://openalex.org/W3003257820","https://openalex.org/W3012326391","https://openalex.org/W3012927825","https://openalex.org/W3025757981","https://openalex.org/W3047916956","https://openalex.org/W3092559221","https://openalex.org/W3103145119","https://openalex.org/W3119078903","https://openalex.org/W3130090991","https://openalex.org/W3131680021","https://openalex.org/W3169281300","https://openalex.org/W3174779269","https://openalex.org/W3183713734","https://openalex.org/W3209194677","https://openalex.org/W4214525752","https://openalex.org/W4225434086","https://openalex.org/W4226515274","https://openalex.org/W4254687493","https://openalex.org/W4283640995","https://openalex.org/W4288369446","https://openalex.org/W4388575241","https://openalex.org/W4399648717"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189"],"abstract_inverted_index":{"BACKGROUND:":[0],"Diverse":[1],"communities":[2,32],"of":[3,13,39,46,53,83,147,163],"microbial":[4,59],"eukaryotes":[5],"in":[6,58],"the":[7,37,81,84,161],"global":[8],"ocean":[9],"provide":[10],"a":[11,63,73,125,156],"variety":[12],"essential":[14],"ecosystem":[15],"services,":[16],"from":[17,139,172],"primary":[18],"production":[19],"and":[20,79,89,107,136,150,168],"carbon":[21],"flow":[22],"through":[23,36],"trophic":[24],"transfer":[25],"to":[26,86,159],"cooperation":[27],"via":[28],"symbioses.":[29],"Increasingly,":[30],"these":[31],"are":[33],"being":[34],"understood":[35],"lens":[38],"omics":[40],"tools,":[41],"which":[42],"enable":[43],"high-throughput":[44],"processing":[45],"diverse":[47],"communities.":[48],"Metatranscriptomics":[49],"offers":[50],"an":[51,98,140],"understanding":[52],"near":[54],"real-time":[55],"gene":[56],"expression":[57,93],"eukaryotic":[60,76,91,129,173],"communities,":[61],"providing":[62],"window":[64],"into":[65],"community":[66,165],"metabolic":[67],"activity.":[68],"RESULTS:":[69],"Here":[70],"we":[71],"present":[72],"workflow":[74],"for":[75,101,105],"metatranscriptome":[77,118,130,148],"assembly,":[78],"validate":[80],"ability":[82],"pipeline":[85],"recapitulate":[87],"real":[88],"manufactured":[90],"community-level":[92],"data.":[94],"We":[95,110,122],"also":[96],"include":[97],"open-source":[99],"tool":[100],"simulating":[102],"environmental":[103],"metatranscriptomes":[104],"testing":[106],"validation":[108,146],"purposes.":[109],"reanalyze":[111],"previously":[112],"published":[113],"metatranscriptomic":[114],"datasets":[115],"using":[116],"our":[117,164],"analysis":[119],"approach.":[120],"CONCLUSION:":[121],"determined":[123],"that":[124],"multi-assembler":[126],"approach":[127],"improves":[128],"assembly":[131,149],"based":[132],"on":[133],"recapitulated":[134],"taxonomic":[135],"functional":[137,169],"annotations":[138],"in-silico":[141],"mock":[142],"community.":[143],"The":[144],"systematic":[145],"annotation":[151],"methods":[152],"provided":[153],"here":[154],"is":[155],"necessary":[157],"step":[158],"assess":[160],"fidelity":[162],"composition":[166],"measurements":[167],"content":[170],"assignments":[171],"metatranscriptomes.":[174]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
