{"id":"https://openalex.org/W2901677030","doi":"https://doi.org/10.1038/s41592-018-0229-2","title":"Deep generative modeling for single-cell transcriptomics","display_name":"Deep generative modeling for single-cell transcriptomics","publication_year":2018,"publication_date":"2018-11-21","ids":{"openalex":"https://openalex.org/W2901677030","doi":"https://doi.org/10.1038/s41592-018-0229-2","mag":"2901677030","pmid":"https://pubmed.ncbi.nlm.nih.gov/30504886"},"language":"en","primary_location":{"id":"doi:10.1038/s41592-018-0229-2","doi":"https://doi.org/10.1038/s41592-018-0229-2","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s41592-018-0229-2","pdf_url":null,"source":{"id":"https://openalex.org/S127827428","display_name":"Nature Methods","issn_l":"1548-7091","issn":["1548-7091","1548-7105"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Methods","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2018/10/14/292037.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021527800","display_name":"Romain Lopez","orcid":"https://orcid.org/0000-0003-0495-738X","observed_orcids":["https://orcid.org/0000-0003-0495-738X"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Romain Lopez","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060925308","display_name":"Jeffrey Regier","orcid":"https://orcid.org/0000-0002-1472-5235","observed_orcids":["https://orcid.org/0000-0002-1472-5235"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey Regier","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-1472-5235","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091824135","display_name":"Michael B. Cole","orcid":"https://orcid.org/0000-0002-5026-1714","observed_orcids":["https://orcid.org/0000-0002-5026-1714"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael B. Cole","raw_affiliation_strings":["Department of Physics, University of California, Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049812527","display_name":"Michael I. Jordan","orcid":"https://orcid.org/0000-0001-8935-817X","observed_orcids":["https://orcid.org/0000-0001-8935-817X"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael I. Jordan","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA","Department of Statistics, University of California, Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Statistics, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026299103","display_name":"Nir Yosef","orcid":"https://orcid.org/0000-0001-9004-1225","observed_orcids":["https://orcid.org/0000-0001-9004-1225"]},"institutions":[{"id":"https://openalex.org/I2802422659","display_name":"Ragon Institute of MGH, MIT and Harvard","ror":"https://ror.org/053r20n13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I48633490","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I4210100286","display_name":"Chan Zuckerberg Biohub San Francisco","ror":"https://ror.org/00knt4f32","country_code":"US","type":"facility","lineage":["https://openalex.org/I180670191","https://openalex.org/I4210100286","https://openalex.org/I4210121800","https://openalex.org/I95457486","https://openalex.org/I97018004"]},{"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/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nir Yosef","raw_affiliation_strings":["Chan Zuckerberg BioHub, San Francisco, CA, USA. niryosef@berkeley.edu","Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA. niryosef@berkeley.edu","Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA. niryosef@berkeley.edu","Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0001-9004-1225","affiliations":[{"raw_affiliation_string":"Chan Zuckerberg BioHub, San Francisco, CA, USA. niryosef@berkeley.edu","institution_ids":["https://openalex.org/I4210100286"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA. niryosef@berkeley.edu","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA. niryosef@berkeley.edu","institution_ids":["https://openalex.org/I2802422659","https://openalex.org/I63966007"]},{"raw_affiliation_string":"Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I2802422659"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5026299103"],"corresponding_institution_ids":["https://openalex.org/I2802422659","https://openalex.org/I4210100286","https://openalex.org/I63966007","https://openalex.org/I95457486"],"apc_list":{"value":12690,"currency":"USD","value_usd":12690},"apc_paid":null,"fwci":38.0733,"has_fulltext":false,"cited_by_count":2498,"citation_normalized_percentile":{"value":0.99917483,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"15","issue":"12","first_page":"1053","last_page":"1058"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T10885","display_name":"Gene expression and cancer classification","score":0.0,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0,"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/single-cell-transcriptomics","display_name":"single-cell transcriptomics","score":0.8769999742507935},{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.9129999876022339},{"id":"https://openalex.org/keywords/deep-generative-models","display_name":"deep generative models","score":0.843999981880188},{"id":"https://openalex.org/keywords/batch-effect-correction","display_name":"batch effect correction","score":0.7250000238418579},{"id":"https://openalex.org/keywords/differential-gene-expression","display_name":"differential gene expression","score":0.6420000195503235},{"id":"https://openalex.org/keywords/cell-clustering","display_name":"cell clustering","score":0.7749999761581421},{"id":"https://openalex.org/keywords/uncertainty-quantification","display_name":"uncertainty quantification","score":0.5979999899864197}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6860049366950989},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.643559455871582},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.532033383846283},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5216165781021118},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.47583484649658203},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4623635411262512},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.4598686397075653},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.45054730772972107},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.44695931673049927},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4436715245246887},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4362605810165405},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4219020903110504},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4202975034713745},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35656875371932983},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.2652164697647095},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006412","descriptor_name":"Hematopoietic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D006412","descriptor_name":"Hematopoietic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D006412","descriptor_name":"Hematopoietic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D006412","descriptor_name":"Hematopoietic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006412","descriptor_name":"Hematopoietic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006412","descriptor_name":"Hematopoietic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D007963","descriptor_name":"Leukocytes, Mononuclear","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D007963","descriptor_name":"Leukocytes, Mononuclear","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D007963","descriptor_name":"Leukocytes, Mononuclear","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D007963","descriptor_name":"Leukocytes, Mononuclear","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007963","descriptor_name":"Leukocytes, Mononuclear","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007963","descriptor_name":"Leukocytes, Mononuclear","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1038/s41592-018-0229-2","doi":"https://doi.org/10.1038/s41592-018-0229-2","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s41592-018-0229-2","pdf_url":null,"source":{"id":"https://openalex.org/S127827428","display_name":"Nature Methods","issn_l":"1548-7091","issn":["1548-7091","1548-7105"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Methods","raw_type":"journal-article"},{"id":"doi:10.1101/292037","doi":"https://doi.org/10.1101/292037","is_oa":true,"landing_page_url":"https://doi.org/10.1101/292037","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2018/10/14/292037.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:30504886","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30504886","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":"Nature methods","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:5508111","doi":null,"is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6289068","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6289068","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6289068","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nat Methods","raw_type":"Text"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt5777r2c7","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/5777r2c7","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nature methods, vol 15, iss 12","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt5777r2c7","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/5777r2c7","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nature Methods, vol 15, iss 12","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1101/292037","doi":"https://doi.org/10.1101/292037","is_oa":true,"landing_page_url":"https://doi.org/10.1101/292037","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2018/10/14/292037.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2525008928","display_name":"Emory R38 Research Training Program","funder_award_id":"R38AI140299","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3926501084","display_name":null,"funder_award_id":"U19AI090023","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320337253","display_name":"Instituto de Ciencias del Mar y Limnolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/040wdye98"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2901677030.pdf","grobid_xml":"https://content.openalex.org/works/W2901677030.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W839653734","https://openalex.org/W1792532087","https://openalex.org/W1956343362","https://openalex.org/W1967327758","https://openalex.org/W1979283544","https://openalex.org/W1981457167","https://openalex.org/W1981641790","https://openalex.org/W1987971958","https://openalex.org/W2059980695","https://openalex.org/W2081942683","https://openalex.org/W2102212449","https://openalex.org/W2106411961","https://openalex.org/W2107665951","https://openalex.org/W2114104545","https://openalex.org/W2122792339","https://openalex.org/W2152692691","https://openalex.org/W2179438025","https://openalex.org/W2190545194","https://openalex.org/W2209349785","https://openalex.org/W2225156818","https://openalex.org/W2273101790","https://openalex.org/W2342016684","https://openalex.org/W2460637143","https://openalex.org/W2510746232","https://openalex.org/W2553303224","https://openalex.org/W2555502666","https://openalex.org/W2555892463","https://openalex.org/W2572662684","https://openalex.org/W2582033455","https://openalex.org/W2605611918","https://openalex.org/W2612502013","https://openalex.org/W2612519453","https://openalex.org/W2618605105","https://openalex.org/W2739492614","https://openalex.org/W2740407064","https://openalex.org/W2741564801","https://openalex.org/W2783644856","https://openalex.org/W2788263670","https://openalex.org/W2794521141","https://openalex.org/W2800392236","https://openalex.org/W2802291136","https://openalex.org/W2805619986","https://openalex.org/W2949272108","https://openalex.org/W2951381561","https://openalex.org/W2951444558","https://openalex.org/W2951506174","https://openalex.org/W2952016241","https://openalex.org/W2953251392","https://openalex.org/W2963135265","https://openalex.org/W3024013192","https://openalex.org/W3104066961","https://openalex.org/W4211177544","https://openalex.org/W4213108508","https://openalex.org/W4255582690","https://openalex.org/W6977390765"],"related_works":["https://openalex.org/W2389214306","https://openalex.org/W2965083567","https://openalex.org/W4235240664","https://openalex.org/W1838576100","https://openalex.org/W2757182831","https://openalex.org/W2095886385","https://openalex.org/W2089704382","https://openalex.org/W1983399550","https://openalex.org/W2381031055","https://openalex.org/W2366070815"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":556},{"year":2025,"cited_by_count":489},{"year":2024,"cited_by_count":409},{"year":2023,"cited_by_count":311},{"year":2022,"cited_by_count":248},{"year":2021,"cited_by_count":239},{"year":2020,"cited_by_count":155},{"year":2019,"cited_by_count":80},{"year":2018,"cited_by_count":11}],"updated_date":"2026-10-15T10:00:46.086208","created_date":"2025-10-10T00:00:00"}
