{"id":"https://openalex.org/W4403883766","doi":"https://doi.org/10.1371/journal.pcbi.1012925","title":"Learning and teaching biological data science in the Bioconductor community","display_name":"Learning and teaching biological data science in the Bioconductor community","publication_year":2025,"publication_date":"2025-04-22","ids":{"openalex":"https://openalex.org/W4403883766","doi":"https://doi.org/10.1371/journal.pcbi.1012925","pmid":"https://pubmed.ncbi.nlm.nih.gov/40160449"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012925","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012925","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1012925","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016517478","display_name":"Jenny Drnevich","orcid":"https://orcid.org/0000-0002-1401-8311"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jenny Drnevich","raw_affiliation_strings":["Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-1401-8311","affiliations":[{"raw_affiliation_string":"Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050762631","display_name":"Frederick J. Tan","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Frederick J. Tan","raw_affiliation_strings":["Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033217984","display_name":"Fabricio Almeida\u2010Silva","orcid":"https://orcid.org/0000-0002-5314-2964"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I4210098178","display_name":"VIB-UGent Center for Plant Systems Biology","ror":"https://ror.org/01qnqmc89","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I32597200","https://openalex.org/I4210098178"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Fabricio Almeida-Silva","raw_affiliation_strings":["Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium","VIB Center for Plant Systems Biology, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"VIB Center for Plant Systems Biology, Ghent, Belgium","institution_ids":["https://openalex.org/I4210098178"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071137998","display_name":"Robert Castelo","orcid":"https://orcid.org/0000-0003-2229-4508"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Robert Castelo","raw_affiliation_strings":["Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0003-2229-4508","affiliations":[{"raw_affiliation_string":"Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082180580","display_name":"Aed\u00edn C. Culhane","orcid":"https://orcid.org/0000-0002-1395-9734"},"institutions":[{"id":"https://openalex.org/I230495080","display_name":"University of Limerick","ror":"https://ror.org/00a0n9e72","country_code":"IE","type":"education","lineage":["https://openalex.org/I230495080"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Aedin C. Culhane","raw_affiliation_strings":["Limerick Digital Cancer Research Centre, School of Medicine, University of Limerick, Limerick, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Limerick Digital Cancer Research Centre, School of Medicine, University of Limerick, Limerick, Ireland","institution_ids":["https://openalex.org/I230495080"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005450827","display_name":"Sean Davis","orcid":"https://orcid.org/0000-0002-8991-6458"},"institutions":[{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sean Davis","raw_affiliation_strings":["University of Colorado Anschutz School of Medicine, Denver, Colorado, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Colorado Anschutz School of Medicine, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077384369","display_name":"Maria Doyle","orcid":"https://orcid.org/0000-0003-4847-8436"},"institutions":[{"id":"https://openalex.org/I230495080","display_name":"University of Limerick","ror":"https://ror.org/00a0n9e72","country_code":"IE","type":"education","lineage":["https://openalex.org/I230495080"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Maria A. Doyle","raw_affiliation_strings":["Limerick Digital Cancer Research Centre, School of Medicine, University of Limerick, Limerick, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Limerick Digital Cancer Research Centre, School of Medicine, University of Limerick, Limerick, Ireland","institution_ids":["https://openalex.org/I230495080"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021558653","display_name":"Ludwig Geistlinger","orcid":"https://orcid.org/0000-0002-2495-5464"},"institutions":[{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ludwig Geistlinger","raw_affiliation_strings":["Core for Computational Biomedicine, Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Core for Computational Biomedicine, Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210155419"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086583333","display_name":"Andrew R. Ghazi","orcid":"https://orcid.org/0000-0002-8888-946X"},"institutions":[{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew R. Ghazi","raw_affiliation_strings":["Core for Computational Biomedicine, Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Core for Computational Biomedicine, Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210155419"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003674456","display_name":"Susan Holmes","orcid":"https://orcid.org/0000-0002-2208-8168"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Susan Holmes","raw_affiliation_strings":["Statistics Department, Stanford University, Stanford, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2208-8168","affiliations":[{"raw_affiliation_string":"Statistics Department, Stanford University, Stanford, California, United States of America","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082648063","display_name":"Leo Lahti","orcid":"https://orcid.org/0000-0001-5537-637X"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Leo Lahti","raw_affiliation_strings":["Department of Computing, University of Turku, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090394262","display_name":"Alexandru Mahmoud","orcid":"https://orcid.org/0000-0002-3779-492X"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexandru Mahmoud","raw_affiliation_strings":["Channing Division of Network Medicine, Harvard Medical School, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Channing Division of Network Medicine, Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034175804","display_name":"Kozo Nishida","orcid":"https://orcid.org/0000-0001-8501-7319"},"institutions":[{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kozo Nishida","raw_affiliation_strings":["RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo, Japan","institution_ids":["https://openalex.org/I4210116810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063530956","display_name":"Marcel Ramos","orcid":"https://orcid.org/0000-0002-3242-0582"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcel Ramos","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3242-0582","affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, New York, United States of America","institution_ids":["https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023984745","display_name":"K\u00e9vin Rue-Albrecht","orcid":"https://orcid.org/0000-0003-3899-3872"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210110594","display_name":"MRC Weatherall Institute of Molecular Medicine","ror":"https://ror.org/01q496a73","country_code":"GB","type":"facility","lineage":["https://openalex.org/I40120149","https://openalex.org/I4210087105","https://openalex.org/I4210110594","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kevin Rue-Albrecht","raw_affiliation_strings":["MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-3899-3872","affiliations":[{"raw_affiliation_string":"MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom","institution_ids":["https://openalex.org/I4210110594","https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008096194","display_name":"David Shih","orcid":"https://orcid.org/0000-0002-9802-4937"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"David J. H. Shih","raw_affiliation_strings":["School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064560423","display_name":"Laurent Gatto","orcid":"https://orcid.org/0000-0002-1520-2268"},"institutions":[{"id":"https://openalex.org/I4210114657","display_name":"de Duve Institute","ror":"https://ror.org/022em3k58","country_code":"BE","type":"facility","lineage":["https://openalex.org/I4210114657"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Laurent Gatto","raw_affiliation_strings":["Computational Biology and Bioinformatics Unit, de Duve Institute, UCLouvain, Brussels, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-1520-2268","affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics Unit, de Duve Institute, UCLouvain, Brussels, Belgium","institution_ids":["https://openalex.org/I4210114657"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008885844","display_name":"Charlotte Soneson","orcid":"https://orcid.org/0000-0003-3833-2169"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I860889466","display_name":"Friedrich Miescher Institute","ror":"https://ror.org/01bmjkv45","country_code":"CH","type":"facility","lineage":["https://openalex.org/I860889466"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Charlotte Soneson","raw_affiliation_strings":["Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-3833-2169","affiliations":[{"raw_affiliation_string":"Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland","institution_ids":["https://openalex.org/I860889466"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":9,"institutions_distinct_count":18,"corresponding_author_ids":["https://openalex.org/A5016517478"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.9959,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.83812926,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"21","issue":"4","first_page":"e1012925","last_page":"e1012925"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9951000213623047,"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":0.9951000213623047,"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":0.9925000071525574,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9879999756813049,"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/bioconductor","display_name":"Bioconductor","score":0.8857535123825073},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.6562280654907227},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5636350512504578},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5553939938545227},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5092552900314331},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.48193883895874023},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42074185609817505},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.20751407742500305},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17570999264717102}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.8857535123825073},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.6562280654907227},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5636350512504578},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5553939938545227},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5092552900314331},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.48193883895874023},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42074185609817505},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.20751407742500305},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17570999264717102},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":10,"locations":[{"id":"doi:10.1371/journal.pcbi.1012925","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012925","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40160449","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40160449","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":"ArXiv","raw_type":null},{"id":"pmid:40261894","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40261894","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:repositori-api.upf.edu:10230/70600","is_oa":true,"landing_page_url":"http://hdl.handle.net/10230/70600","pdf_url":null,"source":{"id":"https://openalex.org/S4306402615","display_name":"Repositori digital de la UPF (Universitat Pompeu Fabra)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I170486558","host_organization_name":"Universitat Pompeu Fabra","host_organization_lineage":["https://openalex.org/I170486558"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:arXiv.org:2410.01351","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2410.01351","pdf_url":"https://arxiv.org/pdf/2410.01351","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":null,"raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12013867","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12013867","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:ef1673d8988b462996f30fcffa1e788d","is_oa":true,"landing_page_url":"https://doaj.org/article/ef1673d8988b462996f30fcffa1e788d","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":"PLoS Computational Biology, Vol 21, Iss 4, p e1012925 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:10763513","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11952580","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,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:4f04e42c-c81d-4172-bc9a-176f07c782fb","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Jisc Publications Router","raw_type":"http://purl.org/coar/resource_type/c_dcae04bc"},{"id":"pmh:oai:www.utupub.fi:10024/185527","is_oa":false,"landing_page_url":"https://www.utupub.fi/handle/10024/185527","pdf_url":null,"source":null,"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:10.1371/journal.pcbi.1012925","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012925","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1554348260","display_name":null,"funder_award_id":"2022-311145","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"},{"id":"https://openalex.org/G2024017800","display_name":null,"funder_award_id":"330887","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G3485400596","display_name":null,"funder_award_id":"2021-237919","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"},{"id":"https://openalex.org/G4855324266","display_name":null,"funder_award_id":"952914","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6066146323","display_name":null,"funder_award_id":"2024- 342820","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"},{"id":"https://openalex.org/G8022961113","display_name":"Eco-evolutionary mechanisms underlying critical transitions in microbial communities","funder_award_id":"330887","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320306192","display_name":"Silicon Valley Community Foundation","ror":"https://ror.org/001ader08"},{"id":"https://openalex.org/F4320310389","display_name":"Novartis Foundation","ror":"https://ror.org/02f9zrr09"},{"id":"https://openalex.org/F4320315474","display_name":"Chan Zuckerberg Initiative","ror":"https://ror.org/02qenvm24"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1533335653","https://openalex.org/W1973094248","https://openalex.org/W2069089843","https://openalex.org/W2131478115","https://openalex.org/W2160697532","https://openalex.org/W2563052372","https://openalex.org/W2618433578","https://openalex.org/W2800392236","https://openalex.org/W2923101443","https://openalex.org/W2953425107","https://openalex.org/W2989807288","https://openalex.org/W2990427812","https://openalex.org/W4212871932","https://openalex.org/W4226051960","https://openalex.org/W4235157788","https://openalex.org/W4237164438","https://openalex.org/W4240098044","https://openalex.org/W4245250485","https://openalex.org/W4308336157","https://openalex.org/W4313880130","https://openalex.org/W4362737480","https://openalex.org/W4385759320","https://openalex.org/W4388522104","https://openalex.org/W4398182689","https://openalex.org/W4399679431","https://openalex.org/W4402902773","https://openalex.org/W4408610678"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2011682793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W2978247079","https://openalex.org/W2140163842","https://openalex.org/W2148708580","https://openalex.org/W2166887457","https://openalex.org/W2982252354","https://openalex.org/W2357879326"],"abstract_inverted_index":{"Modern":[0],"biological":[1,15],"research":[2],"is":[3],"increasingly":[4],"data-intensive,":[5],"leading":[6],"to":[7],"a":[8,48],"growing":[9],"demand":[10],"for":[11,51],"effective":[12],"training":[13],"in":[14,56],"data":[16,42],"science.":[17],"In":[18],"this":[19],"article,":[20],"we":[21],"provide":[22],"an":[23],"overview":[24],"of":[25],"key":[26],"resources":[27],"and":[28,54],"best":[29],"practices":[30],"available":[31],"within":[32],"the":[33,57],"Bioconductor":[34],"project-an":[35],"open-source":[36],"software":[37],"community":[38],"focused":[39],"on":[40],"omics":[41],"analysis.":[43],"This":[44],"guide":[45],"serves":[46],"as":[47],"valuable":[49],"reference":[50],"both":[52],"learners":[53],"educators":[55],"field.":[58]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-05-11T08:15:01.531666","created_date":"2024-10-30T00:00:00"}
