{"id":"https://openalex.org/W4310696458","doi":"https://doi.org/10.1093/bioinformatics/btac781","title":"Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories","display_name":"Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories","publication_year":2022,"publication_date":"2022-12-02","ids":{"openalex":"https://openalex.org/W4310696458","doi":"https://doi.org/10.1093/bioinformatics/btac781","pmid":"https://pubmed.ncbi.nlm.nih.gov/36469345"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac781","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac781","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac781/48520839/btac781.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac781/48520839/btac781.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087851342","display_name":"Jelena Banjac","orcid":"https://orcid.org/0000-0001-7373-4150"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Jelena Banjac","raw_affiliation_strings":["Data Science, Swiss Federal Institute of Technology Lausanne (EPFL) , Lausanne 1015, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-7373-4150","affiliations":[{"raw_affiliation_string":"Data Science, Swiss Federal Institute of Technology Lausanne (EPFL) , Lausanne 1015, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003626384","display_name":"Norbert Sprenger","orcid":"https://orcid.org/0000-0003-4880-2750"},"institutions":[{"id":"https://openalex.org/I4210112383","display_name":"Nestl\u00e9 (Switzerland)","ror":"https://ror.org/01v5xwf23","country_code":"CH","type":"company","lineage":["https://openalex.org/I4210112383"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Norbert Sprenger","raw_affiliation_strings":["Department of Gastrointestinal Health, Nestl\u00e9 Institute of Health Sciences, Nestl\u00e9 Research, Soci\u00e9t\u00e9 des Produits Nestl\u00e9 S.A , Lausanne 1000, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-4880-2750","affiliations":[{"raw_affiliation_string":"Department of Gastrointestinal Health, Nestl\u00e9 Institute of Health Sciences, Nestl\u00e9 Research, Soci\u00e9t\u00e9 des Produits Nestl\u00e9 S.A , Lausanne 1000, Switzerland","institution_ids":["https://openalex.org/I4210112383"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055986987","display_name":"Shaillay Kumar Dogra","orcid":"https://orcid.org/0000-0002-2987-4313"},"institutions":[{"id":"https://openalex.org/I4210112383","display_name":"Nestl\u00e9 (Switzerland)","ror":"https://ror.org/01v5xwf23","country_code":"CH","type":"company","lineage":["https://openalex.org/I4210112383"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Shaillay Kumar Dogra","raw_affiliation_strings":["Department of Gastrointestinal Health, Nestl\u00e9 Institute of Health Sciences, Nestl\u00e9 Research, Soci\u00e9t\u00e9 des Produits Nestl\u00e9 S.A , Lausanne 1000, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-2987-4313","affiliations":[{"raw_affiliation_string":"Department of Gastrointestinal Health, Nestl\u00e9 Institute of Health Sciences, Nestl\u00e9 Research, Soci\u00e9t\u00e9 des Produits Nestl\u00e9 S.A , Lausanne 1000, Switzerland","institution_ids":["https://openalex.org/I4210112383"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5055986987"],"corresponding_institution_ids":["https://openalex.org/I4210112383"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5493,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.61503792,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9641000032424927,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9641000032424927,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.007899999618530273,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.0026000000070780516,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.8424248695373535},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.8156088590621948},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7100784778594971},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6001075506210327},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.505129873752594},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4870193600654602},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.4681330621242523},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.43722668290138245},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.4251863360404968},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4244958758354187},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3316892385482788},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32837170362472534},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2855972647666931},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2752060294151306},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18025898933410645},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12660124897956848}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.8424248695373535},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8156088590621948},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7100784778594971},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6001075506210327},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.505129873752594},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4870193600654602},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.4681330621242523},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.43722668290138245},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.4251863360404968},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4244958758354187},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3316892385482788},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32837170362472534},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2855972647666931},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2752060294151306},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18025898933410645},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12660124897956848},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac781","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac781","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac781/48520839/btac781.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36469345","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36469345","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9825749","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825749","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac781","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac781","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac781/48520839/btac781.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4310696458.pdf","grobid_xml":"https://content.openalex.org/works/W4310696458.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2026006003","https://openalex.org/W2128331389","https://openalex.org/W2166562121","https://openalex.org/W2788488000","https://openalex.org/W2897558112","https://openalex.org/W2999615587","https://openalex.org/W3087727054"],"related_works":["https://openalex.org/W2951327715","https://openalex.org/W2800642158","https://openalex.org/W3209887338","https://openalex.org/W4385545408","https://openalex.org/W1222064643","https://openalex.org/W2474302342","https://openalex.org/W2969529002","https://openalex.org/W4386448373","https://openalex.org/W4296029826","https://openalex.org/W3118380721"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,159,191],"gut":[2],"microbiome":[3,54,62,110,142],"changes":[4,16],"rapidly":[5],"under":[6],"the":[7,59,75,80,141,176,196,199],"influence":[8],"of":[9,52,61,133,175,202],"different":[10,129],"factors":[11],"such":[12,28,64],"as":[13,65,67,69],"age,":[14],"dietary":[15],"or":[17],"medications":[18],"to":[19,43,148,152,198],"name":[20],"just":[21],"a":[22,32,153],"few.":[23],"To":[24],"analyze":[25],"and":[26,41,50,73,89,97,120,131,144,165,189,195],"understand":[27],"changes,":[29],"we":[30],"present":[31],"Microbiome":[33,81,177,203],"Toolbox.":[34],"We":[35],"implemented":[36,166],"several":[37],"methods":[38,84,188],"for":[39,47,85,103,125,183],"analysis":[40,88,124],"exploration":[42],"provide":[44],"interactive":[45,200],"visualizations":[46],"easy":[48],"comprehension":[49],"reporting":[51],"longitudinal":[53,137],"data.":[55],"RESULTS:":[56],"Based":[57],"on":[58,140,207],"abundance":[60],"features":[63],"taxa":[66],"well":[68],"functional":[70],"capacity":[71],"modules,":[72],"with":[74,113,186],"corresponding":[76],"metadata":[77],"per":[78],"sample,":[79],"Toolbox":[82,204],"includes":[83],"(i)":[86],"data":[87,92,213],"exploration,":[90],"(ii)":[91],"preparation":[93],"including":[94],"dataset-specific":[95],"preprocessing":[96],"transformation,":[98],"(iii)":[99],"best":[100],"feature":[101,114],"selection":[102],"log-ratio":[104],"denominators,":[105],"(iv)":[106],"two-group":[107],"analysis,":[108],"(v)":[109],"trajectory":[111,143],"prediction":[112],"importance":[115],"over":[116],"time,":[117],"(vi)":[118],"spline":[119],"linear":[121],"regression":[122],"statistical":[123],"testing":[126],"universality":[127],"across":[128],"groups":[130],"differentiation":[132],"two":[134],"trajectories,":[135],"(vii)":[136],"anomaly":[138,150],"detection":[139],"(viii)":[145],"simulated":[146],"intervention":[147],"return":[149],"back":[151],"reference":[154],"trajectory.":[155],"AVAILABILITY":[156],"AND":[157],"IMPLEMENTATION:":[158],"software":[160],"tools":[161],"are":[162,205,214],"open":[163],"source":[164],"in":[167,172],"Python.":[168],"For":[169],"developers":[170],"interested":[171],"additional":[173],"functionality":[174],"Toolbox,":[178],"it":[179],"is":[180],"modular":[181],"allowing":[182],"further":[184],"extension":[185],"custom":[187],"analysis.":[190],"code,":[192],"python":[193],"package":[194],"link":[197],"dashboard":[201],"available":[206,215],"GitHub":[208],"https://github.com/JelenaBanjac/microbiome-toolbox.":[209],"SUPPLEMENTARY":[210],"INFORMATION:":[211],"Supplementary":[212],"at":[216],"Bioinformatics":[217],"online.":[218]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}