{"id":"https://openalex.org/W4390099273","doi":"https://doi.org/10.1093/bioinformatics/btad766","title":"SOHPIE: statistical approach via pseudo-value information and estimation for differential network analysis of microbiome data","display_name":"SOHPIE: statistical approach via pseudo-value information and estimation for differential network analysis of microbiome data","publication_year":2023,"publication_date":"2023-12-22","ids":{"openalex":"https://openalex.org/W4390099273","doi":"https://doi.org/10.1093/bioinformatics/btad766","pmid":"https://pubmed.ncbi.nlm.nih.gov/38134422"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad766","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad766","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad766/54762900/btad766.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad766/54762900/btad766.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066569055","display_name":"Seungjun Ahn","orcid":"https://orcid.org/0000-0002-4816-8924"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Seungjun Ahn","raw_affiliation_strings":["Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai , New York, NY 10029, United States"],"raw_orcid":"https://orcid.org/0000-0002-4816-8924","affiliations":[{"raw_affiliation_string":"Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai , New York, NY 10029, United States","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003292914","display_name":"Somnath Datta","orcid":"https://orcid.org/0000-0003-4381-1842"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Somnath Datta","raw_affiliation_strings":["Department of Biostatistics, University of Florida , Gainesville, FL 32610, United States"],"raw_orcid":"https://orcid.org/0000-0003-4381-1842","affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Florida , Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5066569055"],"corresponding_institution_ids":["https://openalex.org/I98704320"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2819,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.64336098,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"40","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":0.9541000127792358,"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":0.9541000127792358,"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/T13283","display_name":"Mental Health Research Topics","score":0.005100000184029341,"subfield":{"id":"https://openalex.org/subfields/3205","display_name":"Experimental and Cognitive Psychology"},"field":{"id":"https://openalex.org/fields/32","display_name":"Psychology"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11337","display_name":"Tryptophan and brain disorders","score":0.0032999999821186066,"subfield":{"id":"https://openalex.org/subfields/2803","display_name":"Biological Psychiatry"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/covariate","display_name":"Covariate","score":0.8772549629211426},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.7474381327629089},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5795572996139526},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5788794755935669},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.49643856287002563},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48447299003601074},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.45908987522125244},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.4496243894100189},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4378528594970703},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3481803238391876},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3430885076522827},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.22337126731872559},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22205448150634766},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.20061072707176208},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17879101634025574}],"concepts":[{"id":"https://openalex.org/C119043178","wikidata":"https://www.wikidata.org/wiki/Q320723","display_name":"Covariate","level":2,"score":0.8772549629211426},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.7474381327629089},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5795572996139526},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5788794755935669},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.49643856287002563},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48447299003601074},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.45908987522125244},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.4496243894100189},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4378528594970703},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3481803238391876},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3430885076522827},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.22337126731872559},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22205448150634766},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.20061072707176208},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17879101634025574},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0}],"mesh":[{"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":"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":"D006801","descriptor_name":"Humans","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":"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":"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},{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad766","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad766","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad766/54762900/btad766.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:38134422","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38134422","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:10807904","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10807904","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10807904/pdf/btad766.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad766","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad766","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad766/54762900/btad766.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[{"id":"https://openalex.org/G1722358303","display_name":null,"funder_award_id":"NIH P30CA196521","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2733339061","display_name":null,"funder_award_id":"P30CA196521-01","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2950618573","display_name":null,"funder_award_id":"P30CA196521","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G335978624","display_name":null,"funder_award_id":"P30CA196521","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G94896523","display_name":null,"funder_award_id":"P30 CA196521","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"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":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390099273.pdf"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1577822803","https://openalex.org/W1864161604","https://openalex.org/W1891411045","https://openalex.org/W2105381419","https://openalex.org/W2113977541","https://openalex.org/W2115088843","https://openalex.org/W2125826054","https://openalex.org/W2131186249","https://openalex.org/W2144494558","https://openalex.org/W2152701363","https://openalex.org/W2794407684","https://openalex.org/W2802324602","https://openalex.org/W2904250115","https://openalex.org/W2982906277","https://openalex.org/W2995649573","https://openalex.org/W3022211185","https://openalex.org/W3035423941","https://openalex.org/W3106889297","https://openalex.org/W3110476256","https://openalex.org/W3128701120","https://openalex.org/W3158506552","https://openalex.org/W4392896955"],"related_works":["https://openalex.org/W2606446052","https://openalex.org/W2036021480","https://openalex.org/W2985746494","https://openalex.org/W4206042385","https://openalex.org/W3195777957","https://openalex.org/W2511384863","https://openalex.org/W2080773131","https://openalex.org/W2096089271","https://openalex.org/W2800090224","https://openalex.org/W4311995277"],"abstract_inverted_index":{"SUMMARY:":[0],"The":[1],"SOHPIE":[2,74],"R":[3],"package":[4],"implements":[5],"a":[6,22,51,76],"novel":[7],"functionality":[8],"for":[9,27,30],"\"multivariable\"":[10],"differential":[11],"co-abundance":[12],"network":[13],"(DN,":[14],"hereafter)":[15,62],"analyses":[16,41],"of":[17,54],"microbiome":[18],"data.":[19],"It":[20],"incorporates":[21],"regression":[23],"approach":[24],"that":[25,57],"adjusts":[26],"additional":[28],"covariates":[29],"DN":[31,40],"analyses.":[32],"This":[33],"distinguishes":[34],"from":[35],"previous":[36],"prominent":[37],"approaches":[38],"in":[39],"such":[42],"as":[43],"MDiNE":[44],"and":[45,68,84],"NetCoMi":[46],"which":[47],"do":[48],"not":[49],"feature":[50],"covariate":[52],"adjustment":[53],"finding":[55],"taxa":[56],"are":[58],"differentially":[59],"connected":[60],"(DC,":[61],"between":[63],"individuals":[64],"with":[65,75],"different":[66],"clinical":[67],"phenotypic":[69],"characteristics.":[70],"AVAILABILITY":[71],"AND":[72],"IMPLEMENTATION:":[73],"vignette":[77],"is":[78],"available":[79],"on":[80],"CRAN":[81],"repository":[82],"https://CRAN.R-project.org/package=SOHPIE":[83],"published":[85],"under":[86],"General":[87],"Public":[88],"License":[89],"(GPL)":[90],"version":[91],"3":[92],"license.":[93]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
