{"id":"https://openalex.org/W4392183999","doi":"https://doi.org/10.1093/bioinformatics/btae071","title":"Zero is not absence: censoring-based differential abundance analysis for microbiome data","display_name":"Zero is not absence: censoring-based differential abundance analysis for microbiome data","publication_year":2024,"publication_date":"2024-02-01","ids":{"openalex":"https://openalex.org/W4392183999","doi":"https://doi.org/10.1093/bioinformatics/btae071","pmid":"https://pubmed.ncbi.nlm.nih.gov/38331411"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae071","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae071","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btae071","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039958957","display_name":"Lap Sum Chan","orcid":"https://orcid.org/0000-0003-3206-9064"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lap Sum Chan","raw_affiliation_strings":["Department of Biostatistics, University of Michigan , Ann Arbor, MI 48109, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Michigan , Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100357040","display_name":"Gen Li","orcid":"https://orcid.org/0000-0002-7298-2141"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gen Li","raw_affiliation_strings":["Department of Biostatistics, University of Michigan , Ann Arbor, MI 48109, United States"],"raw_orcid":"https://orcid.org/0000-0002-7298-2141","affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of Michigan , Ann Arbor, MI 48109, United States","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.3201,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.78682615,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"40","issue":"2","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":0.9891999959945679,"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":0.9891999959945679,"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/T11288","display_name":"Clostridium difficile and Clostridium perfringens research","score":0.00139999995008111,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T13410","display_name":"Immune responses and vaccinations","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.7408864498138428},{"id":"https://openalex.org/keywords/censoring","display_name":"Censoring (clinical trials)","score":0.7400318384170532},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5904422998428345},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.5471053719520569},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5462886095046997},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.5131681561470032},{"id":"https://openalex.org/keywords/type-i-and-type-ii-errors","display_name":"Type I and type II errors","score":0.5041805505752563},{"id":"https://openalex.org/keywords/power-analysis","display_name":"Power analysis","score":0.4648992121219635},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4069713056087494},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.369439959526062},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32109421491622925},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27549999952316284},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.20641157031059265},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.19031044840812683},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17855015397071838}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.7408864498138428},{"id":"https://openalex.org/C137668524","wikidata":"https://www.wikidata.org/wiki/Q189813","display_name":"Censoring (clinical trials)","level":2,"score":0.7400318384170532},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5904422998428345},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.5471053719520569},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5462886095046997},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.5131681561470032},{"id":"https://openalex.org/C40696583","wikidata":"https://www.wikidata.org/wiki/Q989120","display_name":"Type I and type II errors","level":2,"score":0.5041805505752563},{"id":"https://openalex.org/C71743495","wikidata":"https://www.wikidata.org/wiki/Q2845210","display_name":"Power analysis","level":3,"score":0.4648992121219635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4069713056087494},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.369439959526062},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32109421491622925},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27549999952316284},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.20641157031059265},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.19031044840812683},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17855015397071838},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C178489894","wikidata":"https://www.wikidata.org/wiki/Q8789","display_name":"Cryptography","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","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":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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/btae071","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae071","pdf_url":null,"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:38331411","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38331411","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:10885211","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10885211","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10885211/pdf/btae071.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/btae071","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae071","pdf_url":null,"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":[{"score":0.6899999976158142,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[{"id":"https://openalex.org/G2948471872","display_name":null,"funder_award_id":"R03 DE027773","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"},{"id":"https://openalex.org/G7579696122","display_name":null,"funder_award_id":"R03 DE031296","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"}],"funders":[{"id":"https://openalex.org/F4320337365","display_name":"National Institute of Dental and Craniofacial Research","ror":"https://ror.org/004a2wv92"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1523266228","https://openalex.org/W1975271432","https://openalex.org/W1985197139","https://openalex.org/W2021880506","https://openalex.org/W2026006003","https://openalex.org/W2139984188","https://openalex.org/W2156975150","https://openalex.org/W2162088497","https://openalex.org/W2179438025","https://openalex.org/W2767984705","https://openalex.org/W2785509713","https://openalex.org/W2949960840","https://openalex.org/W2951061751","https://openalex.org/W2993347499","https://openalex.org/W2995916473","https://openalex.org/W3016136518","https://openalex.org/W3017072931","https://openalex.org/W3017169614","https://openalex.org/W3043062835","https://openalex.org/W3126629478","https://openalex.org/W3198822282","https://openalex.org/W6631383449","https://openalex.org/W6790608273"],"related_works":["https://openalex.org/W2363656491","https://openalex.org/W4376988598","https://openalex.org/W4388007941","https://openalex.org/W1581143638","https://openalex.org/W2884149040","https://openalex.org/W2615598724","https://openalex.org/W154749848","https://openalex.org/W2031189000","https://openalex.org/W2358304601","https://openalex.org/W2159198570"],"abstract_inverted_index":{"MOTIVATION:":[0],"Microbiome":[1],"data":[2,25,61,143],"analysis":[3,54,82,136],"faces":[4],"the":[5,19,78,85],"challenge":[6],"of":[7,21,37,55,80],"sparsity,":[8],"with":[9],"many":[10],"entries":[11],"recorded":[12],"as":[13,65],"zeros.":[14],"In":[15],"differential":[16,91],"abundance":[17,92],"analysis,":[18],"presence":[20],"excessive":[22],"zeros":[23,64],"in":[24,144],"violates":[26],"distributional":[27],"assumptions":[28],"and":[29,41,105,137],"creates":[30],"ties,":[31],"leading":[32],"to":[33,110],"an":[34],"increased":[35],"risk":[36],"type":[38,101],"I":[39,102],"errors":[40],"reduced":[42],"statistical":[43,135],"power.":[44,107],"RESULTS:":[45],"We":[46],"developed":[47],"a":[48,111],"novel":[49],"normalization":[50],"method,":[51],"called":[52],"censoring-based":[53],"microbiome":[56,60,114,142],"proportions":[57],"(CAMP),":[58],"for":[59,90],"by":[62],"treating":[63],"censored":[66],"observations,":[67],"transforming":[68],"raw":[69],"read":[70],"counts":[71],"into":[72,141],"tie-free":[73],"time-to-event-like":[74],"data.":[75],"This":[76],"enables":[77],"use":[79],"survival":[81],"techniques,":[83],"like":[84],"Cox":[86],"proportional":[87],"hazards":[88],"model,":[89],"analysis.":[93],"Extensive":[94],"simulations":[95],"demonstrate":[96],"that":[97],"CAMP":[98,109,129],"achieves":[99],"proper":[100],"error":[103],"control":[104],"high":[106],"Applying":[108],"human":[112],"gut":[113],"dataset,":[115],"we":[116],"identify":[117],"60":[118],"new":[119],"differentially":[120],"abundant":[121],"taxa":[122],"across":[123],"geographic":[124],"locations,":[125],"showcasing":[126],"its":[127],"usefulness.":[128],"overcomes":[130],"sparsity":[131],"challenges,":[132],"enabling":[133],"improved":[134],"providing":[138],"valuable":[139],"insights":[140],"various":[145],"contexts.":[146],"AVAILABILITY":[147],"AND":[148],"IMPLEMENTATION:":[149],"The":[150],"R":[151],"package":[152],"is":[153],"available":[154],"at":[155],"https://github.com/lapsumchan/CAMP.":[156]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-07T14:30:12.667765","created_date":"2025-10-10T00:00:00"}
