{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T19:08:14Z","timestamp":1789931294629,"version":"4.0.1"},"reference-count":22,"publisher":"Cambridge University Press (CUP)","issue":"11","license":[{"start":{"date-parts":[[2016,4,6]],"date-time":"2016-04-06T00:00:00Z","timestamp":1459900800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/www.cambridge.org\/core\/terms"}],"content-domain":{"domain":["journals.cambridge.org"],"crossmark-restriction":true},"short-container-title":["Epidemiol. Infect."],"published-print":{"date-parts":[[2016,8]]},"abstract":"<jats:title>SUMMARY<\/jats:title><jats:p>Altered microbial communities are thought to play an important role in eosinophilic oesophagitis, an allergic inflammatory condition of the oesophagus. Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. However, these data consist of non-negative, highly skewed sequence counts with a large proportion of zeros. In addition, hierarchical study designs are often performed with repeated measurements or multiple samples collected from the same subject, thus requiring approaches to account for within-subject variation, yet only a small number of microbiota studies have applied hierarchical regression models. In this paper, we describe and illustrate the use of a hierarchical regression-based approach to evaluate multiple factors for a small number of organisms individually. More specifically, the zero-inflated negative binomial mixed model with random effects in both the count and zero-inflated parts is applied to evaluate associations with disease state while adjusting for potential confounders for two organisms of interest from a study of human microbiota sequence data in oesophagitis.<\/jats:p>","DOI":"10.1017\/s0950268816000662","type":"journal-article","created":{"date-parts":[[2016,4,6]],"date-time":"2016-04-06T08:21:28Z","timestamp":1459930888000},"page":"2447-2455","update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":40,"title":["Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis"],"prefix":"10.1017","volume":"144","author":[{"given":"R.","family":"FANG","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B. D.","family":"WAGNER","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. K.","family":"HARRIS","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S. A.","family":"FILLON","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2016,4,6]]},"reference":[{"key":"S0950268816000662_ref15","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-79"},{"key":"S0950268816000662_ref18","unstructured":"Greene W . Accounting for excess zeros and sample selection in Poisson and negative binomial regression models. Working paper. Department of Economics, Stern School of Business, New York University, 1994."},{"key":"S0950268816000662_ref5","doi-asserted-by":"publisher","DOI":"10.1101\/gr.096651.109"},{"key":"S0950268816000662_ref20","doi-asserted-by":"publisher","DOI":"10.1080\/02664760802273203"},{"key":"S0950268816000662_ref21","doi-asserted-by":"publisher","DOI":"10.1023\/A:1021594923546"},{"key":"S0950268816000662_ref7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0128346"},{"key":"S0950268816000662_ref13","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-422"},{"key":"S0950268816000662_ref16","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-4"},{"key":"S0950268816000662_ref11","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-10-r106"},{"key":"S0950268816000662_ref10","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-94"},{"key":"S0950268816000662_ref17","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-015-0085-6"},{"key":"S0950268816000662_ref1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1124234"},{"key":"S0950268816000662_ref22","doi-asserted-by":"publisher","DOI":"10.1002\/sim.860"},{"key":"S0950268816000662_ref4","doi-asserted-by":"publisher","DOI":"10.1373\/clinchem.2012.187617"},{"key":"S0950268816000662_ref3","doi-asserted-by":"publisher","DOI":"10.1086\/367657"},{"key":"S0950268816000662_ref12","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp616"},{"key":"S0950268816000662_ref19","doi-asserted-by":"publisher","DOI":"10.1002\/bimj.200390024"},{"key":"S0950268816000662_ref9","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2658"},{"key":"S0950268816000662_ref8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003531"},{"key":"S0950268816000662_ref2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2974"},{"key":"S0950268816000662_ref14","article-title":"The cervical microbiome over 7 years and a comparison of methodologies for its characterization","volume":"7","author":"Smith","year":"2012","journal-title":"PLoS ONE"},{"key":"S0950268816000662_ref6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0042938"}],"container-title":["Epidemiology and Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S0950268816000662","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,4,19]],"date-time":"2019-04-19T01:38:59Z","timestamp":1555637939000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cambridge.org\/core\/product\/identifier\/S0950268816000662\/type\/journal_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,6]]},"references-count":22,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2016,8]]}},"alternative-id":["S0950268816000662"],"URL":"https:\/\/doi.org\/10.1017\/s0950268816000662","relation":{},"ISSN":["0950-2688","1469-4409"],"issn-type":[{"value":"0950-2688","type":"print"},{"value":"1469-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,4,6]]},"assertion":[{"value":"Copyright \u00a9 Cambridge University Press 2016\u00a0","name":"license","label":"License","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}}]}}