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For: Zhang X, Guo B, Yi N. Zero-Inflated gaussian mixed models for analyzing longitudinal microbiome data. PLoS One 2020;15:e0242073. [PMID: 33166356 PMCID: PMC7652264 DOI: 10.1371/journal.pone.0242073] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/26/2020] [Indexed: 01/01/2023]  Open
Number Cited by Other Article(s)
1
Lee J, Kim B. Zero inflated high dimensional compositional data with DeepInsight. PLoS One 2025;20:e0320832. [PMID: 40238826 PMCID: PMC12002526 DOI: 10.1371/journal.pone.0320832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 02/25/2025] [Indexed: 04/18/2025]  Open
2
Saso A, Kanteh E, Jeffries D, Okoye M, Mohammed N, Kumado M, Roetynck S, Jobe H, Faal A, Roberts E, Gageldonk P, Buisman AM, Fröberg J, Cavell B, Lesne E, Barkoff AM, He Q, Tanha K, Bibi S, Kelly D, Diavatopoulos D, Kampmann B. The effect of pertussis vaccination in pregnancy on the immunogenicity of acellular or whole-cell pertussis vaccination in Gambian infants (GaPS): a single-centre, randomised, controlled, double-blind, phase 4 trial. THE LANCET. INFECTIOUS DISEASES 2025:S1473-3099(25)00072-6. [PMID: 40154521 DOI: 10.1016/s1473-3099(25)00072-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 01/21/2025] [Accepted: 01/27/2025] [Indexed: 04/01/2025]
3
Kodikara S, Lê Cao KA. Microbial network inference for longitudinal microbiome studies with LUPINE. MICROBIOME 2025;13:64. [PMID: 40033386 PMCID: PMC11874778 DOI: 10.1186/s40168-025-02041-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 01/17/2025] [Indexed: 03/05/2025]
4
Rahrig H, Beloborodova P, Castro C, Sabet K, Johnson M, Pearce O, Celik E, Brown KW. Examining emotion reactivity to politically polarizing media in a randomized controlled trial of mindfulness training versus active coping training. Sci Rep 2025;15:5209. [PMID: 39939651 PMCID: PMC11822039 DOI: 10.1038/s41598-024-84510-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 12/24/2024] [Indexed: 02/14/2025]  Open
5
Schropp N, Bauer A, Stanislas V, Huang KD, Lesker TR, Bielecka AA, Strowig T, Michels KB. The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial. MICROBIOME 2025;13:52. [PMID: 39940045 PMCID: PMC11817299 DOI: 10.1186/s40168-024-02016-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 12/19/2024] [Indexed: 02/14/2025]
6
Huang J, Lu Y, Tian F, Ni Y. Association of body index with fecal microbiome in children cohorts with ethnic-geographic factor interaction: accurately using a Bayesian zero-inflated negative binomial regression model. mSystems 2024;9:e0134524. [PMID: 39570024 DOI: 10.1128/msystems.01345-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 10/24/2024] [Indexed: 11/22/2024]  Open
7
Martinez-Feria R, Simmonds MB, Ozaydin B, Lewis S, Schwartz A, Pluchino A, McKellar M, Gottlieb SS, Kayatsky T, Vital R, Mehlman SE, Caron Z, Colaianni NR, Ané JM, Maeda J, Infante V, Karlsson BH, McLimans C, Vyn T, Hanson B, Verhagen G, Nevins C, Reese L, Otyama P, Robinson A, Learmonth T, Miller CMF, Havens K, Tamsir A, Temme K. Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize. Sci Rep 2024;14:27754. [PMID: 39532958 PMCID: PMC11557888 DOI: 10.1038/s41598-024-78243-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024]  Open
8
Francis D, Sun F. A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data. BMC Bioinformatics 2024;25:266. [PMID: 39143554 PMCID: PMC11323399 DOI: 10.1186/s12859-024-05883-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 07/29/2024] [Indexed: 08/16/2024]  Open
9
Trecarten S, Fongang B, Liss M. Current Trends and Challenges of Microbiome Research in Prostate Cancer. Curr Oncol Rep 2024;26:477-487. [PMID: 38573440 DOI: 10.1007/s11912-024-01520-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
10
Rahrig H, Beloboradova P, Castro C, Sabet K, Johnson M, Pearce O, Brown KW. Managing emotions in the age of political polarization: A randomized controlled trial comparing mindfulness to cognitive reappraisal. RESEARCH SQUARE 2024:rs.3.rs-3947259. [PMID: 38586010 PMCID: PMC10996818 DOI: 10.21203/rs.3.rs-3947259/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
11
Kibria MK, Ali MA, Yaseen M, Khan IA, Bhat MA, Islam MA, Mahumud RA, Mollah MNH. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals (Basel) 2024;17:432. [PMID: 38675393 PMCID: PMC11053588 DOI: 10.3390/ph17040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]  Open
12
Browndyke JN, Tomalin LE, Erus G, Overbey JR, Kuceyeski A, Moskowitz AJ, Bagiella E, Iribarne A, Acker M, Mack M, Mathew J, O'Gara P, Gelijns AC, Suarez‐Farinas M, Messé SR. Infarct-related structural disconnection and delirium in surgical aortic valve replacement patients. Ann Clin Transl Neurol 2024;11:263-277. [PMID: 38155462 PMCID: PMC10863920 DOI: 10.1002/acn3.51949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/28/2023] [Indexed: 12/30/2023]  Open
13
Ladakis DC, Harrison KL, Smith MD, Solem K, Gadani S, Jank L, Hwang S, Farhadi F, Dewey BE, Fitzgerald KC, Sotirchos ES, Saidha S, Calabresi PA, Bhargava P. Bile acid metabolites predict multiple sclerosis progression and supplementation is safe in progressive disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.17.24301393. [PMID: 38293182 PMCID: PMC10827276 DOI: 10.1101/2024.01.17.24301393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
14
Zhao J, Shi C, Wang L, Han X, Zhu Y, Liu J, Yang X. Functional Trait Responses of Sophora alopecuroides L. Seedlings to Diverse Environmental Stresses in the Desert Steppe of Ningxia, China. PLANTS (BASEL, SWITZERLAND) 2023;13:69. [PMID: 38202378 PMCID: PMC10780927 DOI: 10.3390/plants13010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
15
Paulo AC, Lança J, Almeida ST, Hilty M, Sá-Leão R. The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children. MICROBIOME 2023;11:199. [PMID: 37658443 PMCID: PMC10474643 DOI: 10.1186/s40168-023-01640-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
16
Lampeter T, Love C, Tang TT, Marella AS, Lee HY, Oganyan A, Moffat D, Kareem A, Rusling M, Massmann A, Orr M, Bongiorno C, Yuan LL. Risk of bias assessment tool for systematic review and meta-analysis of the gut microbiome. GUT MICROBIOME (CAMBRIDGE, ENGLAND) 2023;4:e13. [PMID: 39295908 PMCID: PMC11406368 DOI: 10.1017/gmb.2023.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 04/10/2023] [Accepted: 07/01/2023] [Indexed: 09/21/2024]
17
Kim M, Oh HS, Lim Y. Zero-Inflated Time Series Clustering Via Ensemble Thick-Pen Transform. JOURNAL OF CLASSIFICATION 2023;40:1-25. [PMID: 37359508 PMCID: PMC10258486 DOI: 10.1007/s00357-023-09437-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 06/28/2023]
18
Hajihosseini M, Amini P, Saidi-Mehrabad A, Dinu I. Infants' gut microbiome data: A Bayesian Marginal Zero-inflated Negative Binomial regression model for multivariate analyses of count data. Comput Struct Biotechnol J 2023;21:1621-1629. [PMID: 36860341 PMCID: PMC9969297 DOI: 10.1016/j.csbj.2023.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023]  Open
19
Dousti Mousavi N, Yang J, Aldirawi H. Variable Selection for Sparse Data with Applications to Vaginal Microbiome and Gene Expression Data. Genes (Basel) 2023;14:403. [PMID: 36833330 PMCID: PMC9956208 DOI: 10.3390/genes14020403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023]  Open
20
Sokhansanj BA, Rosen GL. Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning. Comput Biol Med 2022;149:105969. [PMID: 36041271 PMCID: PMC9384346 DOI: 10.1016/j.compbiomed.2022.105969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/11/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
21
Kodikara S, Ellul S, Lê Cao KA. Statistical challenges in longitudinal microbiome data analysis. Brief Bioinform 2022;23:bbac273. [PMID: 35830875 PMCID: PMC9294433 DOI: 10.1093/bib/bbac273] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/28/2022] [Accepted: 06/12/2022] [Indexed: 11/13/2022]  Open
22
Gisler A, Korten I, de Hoogh K, Vienneau D, Frey U, Decrue F, Gorlanova O, Soti A, Hilty M, Latzin P, Usemann J. Associations of air pollution and greenness with the nasal microbiota of healthy infants: A longitudinal study. ENVIRONMENTAL RESEARCH 2021;202:111633. [PMID: 34256075 DOI: 10.1016/j.envres.2021.111633] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 05/25/2023]
23
Liu T, Xu P, Du Y, Lu H, Zhao H, Wang T. MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys. Brief Bioinform 2021;23:6409694. [PMID: 34718406 DOI: 10.1093/bib/bbab443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/11/2021] [Accepted: 09/28/2021] [Indexed: 01/02/2023]  Open
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