research-article

Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA

Authors:

Ahmed A. Metwally,

Patricia W. Finn,

David L. PerkinsAuthors Info & Claims

ACM-BCB '17: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics

Pages 295 - 304

https://doi.org/10.1145/3107411.3107429

Published: 20 August 2017 Publication History

Abstract

Metagenomic longitudinal studies have become a widely-used study design to investigate the dynamics of the microbial ecological systems and their temporal effects. One of the important questions to be addressed in longitudinal studies is the identification of time intervals when microbial features show changes in their abundance. We propose a statistical method that is based on a semi-parametric Smoothing Spline ANOVA and negative binomial distribution to model the time-course of the features between two phenotypes. We demonstrate the superior performance of our proposed method compared to the two currently existing methods using simulated data. We present the analysis results of our proposed method in an analysis of a longitudinal dataset that investigates the association between the development of type 1 diabetes in infants and the gut microbiome. The identified significant species and their specific time intervals reveal new information that can be used in improving intervention or treatment plans.

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Cited By

Lutz KJiang SNeugent MDe Nisco NZhan XLi Q(2022)A Survey of Statistical Methods for Microbiome Data AnalysisFrontiers in Applied Mathematics and Statistics10.3389/fams.2022.8848108Online publication date: 14-Jun-2022
https://doi.org/10.3389/fams.2022.884810
Alaa AMetwally A(2018)Cloud-based solution for improving usability and interactivity of metagenomic ensemble taxonomic classification methods2018 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI)10.1109/BHI.2018.8333403(198-201)Online publication date: Mar-2018
https://doi.org/10.1109/BHI.2018.8333403

Index Terms

Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA
1. Applied computing
  1. Life and medical sciences
    1. Bioinformatics
2. Mathematics of computing
  1. Mathematical analysis
    1. Numerical analysis
      1. Interpolation
  2. Probability and statistics
    1. Statistical paradigms
      1. Time series analysis

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cover image ACM Conferences

ACM-BCB '17: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics

August 2017

800 pages

ISBN:9781450347228

DOI:10.1145/3107411

General Chairs:
Nurit Haspel
University of Massachusetts Boston, USA
,
Lenore J. Cowen
Tufts University, USA
,
Program Chairs:
Amarda Shehu
George Mason University, USA
,
Tamer Kahveci
University of Florida, USA
,
Giuseppe Pozzi
Politecnico di Milano, Italy

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Published: 20 August 2017

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BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

August 20 - 23, 2017

Massachusetts, Boston, USA

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Cited By

Lutz KJiang SNeugent MDe Nisco NZhan XLi Q(2022)A Survey of Statistical Methods for Microbiome Data AnalysisFrontiers in Applied Mathematics and Statistics10.3389/fams.2022.8848108Online publication date: 14-Jun-2022
https://doi.org/10.3389/fams.2022.884810
Alaa AMetwally A(2018)Cloud-based solution for improving usability and interactivity of metagenomic ensemble taxonomic classification methods2018 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI)10.1109/BHI.2018.8333403(198-201)Online publication date: Mar-2018
https://doi.org/10.1109/BHI.2018.8333403

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