Microbiomarkers Discovery in Inflammatory Bowel Diseases using Network-Based Feature Selection

Mostafa Abbas, Thanh Le, Halima Bensmail, Vasant Gajanan Honavar, Yasser Elmanzalawi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

Discovery of disease biomarkers is a key step in translating advances in genomics into clinical practice. There is growing evidence that changes in gut microbial composition are associated with the onset and progression of Type 2 Diabetes (T2D), Obesity, and Inflammatory Bowel Disease (IBD). Reliable identification of the most informative features (i.e., microbes) for discriminating metagenomics samples from two or more groups (i.e., phenotypes) is a major challenge in computational metagenomics. We propose a Network-Based Biomarker Discovery (NBBD) framework for detecting disease biomarkers from metagenomics data. NBBD has two major customizable modules: i) A network inference module for inferring ecological networks from the abundances of microbial operational taxonomic units (OTUs); ii) A node importance scoring module for comparing the constructed networks for the chosen phenotypes and assigning a score to each node based on the degree to which the topological properties of the node differ across two networks. We empirically evaluated the proposed NBBD framework, using five network inference methods for inferring gut microbial networks combined with six node topological properties, on the identification of IBD biomarkers using a large dataset from a cohort of 657 and 316 IBD and healthy controls metagenomic biopsy samples, respectively. Our results show that NBBD is very competitive with some of the state-of-the-art feature selection methods including the widely used method based on random forest variable importance scores.

Original languageEnglish (US)
Title of host publicationACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics
PublisherAssociation for Computing Machinery, Inc
Pages172-177
Number of pages6
ISBN (Electronic)9781450357944
DOIs
StatePublished - Aug 15 2018
Event9th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2018 - Washington, United States
Duration: Aug 29 2018Sep 1 2018

Publication series

NameACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

Other

Other9th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2018
CountryUnited States
CityWashington
Period8/29/189/1/18

Fingerprint

Biomarkers
Inflammatory Bowel Diseases
Feature extraction
Metagenomics
Phenotype
Biopsy
Medical problems
Genomics
Type 2 Diabetes Mellitus
Obesity
Chemical analysis

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Software
  • Health Informatics
  • Biomedical Engineering

Cite this

Abbas, M., Le, T., Bensmail, H., Honavar, V. G., & Elmanzalawi, Y. (2018). Microbiomarkers Discovery in Inflammatory Bowel Diseases using Network-Based Feature Selection. In ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 172-177). (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics). Association for Computing Machinery, Inc. https://doi.org/10.1145/3233547.3233602
Abbas, Mostafa ; Le, Thanh ; Bensmail, Halima ; Honavar, Vasant Gajanan ; Elmanzalawi, Yasser. / Microbiomarkers Discovery in Inflammatory Bowel Diseases using Network-Based Feature Selection. ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, 2018. pp. 172-177 (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics).
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Abbas, M, Le, T, Bensmail, H, Honavar, VG & Elmanzalawi, Y 2018, Microbiomarkers Discovery in Inflammatory Bowel Diseases using Network-Based Feature Selection. in ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, Association for Computing Machinery, Inc, pp. 172-177, 9th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2018, Washington, United States, 8/29/18. https://doi.org/10.1145/3233547.3233602

Microbiomarkers Discovery in Inflammatory Bowel Diseases using Network-Based Feature Selection. / Abbas, Mostafa; Le, Thanh; Bensmail, Halima; Honavar, Vasant Gajanan; Elmanzalawi, Yasser.

ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, 2018. p. 172-177 (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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AU - Honavar, Vasant Gajanan

AU - Elmanzalawi, Yasser

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Abbas M, Le T, Bensmail H, Honavar VG, Elmanzalawi Y. Microbiomarkers Discovery in Inflammatory Bowel Diseases using Network-Based Feature Selection. In ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc. 2018. p. 172-177. (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics). https://doi.org/10.1145/3233547.3233602