Translational informatics for human microbiota: data resources, models and applications

Author:

Shen Ke1,Din Ahmad Ud1,Sinha Baivab1,Zhou Yi1,Qian Fuliang23,Shen Bairong1

Affiliation:

1. Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University , Chengdu, 610212 , China

2. Center for Systems Biology, Suzhou Medical College of Soochow University , Suzhou 215123 , China

3. Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development , Suzhou 215123 , China

Abstract

Abstract With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.

Funder

National Natural Science Foundation of China

West China Hospital Sichuan University

Sichuan and Guangxi Provinces

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

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