Computational Challenges in Characterization of Bacteria and Bacteria-Host Interactions Based on Genomic Data

With the rapid development of next-generation sequencing technologies, bacterial identification becomes a very important and essential step in processing genomic data, especially for metagenomic data. Many computational methods have been developed and some of them are widely used to address the prob...

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Bibliographic Details
Published inJournal of computer science and technology Vol. 27; no. 2; pp. 225 - 239
Main Author 张潮 郑国铝 徐顺福 许东
Format Journal Article
LanguageEnglish
Published Boston Springer US 01.03.2012
Springer Nature B.V
Department of Computer Science,Christopher S. Bond Life Sciences Center,University of Missouri,Columbia MO 65201,U.S.A.%Department of Agriculture and Environmental Science,Lincoln University,Jefferson City,MO 65101,U.S.A.%Department of Gastroenterology,The First Affiliated Hospital of Nanjing Medical University,Jiangsu 210029,China
Subjects
Algorithms
Analysis
Artificial Intelligence
Bacteria
Computer Science
Data Structures and Information Theory
E coli
Genomes
Genomics
Information Systems Applications (incl.Internet)
Microorganisms
Pathogens
Software Engineering
Studies
Survey
Taxonomy
Theory of Computation
基因数据
基础
宿主
相互作用
组数
细菌鉴定
表征
计算问题
bacteria
bacteria-host interaction
metagenomics
16S rRNA gene
combinatorial entropy
Helicobacter pylori
Faecalibacterium
Online AccessGet full text
ISSN1000-9000
1860-4749
DOI10.1007/s11390-012-1219-y

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Summary:With the rapid development of next-generation sequencing technologies, bacterial identification becomes a very important and essential step in processing genomic data, especially for metagenomic data. Many computational methods have been developed and some of them are widely used to address the problems in bacterial identification. In this article we review the algorithms of these methods, discuss their drawbacks, and propose future computational methods that use genomic data to characterize bacteria. In addition, we tackle two specific computational problems in bacterial identification, namely, the detection of host-specific bacteria and the detection of disease-associated bacteria, by offering potential solutions as a starting point for those who are interested in the area.
Bibliography:Chao Zhang, Guolu Zheng, Shun-Fu Xu , Dong Xu 1Department of Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia MO 65201, U.S.A. 2Department of Agriculture and Environmental Science, Lincoln University, Jefferson City, MO 65101, U.S.A. 3Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu 210029, China
11-2296/TP
With the rapid development of next-generation sequencing technologies, bacterial identification becomes a very important and essential step in processing genomic data, especially for metagenomic data. Many computational methods have been developed and some of them are widely used to address the problems in bacterial identification. In this article we review the algorithms of these methods, discuss their drawbacks, and propose future computational methods that use genomic data to characterize bacteria. In addition, we tackle two specific computational problems in bacterial identification, namely, the detection of host-specific bacteria and the detection of disease-associated bacteria, by offering potential solutions as a starting point for those who are interested in the area.
bacteria, bacteria-host interaction, metagenomics, 16S rRNA gene, Faecalibacterium, Helicobacter pylori, combinatorial entropy
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ISSN:1000-9000
1860-4749
DOI:10.1007/s11390-012-1219-y