Abstract
Traditionally, studies in microbial genomics have focused on single-genomes from cultured species, thereby limiting their focus to the small percentage of species that can be cultured outside their natural environment. Fortunately, recent advances in high-throughput sequencing and computational analyses have ushered in the new field of metagenomics, which aims to decode the genomes of microbes from natural communities without the need for cultivation. Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic sequence data. Current tools and techniques are reviewed in this paper which address challenges in 1) genomic fragment annotation, 2) phylogenetic reconstruction, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology.
Current Genomics
Title: Signal Processing for Metagenomics: Extracting Information from the Soup
Volume: 10 Issue: 7
Author(s): Gail L. Rosen, Bahrad A. Sokhansanj, Robi Polikar, Mary Ann Bruns, Jacob Russell, Elaine Garbarine, Steve Essinger and Non Yok
Affiliation:
Abstract: Traditionally, studies in microbial genomics have focused on single-genomes from cultured species, thereby limiting their focus to the small percentage of species that can be cultured outside their natural environment. Fortunately, recent advances in high-throughput sequencing and computational analyses have ushered in the new field of metagenomics, which aims to decode the genomes of microbes from natural communities without the need for cultivation. Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic sequence data. Current tools and techniques are reviewed in this paper which address challenges in 1) genomic fragment annotation, 2) phylogenetic reconstruction, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology.
Export Options
About this article
Cite this article as:
Rosen L. Gail, Sokhansanj A. Bahrad, Polikar Robi, Bruns Ann Mary, Russell Jacob, Garbarine Elaine, Essinger Steve and Yok Non, Signal Processing for Metagenomics: Extracting Information from the Soup, Current Genomics 2009; 10 (7) . https://dx.doi.org/10.2174/138920209789208255
DOI https://dx.doi.org/10.2174/138920209789208255 |
Print ISSN 1389-2029 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5488 |
Call for Papers in Thematic Issues
Advanced AI Techniques in Big Genomic Data Analysis
The thematic issue on "Advanced AI Techniques in Big Genomic Data Analysis" aims to explore the cutting-edge methodologies and applications of artificial intelligence (AI) in the realm of genomic research, where vast amounts of data pose both challenges and opportunities. This issue will cover a broad spectrum of AI-driven strategies, ...read more
Advanced Computational Algorithms and Artificial Intelligence in Clinical Pharmacogenomics
In the era of personalized medicine, understanding the relationship between genetics and drug response is crucial. This issue delves into innovative methodologies, leveraging deep computational analysis and artificial intelligence, to enhance the field of Clinical Pharmacogenomics. The interdisciplinary approach harnesses the power of advanced high-throughput genotyping technologies, sophisticated computational analysis, ...read more
Applications of Single-cell Sequencing Technology in Reproductive Medicine
Single cell sequencing (SCS) technology utilizes individual cells' genetic material to sequence their genome, transcriptome, and epigenetics at the molecular level. It offers insights into cell heterogeneity and enables the study of limited biological materials. Since its recognition as a valuable technique in 2011, single cell sequencing has yielded numerous ...read more
Big Data in Cancer Research
Cancer is a significant threat to human life and health, remaining a highly aggressive killer. It is a leading cause of death worldwide and represents a crucial medical issue for humanity. However, in the past decade, the effectiveness of new synthetic anticancer agents has not matched the current clinical speculation. ...read more
Related Journals
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
- Announcements
Related Articles
-
The Multiple Roles of Vitamin D in Human Health. A Mini-Review
Immunology, Endocrine & Metabolic Agents in Medicinal Chemistry (Discontinued) Doxycycline Inhibition of Abdominal Aortic Aneurysm Growth - A Systematic Review of the Literature
Current Vascular Pharmacology Application of Nanohydrogels in Drug Delivery Systems: Recent Patents Review
Recent Patents on Nanotechnology Recent Advances in the Development of Antimicrobial Peptides (AMPs): Attempts for Sustainable Medicine?
Current Medicinal Chemistry A Review of Techniques for Gene Therapy in Bone Healing
Current Stem Cell Research & Therapy Functional and Molecular Changes of MSCs in Aging
Current Stem Cell Research & Therapy Rheumatoid Arthritis: A Clinical Overview of New Diagnostic and Treatment Approaches
Current Topics in Medicinal Chemistry Applications of Mesenchymal Stem Cells in Cartilage Tissue Engineering- Part 1
Recent Patents on Regenerative Medicine Influence of Polymorphic N-Acetyltransferases on Non-Malignant Spontaneous Disorders and on Response to Drugs
Current Drug Metabolism The Lipophilicity, Pharmacokinetics, and Cellular Uptake of Different Chemically-Modified Tetracyclines (CMTs)
Current Medicinal Chemistry Stem Cells as a Novel Tool for Drug Screening and Treatment of Degenerative Diseases
Current Pharmaceutical Design Risk Factors, Mechanisms and Treatments of Thromboangiitis Obliterans: An Overview of Recent Research
Current Medicinal Chemistry Current Applications of Biopolymer-based Scaffolds and Nanofibers as Drug Delivery Systems
Current Pharmaceutical Design Biomarkers for Radiographic Progression in Rheumatoid Arthritis
Current Pharmaceutical Design Aligned Biomimetic Scaffolds as a New Tendency in Tissue Engineering
Current Stem Cell Research & Therapy Alzheimer’s Disease-like Early-phase Brain Pathogenesis: Self-curing Amelioration of Neurodegeneration from Pro-inflammatory ‘Wounding’ to Anti-inflammatory ‘Healing’
Current Alzheimer Research Functions and Mechanisms of Green Tea Catechins in Regulating Bone Remodeling
Current Drug Targets Nutritional Antioxidants and Their Applications in Cardiometabolic Diseases
Infectious Disorders - Drug Targets Epigenetics and Periodontal Disease: Hope to Tame the Untameable
Current Gene Therapy <I>Grewia asiatica</I> Mucilage: A Smart Gelling Polymeric Material for Pharmaceutical Applications <i>In Vitro</i> Studies
Current Materials Science