生物信息学的下一个元挑战。
The next meta-challenge for Bioinformatics.
作者信息
Valdivia-Granda Willy
机构信息
Orion Integrated Biosciences Inc., New York, United States of America.
出版信息
Bioinformation. 2008 May 29;2(8):358-62. doi: 10.6026/97320630002358.
Abstract
The direct sequencing of uncultivable organisms present in complex biological and environmental samples has opportunities to discover new life forms and metabolic processes. This transformational field, known as metagenomics, is generating massive amounts of molecular information that can overwhelm the performance of conventional analysis and visualization algorithms. Here, I briefly highlight some of the emerging challenges this new discipline presents to the computational biology community and point some of the opportunities to develop applications that can translate metagenomic information into biomedical, agricultural, environmental, and industrial applications.
摘要
对复杂生物和环境样本中不可培养的生物体进行直接测序，有机会发现新的生命形式和代谢过程。这个被称为宏基因组学的变革性领域正在产生大量的分子信息，这些信息可能会超出传统分析和可视化算法的性能。在这里，我简要强调这一新学科给计算生物学界带来的一些新出现的挑战，并指出一些开发应用程序的机会，这些应用程序可以将宏基因组信息转化为生物医学、农业、环境和工业应用。
相似文献
1
The next meta-challenge for Bioinformatics.
Bioinformation. 2008 May 29;2(8):358-62. doi: 10.6026/97320630002358.
2
Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization.
PLoS One. 2014 Mar 3;9(3):e89323. doi: 10.1371/journal.pone.0089323. eCollection 2014.
3
Recent Advances in Metagenomic Approaches, Applications, and Challenge.
Curr Microbiol. 2023 Sep 21;80(11):347. doi: 10.1007/s00284-023-03451-5.
4
Big Data Analysis in Computational Biology and Bioinformatics.
Methods Mol Biol. 2024;2719:181-197. doi: 10.1007/978-1-0716-3461-5_11.
5
Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review.
Res Microbiol. 2016 Sep;167(7):529-38. doi: 10.1016/j.resmic.2016.06.007. Epub 2016 Jul 7.
6
ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data.
Front Genet. 2019 May 24;10:469. doi: 10.3389/fgene.2019.00469. eCollection 2019.
8
Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.
Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5.
9
Metagenomic Assembly: Overview, Challenges and Applications.
Yale J Biol Med. 2016 Sep 30;89(3):353-362. eCollection 2016 Sep.
10
[Research in metagenomics and its applications in translational medicine].
Yi Chuan. 2015 Jul;37(7):645-54. doi: 10.16288/j.yczz.14-444.
引用本文的文献
1
Clustering of Isolates Using MLST and Whole-Genome Phylogenetics and Protein Motif Fingerprinting.
Front Public Health. 2019 May 8;7:66. doi: 10.3389/fpubh.2019.00066. eCollection 2019.
2
Biodefense Oriented Genomic-Based Pathogen Classification Systems: Challenges and Opportunities.
J Bioterror Biodef. 2012 Mar 16;3(1):1000113. doi: 10.4172/2157-2526.1000113.
3
Biosurveillance enterprise for operational awareness, a genomic-based approach for tracking pathogen virulence.
Virulence. 2013 Nov 15;4(8):745-51. doi: 10.4161/viru.26893. Epub 2013 Oct 23.
4
Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency.
BMC Bioinformatics. 2010 Nov 18;11:565. doi: 10.1186/1471-2105-11-565.
5
Signal processing for metagenomics: extracting information from the soup.
Curr Genomics. 2009 Nov;10(7):493-510. doi: 10.2174/138920209789208255.
6
ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies.
Database (Oxford). 2009;2009:bap014. doi: 10.1093/database/bap014. Epub 2009 Oct 12.
本文引用的文献
1
Old and new concepts of species differentiation in Aspergillus.
Med Mycol. 2006 Sep 1;44(Supplement_1):S133-S148. doi: 10.1080/13693780600913224.
2
Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time.
Proc Natl Acad Sci U S A. 2007 May 22;104(21):9052-7. doi: 10.1073/pnas.0700496104. Epub 2007 May 14.
3
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
Nat Methods. 2007 Jun;4(6):495-500. doi: 10.1038/nmeth1043. Epub 2007 Apr 29.
4
Targeted access to the genomes of low-abundance organisms in complex microbial communities.
Appl Environ Microbiol. 2007 May;73(10):3205-14. doi: 10.1128/AEM.02985-06. Epub 2007 Mar 16.
5
Distinctive features of large complex virus genomes and proteomes.
Proc Natl Acad Sci U S A. 2007 Mar 20;104(12):5127-32. doi: 10.1073/pnas.0700429104. Epub 2007 Mar 9.
6
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.
PLoS Biol. 2007 Mar;5(3):e16. doi: 10.1371/journal.pbio.0050016.
7
Finding the needles in the metagenome haystack.
Microb Ecol. 2007 Apr;53(3):475-85. doi: 10.1007/s00248-006-9201-2. Epub 2007 Mar 8.
8
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.
Nature. 2007 Mar 29;446(7135):537-41. doi: 10.1038/nature05624. Epub 2007 Mar 7.
9
Quantitative phylogenetic assessment of microbial communities in diverse environments.
Science. 2007 Feb 23;315(5815):1126-30. doi: 10.1126/science.1133420. Epub 2007 Feb 1.
10
The marine viromes of four oceanic regions.
PLoS Biol. 2006 Nov;4(11):e368. doi: 10.1371/journal.pbio.0040368.
Zotero 插件