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bioinformatics

Thursday 7 April 2005

Definition: Bioinformatics is defined as the large-scale storage, retrieval and assessment of data from biological studies. This field draws on high-performance computing, software and information technology.

Genomic information is too voluminous for even a large team of researchers to remember or analyze, so the information is placed in complex databases in which the gene and protein structures and functions can be easily accessed, cross-referenced or queried.

Bioinformatics is the application of computer science and information technology to the field of biology and medicine.

Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software engineering, data mining, image processing, modeling and simulation, signal processing, discrete mathematics, control and system theory, circuit theory, and statistics, for generating new knowledge of biology and medicine, and improving and discovering new models of computation (e.g. DNA computing, neural computing, evolutionary computing, immuno-computing, swarm-computing, cellular-computing).

Java, XML, Perl, C, C++, Python, R, SQL and MatLab are the some of the more prominent software technologies used in this field.

Major applications

- biological databases
- sequence analysis (sequence alignment, sequence database)
- genome annotation
- computational evolutionary biology
- biological litterature analysis (text mining)
- analysis of gene expression
- analysis of gene regulation
- analysis of protein expression
- analysis of mutations in cancer
- comparative genomics
- modeling biological systems (computational systems biology)
- high-throughput image analysis
- in silico biology
- metabolic network modelling
- molecular design software
- computational biomodeling
- computational genomics
- functional genomics
- morphometrics
- phylogenetics
- structural bioinformatics

  • protein structure prediction
  • molecualr interaction prediction

Websites

- NCBI
- infobiogen.fr
- UCSC Genome Bioinformatics
- BioIT Alliance

Journals

- Briefings in Bioinformatics
- Bioinformatics
- PLOS Computational Biology: Translational Bioinformatics

References

- Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends Genet. 2008 Mar;24(3):142-9. PMID: 18262676

- Hanauer DA, Rhodes DR, Sinha-Kumar C, Chinnaiyan AM. Bioinformatics approaches in the study of cancer. Curr Mol Med. 2007 Feb;7(1):133-41. PMID: 17311538

- Hu P, Bader G, Wigle DA, Emili A. Computational prediction of cancer-gene function. Nat Rev Cancer. 2007 Jan;7(1):23-34. PMID: 17167517

- Kanehisa M, Bork P. Bioinformatics in the post-sequence era. Nat Genet. 2003 Mar;33 Suppl:305-10. PMID: 12610540