Bioinformatics

What's Bioinformatics ?

Copyright© Kerstin Wagner

• many names, for instance, boinformatics, biocomputing, biological computing, computational biology, computational genomics, biological data mining ...
• no formal definition of bioinformatics
• field of science in which biology, computer science and information technology merge into a single discipline
• development and application of computing, mathematical and statistical methods to analyze biological, biochemical and biophysical data
• employs computers to store, retrieve, analyze and assist in understanding biological information
• multidisciplinary field required in-depth knowledge of e.g. mathematics, algorithms, statistics, data mining, natural lanquage processing, genome science, sequence analysis, molecular biology, pharmacology, biophysics, hardware engineering and software programming

3 important sub-disciplines

• development and implementation of tools to access and manage different types of information
• analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains and protein structures
• development of new algorithms and statistics to assess relationships in large data sets

• provide new insights into biological function
• understand the functioning of living things
• to apply the knowledge for "improving the quality of life" (in order to understand and fight against diseases)
• databases (design, handling, ...)
• gene and genome mapping
• analysis of gene expression data
• search for gene functions
• identification of genetic risk factors
• pathways, metabolic and regulatoric networks (modelling, simulation, ...)
• structure prediction (protein folding, sequence alignments, homology search, ...)
• target identification
• drug design (docking studies, HTS, screening tests, ...)
• gene therapy
• ...

• sequence data
• structural information
• expression data
• molecular interaction data
• mutation data
• phenotypic data
• ...

• post-genome applications
• sequence analyses
• protein structure prediction
• data processing, data management
• database searches
• phylogentic analyses
• gene expression, expression data analysis
• recognition of genes and regulatory elements
• visualization, modelling and simulation of metabolic pathways and regulatory networks
• software tools
• ...

Biological Information Flow

Bioinformatics attempts to model and interprets this pathway:

genome -> introns/exons -> gene sequence -> protein sequence -> protein structure -> protein function - cellular pathways & networks

Genomics	sequencing, comparative genomics, genome annotation, microarray technology
Proteomics	protein structure, 3D structural prediction, cellular pathways & networks (regulatory and metabolic

Additional Information

• Bioinformatik: Jäger, Sammler und Forscher im Daten-Dschungel der Molekularbiologie. Evers, D.; R. Giegerich, Bericht - Forschung an der Univ. Bielefeld 1998, 17, 49-57. [PDF]
• Bioinformatik: Werkzeug und Schlüssel zur Genomanalyse. Mewes, H.-W.; Mensch+Umwelt (GSF Special) 2003, 16, 26-29. [PDF]
• Bioinformatik als Werkzeug und Schlüssel zur Genomanalyse. Vom Schlüssel zur Funktion - Genforschung in der GSF, 2002, 56-60. [PDF]
• Bioinformatik - Eine Schlüsseltechnologie. Martin, W.; Jahrbuch der Heinrich Heine Universität Düsseldorf 2001, 157-182. [HTML I PDF]

• Bioinformatics. A user's perspective. Kaminski, N.; Am. J. Respir. Cell Mol. Biol. 2000, 23(6), 705-711. [PDF I PubMed]
• Bioinformatics: bringing it all together. Chicurel, M.; Nature 2002, 419(6908), 751-757. [PDF I PubMed]
• Bioinformatics in the post-sequence era. Kanehisa, M.; Bork, P.; Nat. Genet. 2003, 33(Suppl.), 305-310. [PDF I PubMed]
• Disease proteomics. Hanash, S.; Nature 2003, 422(6928), 226-232. [PDF I PubMed]
• Functional genomics and proteomics as a foundation for systems biology. Aggarwal, K.; Lee, K.H.; Briefings in Functional Genomics and Proteomics 2003, 2(3), 175-184. [PDF]
• Systems biology. Life's complexity pyramid. Oltvai, Z.N.; Barabasi, A.L.; Science 2002, 298(5594), 763-764. [PDF I PubMed]
• Taking a functional genomics approach in molecular medicine. Yaspo, M.L.; Trends Mol. Med. 2001, 7(11), 494-501. [PDF I PubMed]
• What is bioinformatics? An introduction and overview. Luscombe, N.M.; Greenbaum, D.; Gerstein, M.; Yearbook of Medial Informatics, Intl. Medical Informatics Association 2001, 83-100. [PDF]

• BIOINFORMATICS - Introduction. (by Mark Gerstein, Yale University) [PDF]

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