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Bioinformatics

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Bioinformatics involves the use of techniques including applied mathematics, informatics, statistics, computer science, chemistry, and biochemistry to solve biological problems. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution.

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Introduction

The terms bioinformatics and computational biology are often used interchangeably. However bioinformatics more properly refers to the creation and advancement of algorithms, computational and statistical techniques, and theory to solve formal and practical problems inspired from the management and analysis of biological data. Computational biology, on the other hand, refers to hypothesis-driven investigation of a specific biological problem using computers, carried out with experimental or simulated data, with the primary goal of discovery and the advancement of biological knowledge. Put more simply, bioinformatics is concerned with the information while computational biology is concerned with the hypotheses. A similar distinction is made by National Institutes of Health in their working definitions of Bioinformatics and Computational Biology, where it is further emphasized that there is a tight coupling of developments and knowledge between the more hypothesis-driven research in computational biology and technique-driven research in bioinformatics.

Evolutionary biology is the study of the origin and descent of species, as well as their change over time. Informatics has assisted evolutionary biologists in several key ways; it has enabled researchers to:

<ul>

<li>trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone, </li> <li>more recently, compare entire genomes, which permits the study of more complex evolutionary events, such as gene duplication, lateral gene transfer, and the prediction of bacterial speciation factors, </li> <li>build complex computational models of populations to predict the outcome of the system over time </li> <li>track and share information on an increasingly large number of species and organisms </li>

</ul>

Future work endeavours to reconstruct the now more complex tree of life.

Computational technologies are used to accelerate or fully automate the processing, quantification and analysis of large amounts of high-information-content biomedical imagery. Modern image analysis systems augment an observer's ability to make measurements from a large or complex set of images, by improving accuracy, objectivity, or speed. A fully developed analysis system may completely replace the observer. Although these systems are not unique to biomedical imagery, biomedical imaging is becoming more important for both diagnostics and research. Some examples are:

<ul>

<li>high-throughput and high-fidelity quantification and sub-cellular localization (high-content screening, cytohistopathology) </li> <li>morphometrics </li> <li>clinical image analysis and visualization </li> <li>determining the real-time air-flow patterns in breathing lungs of living animals </li> <li>quantifying occlusion size in real-time imagery from the development of and recovery during arterial injury </li> <li>making behavioral observations from extended video recordings of laboratory animals </li> <li>infrared measurements for metabolic activity determination </li>

</ul>

<ul>

<li>Biocybernetics </li> <li>Bioinformatics companies </li> <li>Biologically-inspired computing </li> <li>Biomedical informatics </li> <li>Computational biology </li> <li>Computational biomodeling </li> <li>Computational genomics </li> <li>Dot plot (bioinformatics) </li>

</ul>

</td>

<ul>

<li>Metabolic network modelling </li> <li>Molecular modelling </li> <li>Morphometrics </li> <li>Natural computation </li> <li>Pharmaceutical company </li> <li>Protein-protein interaction prediction </li> <li>List of numerical analysis software </li>

</ul>

</td>

<ul>

<li>Applied mathematics </li> <li>Artificial intelligence </li> <li>Biology </li> <li>Cheminformatics </li> <li>Computational biology </li>

</ul>

</td>

<ul>

<li>Computational science </li> <li>Computer science </li> <li>Cybernetics </li> <li>Informatics </li> <li>Mathematical biology </li>

</ul>

</td>

<ul>

<li>Neuroinformatics </li> <li>Scientific computing </li> <li>Statistics </li> <li>Systems biology </li> <li>Theoretical biology </li>

</ul>

</td>

References

<ul>

<li>Aluru, Srinivas, ed. Handbook of Computational Molecular Biology. Chapman & Hall/Crc, 2006. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=1584884061">ISBN 1584884061</a> (Chapman & Hall/Crc Computer and Information Science Series) </li> <li>Baldi, P and Brunak, S, Bioinformatics: The Machine Learning Approach, 2nd edition. MIT Press, 2001. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=026202506X">ISBN 0-262-02506-X</a> </li> <li>Barnes, M.R. and Gray, I.C., eds., Bioinformatics for Geneticists, first edition. Wiley, 2003. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0470843942">ISBN 0-470-84394-2</a> </li> <li>Baxevanis, A.D. and Ouellette, B.F.F., eds., Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, third edition. Wiley, 2005. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0471478784">ISBN 0-471-47878-4</a> </li> <li>Baxevanis, A.D., Petsko, G.A., Stein, L.D., and Stormo, G.D., eds., Current Protocols in Bioinformatics. Wiley, 2007. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0471250937">ISBN 0-471-25093-7</a> </li> <li>Claverie, J.M. and C. Notredame, Bioinformatics for Dummies. Wiley, 2003. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0764516965">ISBN 0-7645-1696-5</a> </li> <li>Cristianini, N. and Hahn, M. <a class="external text" title="http://www.computational-genomics.net/" rel="nofollow" href="http://www.computational-genomics.net/">Introduction to Computational Genomics</a>, Cambridge University Press, 2006. (<a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=9780521671910">ISBN 9780521671910</a> | <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0521671914">ISBN 0521671914</a>) </li> <li>Durbin, R., S. Eddy, A. Krogh and G. Mitchison, Biological sequence analysis. Cambridge University Press, 1998. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0521629713">ISBN 0-521-62971-3</a> </li> <li>Gilbert, D. <a class="external text" title="http://bib.oxfordjournals.org/cgi/content/abstract/5/3/300" rel="nofollow" href="http://bib.oxfordjournals.org/cgi/content/abstract/5/3/300">Bioinformatics software resources</a>. Briefings in Bioinformatics, Briefings in Bioinformatics, 2004 5(3):300-304. </li> <li>Keedwell, E., Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques to Bioinformatics Problems. Wiley, 2005. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0470021756">ISBN 0-470-02175-6</a> </li> <li>Kohane, et al. Microarrays for an Integrative Genomics. The MIT Press, 2002. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=026211271X">ISBN 0-262-11271-X</a> </li> <li>Lund, O. et al. Immunological Bioinformatics. The MIT Press, 2005. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0262122804">ISBN 0-262-12280-4</a> </li> <li>Michael S. Waterman, Introduction to Computational Biology: Sequences, Maps and Genomes. CRC Press, 1995. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0412993910">ISBN 0-412-99391-0</a> </li> <li>Mount, David W. Bioinformatics: Sequence and Genome Analysis Spring Harbor Press, May 2002. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0879696087">ISBN 0-87969-608-7</a> </li> <li>Pachter, Lior and <a title="Bernd Sturmfels" href="http://en.wikipedia.org/wiki/Bernd_Sturmfels">Sturmfels, Bernd</a>. "Algebraic Statistics for Computational Biology" Cambridge University Press, 2005. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0521857007">ISBN 0-521-85700-7</a> </li> <li>Pevzner, Pavel A. Computational Molecular Biology: An Algorithmic Approach The MIT Press, 2000. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0262161974">ISBN 0-262-16197-4</a> </li>

</ul>

External links

</div>

</div>

<li>[http://bioinformatics.ws Bioinformatics.ws]: Bioinformatics wiki site.</li>

<li>[http://biomatics.org Biomatics.org]</li>

<li><a class="external text" title="http://bioinformatics.org/" rel="nofollow" href="http://bioinformatics.org/">Bioinformatics Organization (Bioinformatics.Org): The Open-Access Institute</a> </li> <li><a class="external text" title="http://www.embnet.org/" rel="nofollow" href="http://www.embnet.org/">EMBnet</a> </li> <li><a class="external text" title="http://www.ebi.ac.uk/" rel="nofollow" href="http://www.ebi.ac.uk/">European Bioinformatics Institute</a> </li> <li><a class="external text" title="http://www.embl.org/" rel="nofollow" href="http://www.embl.org/">European Molecular Biology Laboratory</a> </li> <li><a class="external text" title="http://www.iscb.org/" rel="nofollow" href="http://www.iscb.org/">The International Society for Computational Biology</a> </li> <li><a class="external text" title="http://www.ncbi.nlm.nih.gov/" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/">National Center for Biotechnology Information</a> </li> <li><a class="external text" title="http://www.nih.gov" rel="nofollow" href="http://www.nih.gov/">National Institutes of Health homepage</a> </li> <li><a class="external text" title="http://www.open-bio.org/" rel="nofollow" href="http://www.open-bio.org/">Open Bioinformatics Foundation: umbrella non-profit organization supporting certain open-source projects in bioinformatics</a> </li> <li><a title="Swiss Institute of Bioinformatics" href="http://en.wikipedia.org/wiki/Swiss_Institute_of_Bioinformatics">Swiss Institute of Bioinformatics</a> </li> <li><a title="Wellcome Trust Sanger Institute" href="http://en.wikipedia.org/wiki/Wellcome_Trust_Sanger_Institute">Wellcome Trust Sanger Institute</a> </li>

</ul>

</li>

<li>Major Journals

<ul>

<li><a class="external text" title="http://www.almob.org/" rel="nofollow" href="http://www.almob.org/">Algorithms in Molecular Biology</a> </li> <li><a class="external text" title="http://bioinformatics.oupjournals.org/" rel="nofollow" href="http://bioinformatics.oupjournals.org/">Bioinformatics journal</a> </li> <li><a class="external text" title="http://www.biomedcentral.com/bmcbioinformatics" rel="nofollow" href="http://www.biomedcentral.com/bmcbioinformatics">BMC Bioinformatics journal</a> </li> <li><a class="external text" title="http://bib.oxfordjournals.org/" rel="nofollow" href="http://bib.oxfordjournals.org/">Briefings in Bioinformatics</a> </li> <li><a class="external text" title="http://www.la-press.com/evolbio.htm" rel="nofollow" href="http://www.la-press.com/evolbio.htm">Evolutionary Bioinformatics</a> </li> <li><a class="external text" title="http://www.genome.org" rel="nofollow" href="http://www.genome.org/">Genome Research</a> </li> <li><a class="external text" title="http://www.bepress.com/ijb/" rel="nofollow" href="http://www.bepress.com/ijb/">The International Journal of Biostatistics</a> </li> <li><a class="external text" title="http://www.liebertpub.com/publication.aspx?pub_id=31" rel="nofollow" href="http://www.liebertpub.com/publication.aspx?pub_id=31">Journal of Computational Biology</a> </li> <li><a class="external text" title="http://www.nature.com/msb/index.html" rel="nofollow" href="http://www.nature.com/msb/index.html">Molecular Systems Biology</a> </li> <li><a class="external text" title="http://compbiol.plosjournals.org" rel="nofollow" href="http://compbiol.plosjournals.org/">PLoS Computational Biology</a> </li> <li><a class="external text" title="http://www.bepress.com/sagmb/" rel="nofollow" href="http://www.bepress.com/sagmb/">Statistical Applications in Genetic and Molecular Biology</a> </li>

</ul>

</li>

<li>Other sites

<ul>

<li><a class="external text" title="http://www.biostatsresearch.com/repository/" rel="nofollow" href="http://www.biostatsresearch.com/repository/">The Collection of Biostatistics Research Archive</a> </li> <li><a class="external text" title="http://www.ornl.gov/TechResources/Human_Genome/research/informatics.html" rel="nofollow" href="http://www.ornl.gov/TechResources/Human_Genome/research/informatics.html">Human Genome Project and Bioinformatics</a> </li> <li><a class="external text" title="http://dmoz.org/Science/Biology/Bioinformatics/Research_Groups/" rel="nofollow" href="http://dmoz.org/Science/Biology/Bioinformatics/Research_Groups/">List of Bioinformatics Research Groups</a> at the <a title="Open Directory Project" href="http://en.wikipedia.org/wiki/Open_Directory_Project">Open Directory Project</a> </li>

</ul>

</li>

[http://bioinformatics.ws Bioinformatics.ws] | [http://biomics.org Biomics.org]

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