Medical Bioinformatics and e-Bioscience

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Bioinformatics and e-Bioscience show cases Ratings The show cases Phylogenetics: SARS Natural selection: HIV Comparative genomics / microarray analysis: dioxin Use of sequence databases: prion genes

Bioinformatics and e-Bioscience show cases

This page contains lectures, publications, and/or other material that show how bioinformatics and e-Bioscience is used to answer relevant/current biological/biomedical questions. Some of these cases are or were used as part of our course. Feel free to improve these presentations (provide versioning).

Ratings

All cases shown on this page should be suitable for demonstrating bioinformatics and e-BioScience. Nevertheless, a rating is given to all these cases:

• : Nice biomedical problem with background story but bioinformatics/e-Bioscience is not sufficiently worked out (yet)
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• : Good biomedical problem, societal relevance, excellent demonstration of power of bioinformatics/e-Bioscience, not too complex.

The show cases

Phylogenetics: SARS

• Title: Severe Acute Respiratory Syndrome (SARS): A post-genomic epidemic
• Aim: application of phylogenetic analysis to SARS
• Added by: Antoine van Kampen
• Rating:
• Source: Book: Introduction to computational genomics, a case study approach, Nello Cristianini and Matthew W. Hahn, ISBN 0 521 67191-4 (Cambridge University Press).
• Remarks:
• DOCUMENTS

Natural selection: HIV

• Title: Fighting the Human Immunodeficiency Virus (HIV): Natural selection at the molecular level
• Aim: Use of Ka / Ks ratio
• Added by: Antoine van Kampen
• Rating:
• Source: Book: Introduction to computational genomics, a case study approach, Nello Cristianini and Matthew W. Hahn, ISBN 0 521 67191-4 (Cambridge University Press).
• Remarks:
• DOCUMENTS

Comparative genomics / microarray analysis: dioxin

• Title: unraveling the molecular mechanisms of dixion toxification
• Aim: comparison of human, rat, mouse genomic sequences in combination with microarray analysis.
• Added by: Antoine van Kampen
• Rating:
• Source: Book: Introduction to computational genomics, a case study approach, Nello Cristianini and Matthew W. Hahn, ISBN 0 521 67191-4 (Cambridge University Press).
• Remarks: nice example of bioinformatics but unfortunately the outcome of this study is not very strong.
• DOCUMENTS

Use of sequence databases: prion genes

• Title: evidence for retrogene origins of the prion gene family
• Aim: unraveling the evolutionary and molecular mechanisms that led to prion genes in vertebrates.
• Added by: Antoine van Kampen
• Rating:
• Source: Associated PLoS ONE paper
• Remarks: nice example of use of sequence databases but argumentation may be difficult to follow if details are left out. Additional notes have been included with the powerpoint presentation.
• DOCUMENTS