CSB Assignment Week 8

Assignments for Week 8

Note! This assignment is currently active. All significant changes will be announced on the mailing list.

 
 

Exercises for this week relate to this week's lecture.
Pre-reading for this week will prepare next week's lecture.
Exercises and pre-reading will be topics on next week's quiz.

Exercises

None for this week.

Pre-reading

Villaverde & Banga (2014) Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J R Soc Interface 11:20130505. (pmid: 24307566)

[ PubMed ] [ DOI ] Abstract The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology?

Here is a useful introduction to the use of information theory, in particular mutual information for the analysis of signal transduction networks.

Waltermann & Klipp (2011) Information theory based approaches to cellular signaling. Biochim Biophys Acta 1810:924-32. (pmid: 21798319)

[ PubMed ] [ DOI ] Abstract BACKGROUND: Cells interact with their environment and they have to react adequately to internal and external changes such changes in nutrient composition, physical properties like temperature or osmolarity and other stresses. More specifically, they must be able to evaluate whether the external change is significant or just in the range of noise. Based on multiple external parameters they have to compute an optimal response. Cellular signaling pathways are considered as the major means of information perception and transmission in cells. SCOPE OF REVIEW: Here, we review different attempts to quantify information processing on the level of individual cells. We refer to Shannon entropy, mutual information, and informal measures of signaling pathway cross-talk and specificity. MAJOR CONCLUSIONS: Information theory in systems biology has been successfully applied to identification of optimal pathway structures, mutual information and entropy as system response in sensitivity analysis, and quantification of input and output information. GENERAL SIGNIFICANCE: While the study of information transmission within the framework of information theory in technical systems is an advanced field with high impact in engineering and telecommunication, its application to biological objects and processes is still restricted to specific fields such as neuroscience, structural and molecular biology. However, in systems biology dealing with a holistic understanding of biochemical systems and cellular signaling only recently a number of examples for the application of information theory have emerged. This article is part of a Special Issue entitled Systems Biology of Microorganisms.

Mutual information is at the core of a novel approach to quantify non-linear correlations in data. Read the perspective on this recent work here:

Speed (2011) Mathematics. A correlation for the 21st century. Science 334:1502-3. (pmid: 22174235)

[ PubMed ] [ DOI ]