Research Topics For Metabolic Network Reconstruction?

Question

[Ninhnn]

Hi guys,

I'm a newbie to computational biology. I can do algorithms, but am quite confusing with biology... I want to ask you guys this naive question:

What are the major research topics for metabolic network reconstruction?

Thank you!

ninh-n-n.

Answer 1

[Larry_Parnell]

One, describe the metabolic network of a drug taken orally. How is that compound metabolized by human and bacterial enzymes? How are the metabolites further metabolized?

Two, describe the metabolic networks involved in (important) bioactive food components? What happens to resveratrol, for example, as it passes through the human gut and is absorbed? How does the microbiome influence the digestion and absorption of dietary fatty acids? Polyphenols? Complex carbohydrates?

Admittedly, these two topics are complex, but they are topics to which those in pharmacokinetics and nutrition are increasingly turning their attention.

Answer 2

[Alex Paciorkowski]

An area of research interest might be the interface of metabolic networks with gene regulatory networks that are important for organism development. Specifically, there are brain malformations that are more common in patients with certain inherited disorders of metabolism (ie glycine encephalopathy and agenesis of the corpus callosum, just to give one example; another good one that's not understood are the multiple brain malformations seen associated with congenital disorders of glycosylation). It's not well understood how metabolic derangements during early embryonic development contribute to these types of recurrent structural malformations. These are just a couple of examples, and related to brain development, but there are multiple other metabolic pathways that would appear to intersect with development of other organ systems.

These are also complex, since they involve understanding not just a given metabolic network, but also the regulatory networks critical to correct patterning of the organism.

Answer 3

[Gjain]

some of the metabolic and biological network related articles that I find interesting:

biological networks

• Genome-scale metabolic networks
• A Survey on Methods for Modeling and Analyzing Integrated Biological Networks
• Reverse Engineering of Molecular Networks from a Common Combinatorial Approach
• Reverse engineering: the architecture of biological networks

metabolic networks

• Exploring the connectivity structure in metabolic networks
• The Evolution of Connectivity in Metabolic Networks
• The large-scale organization of metabolic networks
• Functional and topological characterization of protein interaction networks
• NETWORK BIOLOGY:UNDERSTANDING THE CELL’S FUNCTIONAL ORGANIZATION this is one of my fav paper
• Chemical Basis of Metabolic Network Organization

There are many more resources available. I think its a good start in a very interesting field.