First Meeting

Some impressions from the meeting in Uppsala. Firstly Eva Kisdi and Philip Maini delivered excellent tutorials on Adaptive Dynamics and Pattern Formation respectively. The second day of the meeting offered talks from participants, and it was interesting to see how broad the field of maths biology is in Sweden, ranging from population dynamics to biofilm modelling. Already looking forward to next years meeting to be held in Göteborg.

Meeting in Uppsala and Holidays

Tomorrow I'm travelling to the meeting in Uppsala on Mathematical Biology, and after that it's Christmas time.

Back from Florida

I'm just back from a 2 week research visit at the Moffitt Cancer Center, where I have been working on cancer modelling, or more specifically, the relation between tissue homeostasis and cancer initiation. At the moment we're trying to develop a model in which we hope to analyse different modes of homeostasis, which in the long run will be used as a starting point for models of cancer.

The subject and object

Richard Lewontin is in my opinion a very fine scientist, so I thought I'd share my enthusiasm for one of his papers "The organism as the subject and object of evolution" in which he discusses the extent to which organisms themselves decide which "adaptive problems" to solve. Its very well written and one of my favourite papers ever. Enjoy!

First Swedish meeting on Theory and Mathematics in Biology and Medicine

The meeting takes place the 17-18th Dec in Uppsala and hopefully I'll make it there.

http://www.math.uu.se/cim/events/meeting2009.html

Pathway identification by network pruning in the metabolic network of Escherichia coli

New paper just accepted by Bioinformatics today! Link to the pdf, abstract below:

Motivation:
All metabolic networks contain metabolites which take part in many reactions, such as ATP and NAD, known as currency metabolites. These are often removed in the study of these networks, but no consensus exists on what actually constitutes a currency metabolite, and it is also unclear how these highly connected nodes contribute to the global structure of the network.

Results:
In this paper we analyse how the Escherichia coli metabolic network responds to pruning in the form of sequential removal of metabolites with highest degree. As expected this leads to network fragmentation, but the process by which it occurs suggest modularity and long range correlations within the network. We find that the pruned networks contain longer paths than the random expectation, and that the paths that survive the pruning also exhibit a lower cost (no. of involved metabolites) compared to random paths in the full metabolic network. Finally we confirm that paths detected by pruning overlap with known metabolic pathways.
We conclude that pruning reveals functional pathways in metabolic networks, where currency metabolites may be seen as ingredients in a well-balanced soup in which main metabolic production lines are immersed.

Sorry science....

...but the weather is better than in ages, and I'm dying for a spin on my fixie. I'll make it up to you tomorrow with some great discoveries!

Doing science at the Integrative Mathematical Oncology group in Tampa.

Accepted!

I just got a paper accepted in the "Journal of the Royal Society Interface" a fairly new interdisciplinary journal. The paper is on evolution of genetic architecture in yeast and digital organism, looking at similarities between real and digital evolution. I'm not sure when it will be published, but keep your eyes open!

Tampa, FL

At the moment I'm visiting my former supervisor Alexander "Sandy" Anderson, who's now at the H. Lee Moffitt Cancer Center & Research Institute. We've been working on the revision of a paper from my PhD-work called "Evolution of cell motility in an individual-based model of tumour growth", which hopefully will be out soon. Apart from that we're also starting on a new project which you'll hopefully hear more about soon.