Philip Gerlee's Research

Tree of Life

2011-11-02T03:24:00.000-07:00

The posts on the blog have unfortunately been far and few between, but here's a tip about nice homepage about evolution and the tree of life:

http://tolweb.org/tree/

Kepler Workshop in Heidelberg

2011-05-27T02:05:00.001-07:00

Last week I attended a highly interesting workshop organised by Marcello Delitala in Heidelberg. The topic was "Managing complexity, reducing perplecity" and included talks by both mathematicians and biologists. Some visual impressions:

Gösta Mittag-Leffler

2011-05-27T02:02:00.000-07:00

The old man himself:

Tampa

2011-05-27T01:59:00.000-07:00

A couple of weeks ago I visited the IMO group in Tampa. Here's a picture of me in their "collaboratorium".

Books, books and books

2011-01-20T00:39:00.001-08:00

Just received my latest shipment of books.

Mathematical stability

2011-01-13T05:46:00.000-08:00

The above plot was generated by Google ngrams which, based on all documents in Google Books, calculates the relative usage of a word or sequence of words. Some subjects gain, and subsequently loose popularity, while others seem more stable.

New year and old challenges

2011-01-05T05:17:00.000-08:00

More than a month of snow and ice, and now end to it in sight. Good times for staying indoors and reading. My aim is to read through "Towards a theoretical biology" vol. 1-4 from the 1960s. This series was the result of 4 biyearly symposia organised by Waddington and try to define the challenges and set the course for theoretical biology as a discipline. I wonder if we succeeded?

New place

2010-08-05T05:49:00.000-07:00

On Monday I started my new position at Sahlgrenska/Chalmers. Settling in slowly and enjoying being back in Gothenburg after 5 years abroad. A few conferences coming up: first the IMS in Gbg, then going to a workshop in Smögen on Spatio-temporal modelling, and then finally to the most anticipated meeting this year: Alife XII in Odense.

Holidays

2010-06-23T06:24:00.000-07:00

Holidays are approaching fast, and at the other end of relaxing, swimming and going on road trips, I'll reappear in Gothenburg for my new job as a post-doc with Sven Nelander funded by the Assar Gabrielsson foundation.

Cycling

2010-04-28T11:47:00.000-07:00

Fixed gear race in the south of Sweden. 110 km full of sweat, gravel and sunshine. Does it get any better?

Word cloud

2010-03-23T07:30:00.000-07:00

This was created with wordle and is based on the full text from all my papers so far. Probably gives a good picture of what I spend my time on.

Evolution

2010-03-18T01:04:00.000-07:00

Yesterday I got a paper accepted in the journal Evolution. The title of paper is "Productivity and diversity in a cross-feeding population of artificial organisms" and investigates the dynamics and properties of a new Alife-platform called Urdar. Please have a look at the preprint and the very nice applet.

Various Aspects of Evolution

2010-02-01T00:32:00.000-08:00

On February the 4th I'm going to Gothenburg University for a whole day of talk on various aspects of evolution. Looking forward to it.

http://www.science.gu.se/infoglueCalendar/digitalAssets/1768968428_BifogadFil_researchday2010.pdf

First Meeting

2009-12-20T12:00:00.000-08:00

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

2009-12-15T02:44:00.000-08:00

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

Back from Florida

2009-12-08T02:14:00.000-08:00

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

2009-10-21T00:56:00.000-07:00

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

2009-09-29T00:55:00.000-07:00

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

2009-09-29T00:47:00.000-07:00

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....

2009-03-18T07:18:00.000-07:00

...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!

2009-02-13T10:47:00.000-08:00

Doing science at the Integrative Mathematical Oncology group in Tampa.

Accepted!

2009-02-11T07:25:00.000-08:00

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

2009-02-11T07:20:00.000-08:00

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.

Holidays!

2008-12-19T06:29:00.000-08:00

For 3 weeks I'm going to swap hectic and intense research for relaxing holidays and expect to come back with fresh ideas and new enthusiasm. God jul!

The opening night

2008-12-01T05:31:00.000-08:00

After months of intense preparation and planning I finally pulled myself together and got my new homepage online. In an effort to minimise effort and thus maximise output I've decided to make use of the blogg format, hopefully it'll mean more frequent updates than before, so please check back soon...