home::research Last update: November 2009

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Research topics

Systems biology (*): Structure and function of modules in biological networks

In a great paper, Hartwell & co explain the principle that cellular functions are carried out by modules. Modules are composed of many types of molecules and have discrete functions that arise from the interactions among their components. Modules can be

The main questions in the study of biological modules are:

My current research focuses on the first question, more precisely on developing computational methods for the automatic identification of modules from various kinds of biological networks. In our group, we have developed a software package for learning module networks from gene expression data [paper 1, paper 2, paper 3]. Recently, I have started working on matrix and tensor methods for identifying modules in integrated networks [poster]. An initial matrix algorithm is already available. For more information, have a look at this recent presentation.

(*) What is systems biology?

"Systems biology is the study of dynamic networks of interacting biological elements."
R. Aebersold, Molecular Systems Biology: a new journal for a new biology?, Molecular Systems Biology 1:2005.0005 (2005).

"We expect to encounter fascinating and, I believe, very fundamental questions at each stage in fitting together less complicated pieces into the more complicated system and understanding the basically new types of behavior which can result."
P.W. Anderson, More is Different, Science 177:393 (1972).

"Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better."
J.E. Cohen, PLoS Biol 2:e439 (2004).

Statistical physics of DNA

The computation of the thermal stability and statistical physics of nucleic acids is a classical problem going back to the 1960's, with recent results relating the physics of denaturation (DNA strand separation) to the biology of genomes. Other experimental developments, which can also be modeled accurately by statistical physics, have made it possible to manipulate single polymeric molecules directly and offer access to a whole new range of DNA properties. Coming from physics, this topic was a nice introduction into the world of biology. I developed a Matlab toolbox for analyzing the melting properties of a non-linear helicoidal DNA model [paper].

Quantum statistical mechanics

This is the area where I worked for my PhD (at the ITF in Leuven) and first postdoc (at UCDavis). I still have a pleasant collaboration with Bruno Nachtergaele and Wolfgang Spitzer on this topic, nowadays mostly limited to writing code for numerical analysis, leaving the difficult mathematics to them. In our latest project we studied the transport of domain walls in quantum spin systems by moving external fields [paper]. For this study we developed a Matlab toolbox for performing ground state and time-dependent Density Matrix Renormalization Group computations for one-dimensional quantum spin systems which need not be translation invariant.

Publications

The links below lead to an abstract of the paper and a choice of download formats. [arXiv] points to the arXiv Preprint server and [journal] to the publisher of the paper; you can also download a [PDF] file directly.

Software

The links below lead to a [download] location of the software package and a list of [paper]'s which have used it.

Recent presentations

Service as reviewer

Genome Biology, PLoS Computational Biology, Bioinformatics, BMC Systems Biology, BMC Bioinformatics, Journal of Mathematical Physics, EURASIP Journal on Bioinformatics and Systems Biology, Current Proteomics

Lecture notes

C.V.