6,714 research outputs found
Reconstruction of Causal Networks by Set Covering
We present a method for the reconstruction of networks, based on the order of
nodes visited by a stochastic branching process. Our algorithm reconstructs a
network of minimal size that ensures consistency with the data. Crucially, we
show that global consistency with the data can be achieved through purely local
considerations, inferring the neighbourhood of each node in turn. The
optimisation problem solved for each individual node can be reduced to a Set
Covering Problem, which is known to be NP-hard but can be approximated well in
practice. We then extend our approach to account for noisy data, based on the
Minimum Description Length principle. We demonstrate our algorithms on
synthetic data, generated by an SIR-like epidemiological model.Comment: Under consideration for the ECML PKDD 2010 conferenc
Adaptive evolution of transcription factor binding sites
The regulation of a gene depends on the binding of transcription factors to
specific sites located in the regulatory region of the gene. The generation of
these binding sites and of cooperativity between them are essential building
blocks in the evolution of complex regulatory networks. We study a theoretical
model for the sequence evolution of binding sites by point mutations. The
approach is based on biophysical models for the binding of transcription
factors to DNA. Hence we derive empirically grounded fitness landscapes, which
enter a population genetics model including mutations, genetic drift, and
selection. We show that the selection for factor binding generically leads to
specific correlations between nucleotide frequencies at different positions of
a binding site. We demonstrate the possibility of rapid adaptive evolution
generating a new binding site for a given transcription factor by point
mutations. The evolutionary time required is estimated in terms of the neutral
(background) mutation rate, the selection coefficient, and the effective
population size. The efficiency of binding site formation is seen to depend on
two joint conditions: the binding site motif must be short enough and the
promoter region must be long enough. These constraints on promoter architecture
are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive
evolution of genetic switches and of signal integration through binding
cooperativity between different sites. Experimental tests of this picture
involving the statistics of polymorphisms and phylogenies of sites are
discussed.Comment: published versio
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