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SUMMARY TOPALi is a new Java graphical analysis application that allows the user to identify recombinant sequences within a DNA multiple alignment (either automatically or via manual investigation). TOPALi allows a choice of three statistical methods to predict the positions of breakpoints due to past recombination. The breakpoint predictions are then used(More)
MOTIVATION Bayesian networks have been applied to infer genetic regulatory interactions from microarray gene expression data. This inference problem is particularly hard in that interactions between hundreds of genes have to be learned from very small data sets, typically containing only a few dozen time points during a cell cycle. Most previous studies(More)
MOTIVATION An important problem in systems biology is the inference of biochemical pathways and regulatory networks from postgenomic data. Various reverse engineering methods have been proposed in the literature, and it is important to understand their relative merits and shortcomings. In the present paper, we compare the accuracy of reconstructing gene(More)
—A Bayesian-based methodology is presented which automatically penalizes overcomplex models being fitted to unknown data. We show that, with a Gaussian mixture model, the approach is able to select an " optimal " number of components in the model and so partition data sets. The performance of the Bayesian method is compared to other methods of optimal model(More)
There have been various attempts to improve the reconstruction of gene regulatory networks from microarray data by the systematic integration of biological prior knowledge. Our approach is based on pioneering work by Imoto et al. where the prior knowledge is expressed in terms of energy functions, from which a prior distribution over network structures is(More)
UNLABELLED TOPALi v2 simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments. Jobs are submitted from a Java graphical user interface as TOPALi web services to either run remotely on high-performance computing clusters or locally (with multiple cores supported). Methods available include model(More)
MOTIVATION Short well-defined domains known as peptide recognition modules (PRMs) regulate many important protein-protein interactions involved in the formation of macromolecular complexes and biochemical pathways. Since high-throughput experiments like yeast two-hybrid and phage display are expensive and intrinsically noisy, it would be desirable to more(More)
Parameter inference in mechanistic models based on systems of coupled differential equations is a topical yet computationally challenging problem, due to the need to follow each parameter adaptation with a numerical integration of the differential equations. Techniques based on gradient matching , which aim to minimize the discrepancy between the slope of a(More)
MOTIVATION A promising sliding-window method for the detection of interspecific recombination in DNA sequence alignments is based on the monitoring of changes in the posterior distribution of tree topologies with a probabilistic divergence measure. However, as the number of taxa in the alignment increases or the sliding-window size decreases, the posterior(More)