Affiliation: Biomathematics and Statistics Scotland
- Probabilistic divergence measures for detecting interspecies recombinationD Husmeier
Biomathematics and Statistics Scotland, SCRI, Invergowrie, Dundee, DD2 5DA, UK
Bioinformatics 17:S123-31. 2001..The method is compared with established detection methods on a set of synthetic benchmark sequences and two real-world DNA sequence alignments...
- Addressing the shortcomings of three recent Bayesian methods for detecting interspecific recombination in DNA sequence alignmentsDirk Husmeier
Biomathematics and Statistics Scotland
Stat Appl Genet Mol Biol 7:Article 34. 2008..We then propose a revised model that addresses these shortcomings, and compare it with the aforementioned models on a set of synthetic DNA sequence alignments systematically generated around the Felsenstein zone...
- Modelling transcriptional regulation with a mixture of factor analyzers and variational bayesian expectation maximizationKuang Lin
Biomathematics and Statistics Scotland BioSS, Edinburgh EH93JZ, UK
EURASIP J Bioinform Syst Biol 2009:601068. 2009..We have evaluated the performance of the proposed method on three criteria: activity profile reconstruction, gene clustering, and network inference...
- Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov modelsDirk Husmeier
Biomathematics and Statistics, Scotland, Edinburgh, UK
Bioinformatics 21:ii166-72. 2005..Inference is done in terms of a hierarchical Bayesian model, where parameters and hidden states are sampled from the posterior distribution with Gibbs sampling...
- Detecting interspecific recombination with a pruned probabilistic divergence measureDirk Husmeier
Biomathematics and Statistics Scotland, JCMB The King s Buildings, Edinburgh, UK
Bioinformatics 21:1797-806. 2005..The present study investigates how this shortcoming can be redeemed with a pruning method based on post-processing clustering, using the Robinson-Foulds distance as a metric in tree topology space...
- Detecting recombination with MCMCDirk Husmeier
Biomathematics and Statistics Scotland BioSS, JCMB, The King s Buildings, Edinburgh EH9 3JZ, UK
Bioinformatics 18:S345-53. 2002..RESULTS: The method was tested on a synthetic and three real DNA sequence alignments, where it was found to outperform the established detection methods PLATO, RECPARS, and TOPAL...
- Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networksDirk Husmeier
Biomathematics and Statistics Scotland, JCMB, The King s Buildings, Edinburgh, EH9 3JZ, UK
Bioinformatics 19:2271-82. 2003..Then, interaction networks are inferred from these data in a reverse engineering approach, using Bayesian networks and Bayesian learning with Markov chain Monte Carlo...
- Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte CarloDirk Husmeier
Biomathematics and Statistics Scotland, JCMB, King s Buildings, Edinburgh, United Kingdom
Mol Biol Evol 20:315-37. 2003....
- A Bayesian approach to discriminate between alternative DNA sequence segmentationsDirk Husmeier
Biomathematics and Statistics Scotland, SCRI, Invergowrie, Dundee DD2 5DA, UK
Bioinformatics 18:226-34. 2002..On the synthetic data, the algorithm identified the true mosaic structure in nine out of ten cases. On the real-world sequence alignments, it selected the same mosaic structures as predicted in the literature...
- Bayesian integration of biological prior knowledge into the reconstruction of gene regulatory networks with Bayesian networksDirk Husmeier
Biomathematics and Statistics Scotland, Edinburgh, United Kingdom
Comput Syst Bioinformatics Conf 6:85-95. 2007..We have assessed the viability of this approach by reconstructing the RAF pathway from cytometry protein concentrations and prior knowledge from KEGG...
- TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktopsIain Milne
Scottish Crop Research Institute, Invergowrie, Dundee, UK
Bioinformatics 25:126-7. 2009..Phylogenetic software available includes PhyML, RAxML and MrBayes. AVAILABILITY: Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris...
- TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignmentsIain Milne
Biomathematics and Statistics Scotland, SCRI, Dundee, DD2 5DA, UK
Bioinformatics 20:1806-7. 2004..AVAILABILITY: TOPALi is freely available from http://www.bioss.ac.uk/software.html..
- Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networksAdriano V Werhli
Biomathematics and Statistics Scotland, Edinburgh, UK
Bioinformatics 22:2523-31. 2006..We use both laboratory data from cytometry experiments as well as data simulated from the gold-standard network. We also compare passive observations with active interventions...
- Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation samplerMarco Grzegorczyk
School of Biological Sciences, The University of Edinburgh, Swann Building, King s Buildings, Edinburgh, UK
Bioinformatics 24:2071-8. 2008....
- Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticumKuang Lin
Biomathematics and Statistics Scotland, Edinburgh and Aberdeen, UK
Methods Mol Biol 673:253-81. 2010..The chapter concludes with a biological evaluation of the predicted network structures...
- Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledgeAdriano V Werhli
Biomathematics and Statistics Scotland BioSS and Edinburgh University, UK
Stat Appl Genet Mol Biol 6:Article15. 2007....
- Segregation and recombination of a multipartite mitochondrial DNA in populations of the potato cyst nematode Globodera pallidaMiles R Armstrong
Plant Pathogen Programme, Scottish Crop Research Institute, Invergowrie, Dundee, UK
J Mol Evol 64:689-701. 2007..The mosaic structure of P4A scmtDNA IV sequences was revealed using several detection methods and recombination breakpoints were independently detected by maximum likelihood and Bayesian MCMC methods...
- Gene regulatory network reconstruction by Bayesian integration of prior knowledge and/or different experimental conditionsAdriano V Werhli
Department of Computing Science, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
J Bioinform Comput Biol 6:543-72. 2008..We have assessed the viability of all proposed methods on data related to the Raf signaling pathway, generated both synthetically and in cytometry experiments...
- A regularized discriminative model for the prediction of protein-peptide interactionsWolfgang P Lehrach
University of Edinburgh, Edinburgh EH1 2QL, UK
Bioinformatics 22:532-40. 2006..As proposed by Williams, we overcome the problem of susceptibility to over-fitting by adopting a Bayesian a posteriori approach based on a Laplacian prior in parameter space...
- A heuristic Bayesian method for segmenting DNA sequence alignments and detecting evidence for recombination and gene conversionAnna Kedzierska
Wroclaw University of Technology, Poland
Stat Appl Genet Mol Biol 5:Article27. 2006..To this end, we apply reversible jump MCMC, and sample the number of hidden states from the respective posterior distribution...