Dirk Husmeier

Summary

Affiliation: Biomathematics and Statistics Scotland
Country: UK

Publications

  1. ncbi request reprint Probabilistic divergence measures for detecting interspecies recombination
    D Husmeier
    Biomathematics and Statistics Scotland, SCRI, Invergowrie, Dundee, DD2 5DA, UK
    Bioinformatics 17:S123-31. 2001
  2. doi request reprint Addressing the shortcomings of three recent Bayesian methods for detecting interspecific recombination in DNA sequence alignments
    Dirk Husmeier
    Biomathematics and Statistics Scotland
    Stat Appl Genet Mol Biol 7:Article 34. 2008
  3. pmc Modelling transcriptional regulation with a mixture of factor analyzers and variational bayesian expectation maximization
    Kuang Lin
    Biomathematics and Statistics Scotland BioSS, Edinburgh EH93JZ, UK
    EURASIP J Bioinform Syst Biol 2009:601068. 2009
  4. ncbi request reprint Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models
    Dirk Husmeier
    Biomathematics and Statistics, Scotland, Edinburgh, UK
    Bioinformatics 21:ii166-72. 2005
  5. ncbi request reprint Detecting interspecific recombination with a pruned probabilistic divergence measure
    Dirk Husmeier
    Biomathematics and Statistics Scotland, JCMB The King s Buildings, Edinburgh, UK
    Bioinformatics 21:1797-806. 2005
  6. ncbi request reprint Detecting recombination with MCMC
    Dirk Husmeier
    Biomathematics and Statistics Scotland BioSS, JCMB, The King s Buildings, Edinburgh EH9 3JZ, UK
    Bioinformatics 18:S345-53. 2002
  7. ncbi request reprint Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
    Dirk Husmeier
    Biomathematics and Statistics Scotland, JCMB, The King s Buildings, Edinburgh, EH9 3JZ, UK
    Bioinformatics 19:2271-82. 2003
  8. ncbi request reprint Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo
    Dirk Husmeier
    Biomathematics and Statistics Scotland, JCMB, King s Buildings, Edinburgh, United Kingdom
    Mol Biol Evol 20:315-37. 2003
  9. ncbi request reprint A Bayesian approach to discriminate between alternative DNA sequence segmentations
    Dirk Husmeier
    Biomathematics and Statistics Scotland, SCRI, Invergowrie, Dundee DD2 5DA, UK
    Bioinformatics 18:226-34. 2002
  10. ncbi request reprint Bayesian integration of biological prior knowledge into the reconstruction of gene regulatory networks with Bayesian networks
    Dirk Husmeier
    Biomathematics and Statistics Scotland, Edinburgh, United Kingdom
    Comput Syst Bioinformatics Conf 6:85-95. 2007

Detail Information

Publications20

  1. ncbi request reprint Probabilistic divergence measures for detecting interspecies recombination
    D 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...
  2. doi request reprint Addressing the shortcomings of three recent Bayesian methods for detecting interspecific recombination in DNA sequence alignments
    Dirk 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...
  3. pmc Modelling transcriptional regulation with a mixture of factor analyzers and variational bayesian expectation maximization
    Kuang 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...
  4. ncbi request reprint Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models
    Dirk 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...
  5. ncbi request reprint Detecting interspecific recombination with a pruned probabilistic divergence measure
    Dirk 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...
  6. ncbi request reprint Detecting recombination with MCMC
    Dirk Husmeier
    Biomathematics and Statistics Scotland BioSS, JCMB, The King s Buildings, Edinburgh EH9 3JZ, UK
    Bioinformatics 18:S345-53. 2002
    ..The algorithm returns the site-dependent posterior probability of each tree topology, which is used for detecting recombinant regions and locating their breakpoints...
  7. ncbi request reprint Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
    Dirk 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...
  8. ncbi request reprint Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo
    Dirk Husmeier
    Biomathematics and Statistics Scotland, JCMB, King s Buildings, Edinburgh, United Kingdom
    Mol Biol Evol 20:315-37. 2003
    ....
  9. ncbi request reprint A Bayesian approach to discriminate between alternative DNA sequence segmentations
    Dirk Husmeier
    Biomathematics and Statistics Scotland, SCRI, Invergowrie, Dundee DD2 5DA, UK
    Bioinformatics 18:226-34. 2002
    ..The objective of the present article is to devise an approximate Bayesian hypothesis test to discriminate between alternative candidate mosaic structures...
  10. ncbi request reprint Bayesian integration of biological prior knowledge into the reconstruction of gene regulatory networks with Bayesian networks
    Dirk 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...
  11. pmc TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
    Iain Milne
    Scottish Crop Research Institute, Invergowrie, Dundee, UK
    Bioinformatics 25:126-7. 2009
    ..Phylogenetic software available includes PhyML, RAxML and MrBayes...
  12. ncbi request reprint TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments
    Iain Milne
    Biomathematics and Statistics Scotland, SCRI, Dundee, DD2 5DA, UK
    Bioinformatics 20:1806-7. 2004
    ..In addition to its sophisticated interface, TOPALi can import many sequence formats, estimate and display phylogenetic trees and allow interactive analysis and/or automatic HTML report generation...
  13. ncbi request reprint Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
    Adriano 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...
  14. doi request reprint Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler
    Marco Grzegorczyk
    School of Biological Sciences, The University of Edinburgh, Swann Building, King s Buildings, Edinburgh, UK
    Bioinformatics 24:2071-8. 2008
    ....
  15. doi request reprint Reverse engineering gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum
    Kuang 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...
  16. ncbi request reprint Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge
    Adriano V Werhli
    Biomathematics and Statistics Scotland BioSS and Edinburgh University, UK
    Stat Appl Genet Mol Biol 6:Article15. 2007
    ....
  17. ncbi request reprint Segregation and recombination of a multipartite mitochondrial DNA in populations of the potato cyst nematode Globodera pallida
    Miles 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...
  18. ncbi request reprint Gene regulatory network reconstruction by Bayesian integration of prior knowledge and/or different experimental conditions
    Adriano 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...
  19. ncbi request reprint A regularized discriminative model for the prediction of protein-peptide interactions
    Wolfgang 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...
  20. ncbi request reprint A heuristic Bayesian method for segmenting DNA sequence alignments and detecting evidence for recombination and gene conversion
    Anna 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...