Biomathematics & Statistics Scotland

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Dirk's Talks

Invited talks and presentations

• Machine learning and Bayesian statistics in computational systems biology. Third Southern conference on informatics and engineering, University of Rio Grande, Brazil, 23-25 November 2009
• Learning gene regulatory networks from gene expression time series with non-stationary dynamic Bayesian networks. International workshop on integrative network inference in systems biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany, 8-9 October 2009
• Lecture on learning gene regulatory networks from gene expression time series with non-linear/non-stationary dynamic Bayesian networks. EPSRC Symposium Workshop on Information extraction from complex data sets (INF), University of Warwick, 14-17 September 2009
• Systems biology in plant science. EUCARPIA XIV Meeting of the Biometrics in Plant Breeding Section, SCRI, Dundee, 2-4 September 2009
• Overview of computational systems biology at BioSS. Biweekly seminar, Moredun Research Institute, Edinburgh, 1 September 2009
• Network inference in systems genetics. StoMP: Noisy bugs - modelling and microbiology, eScience Centre Edinburgh, 14 July 2009
• Probabilistic models and Bayesian inference in systems biology. Invited talk in the Mathematics and Computer Science Seminar, Heriot-Watt University, 20 February 2009.
• Probabilistic models for learning gene regulatory networks. Invited talk. Queens University Belfast, 12 February 2009.
• Probabilistic models in systems biology. CSBE scientific advisory board meeting, University of Edinburgh, December 2008
• A Bayesian Method for Reconstructing Gene Regulatory Networks from Gene Expression Data and Biological Prior Knowledge.
  Joint Statistical Meetings - JSM 2008, Denver, Colorado, USA, August 2008.
• Learning Bayesian networks from postgenomic data with an improved structure MCMC sampling scheme. Workshop: Learning and Inference in Computational Systems Biology, University of Warwick, Centre for Systems Biology, June 2008.
• Probabilistic methods and graphical models in systems biology. Bioinformatics and Systems Biology in Scotland, Royal Society of Edinburgh, June 2008.
• Prior distributions and MCMC in systems biology
  Workshop on "Bridging Mathematics and Biology", International Centre for Mathematics Sciences, Edinburgh, UK, 22 April 2008
• Learning Bayesian networks from postgenomic data with an improved structure MCMC sampling scheme.
  Workshop on "Learning and Inference in Computational Systems Biology" , Glasgow, 26-27 March 2008
• Overview of BioSS's work on systems biology.
  CSBE retreat, Bush, Edinburgh, 13 December 2007
• Learning gene regulatory networks from postgenomic data and prior knowledge
  Workshop on Statistical Methods in Bioinformatics, Munich, 22-23 November 2007
• Comparing different machine learning approaches to mine for gene and protein associating patterns.
  Internal seminar at the MRC Human Genetics Unit, Western General Hospital, Edinburgh, 2 October 2007.
• Molecular regulatory network reconstruction by Bayesian integration of prior knowledge and/or different experimental conditions
  Pascal workshop on Practical Inference Methods for Mechanistic Modelling of Biological Systems Glasgow, 18-19 September 2007
• Lecture and talk on probabilistic models in systems biology.
  Regenstrief Institute for Medical Informatics, University of Indiana, Indianapolis, USA, 9 August 2007
• Analysis of high-dimensional data in bioinformatics
  Royal Statistical Society, St Leonard's Hall, Pollock Hall, Edinburgh, 13 July 2007
• Learning gene regulatory networks from postgenomic data using active interventions and biological prior knowledge.
  Lunchtime seminar, Roslin Insitute, 8 March 2007
• Inferring gene regulatory networks from expression data with Bayesian networks.
  Lunchtime seminar on complex systems Department of Mathematics, University of Bath, 26 February 2007
• Segmenting DNA sequence alignments with Bayesian factorial Hidden Markov models
  Workshop on Statistical Modelling in Complex Systems, organized by "Sonderforschungsbereich 386: Statistical Analysis of Discrete Structures", Munich, October 12-14, 2006
• Bayesian methods for detecting recombination in DNA sequence alignments
  Invited talk, University of Warwick, 14 February 2006
• Detecting Mosaic Structures in DNA Sequence Alignments
  (Click here for an abstract )
  Workshop on Statistics in Genomics and Proteomics
  Monte Estoril, Portugal, 5-8 October 2005
• Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial HMMs
  European Conference on Computational Biology , Madrid, 28 September - 1 October 2005
• Report on ISMB 2005
  Presentation given to the BioSS Bioinformatics Taskforce meeting, 21 July 2005
• Probabilistic methods for post-genomic data integration
  Ednburgh Systems Biology club , 26 May 2005
• Reverse engineering of gene regulatory networks.
  Ednburgh Systems Biology club , 12 May 2005
• Learning local gene interaction networks from noisy gene expression data with probabilistic graphical models
  Invited tutorial given at CMSB 05 , Edinburgh, 3 April 2005
• Detecting mosaic structures in DNA sequence alignments
  Presentation to the Royal Statistical Society North Eastern local group , Newcastle, 25 February 2005
• Learning genetic networks from gene expression data
  Herbstkolloquien im Universitaetskolleg Bommerholz
  Department of Statistics, University of Dortmund, November 2004
• Detecting interspecific recombination in DNA sequence alignemnts
  Adaptive & Neural Computation seminar
  Institute for Neural & Adaptive Computation ,
  School of Informatics, Edinburgh University, 11 May 2004
  Click here for an abstract .
• Detecting interspecific recombination in DNA sequence alignments
  Mathematical Genetics and Bioinformatics Seminar
  Department of Statistics, Oxford University, 4 May 2004
• Application of Bayesian networks and MCMC in computational molecular biology
  Department of Computer Science , University of Sheffield, November 2003
• Can we infer genetic networks from gene expression data with Bayesian networks?
  Biochemical Society Focused Meeting on Systems Biology , Sheffield, July 2003
• Statistical Methods for Detecting Recombination in DNA Sequence Alignments
  49th German Biometric Conference , Wuppertal, March 2003
• Inferring genetic networks from microarray gene expression data
  Presentation given at the BioSS annual staff meeting, November 2002
• Detecting recombination with MCMC
  Talk held at the 10th International Conference on Intelligent Systems for Molecular Biology (ISMB) , Edmonton, Canada, 3-7 August 2002
• Statistical methods for phylogenetic inference and the detection of recombination
  Talk held at the Annual Meeting of the Scottish and Northumbrian Academic Statisticians
  May 2002
• Machine learning and bioinformatics
  Presentation given to the SEERAD Management and Advisory Committee
  May 2002
• Detecting Recombination in DNA Sequence Alignments
  Talk held at the Manchester Bioinformatics Week , March 2002
• Statistical methods for detecting recombination and gene conversion in DNA sequence alignments.
  Talk held at the Statistics Department of the University of Glasgow, 13 December 2001.
• Probabilistic Divergence Measures for Detecting Interspecies Recombination
  Talk held at the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB) , Copenhagen, Denmark, 21-25 July 2001
• Approximate Bayesian Discrimination between Alternative Mosaic Structures of DNA Sequence Alignments
  BioSS staff meeting, SCRI, Dundee, 19 June 2001.
• Detection and selection of DNA mosaic structures.
  Invited seminar. Department of Biomolecular Sciences, UMIST Manchester , June 2001
• Statistical Methods to Detect Sporadic Recombination in DNA Sequence Alignments
  Presentation given to the SCRI senior staff committee on 1 June 2001.
• Statistical methods for detecting sporadic recombination in DNA sequence alignments
  Talk held at the BBSRC grantholders' workshop in Hinxton, 21-23 February 2001, and at the workshop Mathematical and Statistical Aspects of Molecular Biology , Isaac Newton Institute for Mathematical Sciences, Cambridge, 20-21 March 2001
• Paradigm Shifts in Statistical Bioinformatics
  BioSS staff meeting, BioSS HQ Edinburgh, 13 November 2000.
  Also available in a paper-saving version (4 pages printed on one).
• Detection of Recombination with Hidden Markov Models
  Poster presented on the Bioinformatics workshop at the Isaac Newton Institute , 4-5 April 2000.
• Detection of Recombination in Phylogenetic Data Sets
  ROAM research meeting at the Scottish Crop Research Institute , 2 March 2000.
• Regularisation of Mixture Models with the Bayesian Evidence Scheme
  Gatsby Computational Neuroscience Unit, University College London , 16 April 1999.
• Bayesian Methods for Neural Network Classifiers
  Max-Planck Institute fuer Stroemungsforschung , 5 February 1999.

Invited lectures and tutorials

• Multivariate statistics and machine learning applications in Pathway Medicine. Lectures in Pathway Medicine at DPM, University of Edinburgh, Royal Infirmery, Little France, Edinburgh, November 2008.
• Tutorial: how do we get networks from data? GENESYS: workshop on "Exploiting Genetic Variation in Reverse Engineering of Regulatory Networks", eScience Centre Edinburgh, October 2008.
• Statistical pattern recognition and network reconstruction from postgenomic data.
  Lecture within the MRes training programme on Genomics and Pathway Biology, Department of Pathway Medicine, Edinburgh, 8 November 2007.
• Bayesian inference for pathway structures in systems biology.
  Tutorial given at QEST 2007: International conference on Quantitative Evaluation of Systems, Edinburgh, 16 September 2007
• Machine learning applications in phylogenetics and systems biology.
  Lecture to MSc students in Informatics, Edinburgh, 8 March 2006.
• Introduction to statistical pattern recognition and machine learning.
  Lecture within the MRes training programme on Genomics and Pathway Biology, Department of Pathway Medicine, Edinburgh, 26 January 2006.
• Introduction to machine learning and multivariate statistics in systems biology.
  Lecture within the MRes training programme on Genomics and Pathway Biology, GTI, Edinburgh, 7 February 2007
• Notes on RJMCMC
  BioSS journal club, 4 March 2005
• Probabilistic modelling in bioinformatics
  Guest lecture given to M.Sc. students in the Division of Informatics , University of Edinburgh, on 2 March 2005
• Interpreting gene expression data
  4 lectures given to postgraduate students in biology as part of the module on Postgenomic and Pathway Biology at GTI , January 2004, repeated January 2005.
• A case study in object-oriented programming
  Presentation given as part of a workshop on object-oriented programming, organized by Glenn Marion at the BioSS staff meeting in December 2003.
• Introduction to Bayesian networks and the reverse engineering of genetic networks
  University of Dortmund, Statistics Department, July 2003
• Introduction to statistical phylogenetics
  Guest lecture given to M.Sc. students in the Division of Informatics , University of Edinburgh, on 24 February 2003
• Statistical methods for detecting recombination in DNA sequence alignments
  Invited lecture held at the International School on Computational Biology , Le Havre, France 2002
• A short course on statistical bioinformatics
  Regenstrief Institute , Indianapolis (USA), July 2002
• Introduction to statistical bioinformatics
  Lectures held at the Statistics Department of Dortmund University, January 2002
• A tutorial on the statistical aspects of BLAST
  Internal BioSS workshop, January 2002
• Three lectures given at the Statistics Department of the University of Dortmund (Germany) on 9/10 January 2001
  1. Introduction to hidden Markov models
  (Also available in a paper-saving version .)
  2. Application of hidden Markov models in Bioinformatics
  (Also available in a paper-saving version .)
  3. Introduction to phylogenetics
  (Also available in a paper-saving version .)
  4. Exercises

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