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Sie sind hier:

Prof. Dr. Marco Grzegorczyk

Statistische Methoden in der Genetik und Chemometrie

Kontakt

Marco Grzegorczyk


My new affiliation since 12/2013:

Johann Bernoulli Institute,

Groningen University

[weblink]

E-mail: m.a.grzegorczyk@rug.nl

 

Studies (Dipl.-Stat.)

  • Diplom in Statistics with special focus on Biometrics ("Studienschwerpunkt: Biometrie"), Department of Statistics, Dortmund University, Title of Diplom thesis: "Auswertung einer Brustkrebsstudie mit logistischen Regressionsmodellen" (2/2003) [Diplom thesis]

 

Graduation (Dr. rer. nat.)

  • Department of Statistics, Dortmund University, Title of doctoral thesis: "Comparative evaluation of different Graphical Models for the Analysis of Gene Expression Data." (8/2006) [Doctoral thesis]

 

Habilitation ("Venia Legendi für das Fach Statistik")

  • Department of Statistics, TU Dortmund University, Title of thesis: "Bayesian Networks for Reconstructing Gene Regulatory Networks in Systems Biology" (6/2012) [Habilitationsschrift]

 

Curriculum Vitae

  • SINCE 12/2013 Assistant Professor, Johann Bernoulli Institute,  Groningen University, Netherlands
  • 10/2011-11/2013 Personal Research Grant, funded by the German Research Foundation (DFG), project title: "Development of new Bayesian network models for systems biology research" (GR3853/1-1)
  • 04/2011-09/2011 Interim guest lectureship for Applied Statistics, Department of Mathematics, Carl von Ossietzky University Oldenburg. [weblink]
  • 01/2011-03/2011 Post-doctoral research fellow, Department of Statistics, TU Dortmund University.
  • 01/2009-12/2010 Post-doctoral research fellow in the Graduate School 'Statistical Modelling' [webpage], Department of Statistics, TU Dortmund University.
  • 07/2007-12/2008 Post-doctoral research fellow at the Centre for Systems Biology at Edinburgh [CSBE webpage], School of Biological Sciences, Edinburgh University, UK and Associate at Biomathematics and Statistics Scotland (BioSS), Edinburgh, Scotland, UK (7/2007-12/2011).  
  • 07/2003-06/2007 Research Fellow (PhD student and later post-doctoral fellow) in the research projet 'Chemical Biology and Biotechnology' at the Department of Statistics, Dortmund University.

 

Research Interests

  • Bayesian networks and other graphical models for extracting gene-regulatory networks and protein pathways in systems biology research.

 

Publications (till 2013) 

  • Aderhold, A., Husmeier, D., Smith, A.V., Millar, A.J., and Grzegorczyk, M. (2013): Assessement of regression methods for inference of regulatory networks involved in circadian regulation. Proceedings of the Tenth International Workshop on Computational Systems Biology, WCSB 2013, Tampere, Finland, 29-33. [proceedings available here]
  • Grzegorczyk, M. and Husmeier, D. (2013): Regularization of Non-Homogeneous Dynamic Bayesian Networks with Global Information-Coupling based on Hierarchical Bayesian modelsMachine Learning, vol. 91 (1), 105-154. [available here]
  • Grzegorczyk, M. and Husmeier, D. (2012): Bayesian regularization of non-homogeneous dynamic Bayesian networks by globally coupling interaction parameters. Journal of Machine Learning Research (JMLR) Workshop and Conference Proceedings (AISTATS2012), 22, 467-476. [available here] [supplement]
  • Grzegorczyk, M. and Husmeier, D. (2012): A non-homogeneous dynamic Bayesian network model with sequentially coupled interaction parameters for applications in systems and synthetic biology. Statistical Applications in Genetics and Molecular Biology (SAGMB), vol. 11 (4), Article 7. [abstract]
  • Grzegorczyk, M. (2012): Modelling regulatory processes during morphogenesis in Drosophila melanogaster with an improved version of the BGMD dynamic Bayesian network model. Proceedings of the Nineth International Conference on Computational Systems Biology, WCSB 2012, Ulm, Germany, 27-30. [proceedings available here]
  • Marbach, D., Costello J.C., Küffner, R., Vega, N.M., Prill, P.J., Camacho, D.M., Allison, K.R., The DREAM5 Consortium, Kellis, M., Collins, J.J., and Stolovitzky, G. (2012): Wisdom of crowds for robust gene network inference. Nature Methods, 9, 796-804. [abstract]
  • Grzegorczyk, M. (2011): Bayesian networks for reconstructing gene regulatoy networks in system biology research. Habilitation thesis, Department of Statistics, TU Dortmund University. [available here]
  • Dondelinger, F., Aderhold, A., Lèbre, S., Grzegorczyk, M., and Husmeier, D. (2011): A Bayesian regression and multiple changepoint model for systems biology. In Conesa, D. et al. (editors) Proceedings of the 26th International Workshop on Statistical Modelling (IWSM2011), Copiformes S.L., Valencia, ISBN 978-84-694-5129-8, 189-194. [proceedings]
  • Husmeier, D.,  Werhli, A.V., and Grzegorczyk, M. (2011): Chapter 13: Advanced Applications of Bayesian networks in Systems Biology. In D.J. Balding et al. (editors): Handbook of Statistical Systems Biology, 270-289, Wiley, Chichester, UK. [book contents]  
  • Grzegorczyk, M. and Husmeier, D. (2011): Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes. Bioinformatics,  27 (5), 693-699. [available here] [supplement]
  • Grzegorczyk, M. and Husmeier, D. (2011): Non-homogeneous dynamic Bayesian networks for continuous data. Machine Learning, 83 (3), 355-419. [abstract]
  • Grzegorczyk, M., Husmeier, D., and Rahnenführer, J. (2011): Modelling non-stationary dynamic gene regulatory processes with the BGM model. Computational Statistics, 26 (2), 199-218. [abstract] [supplement]
  • Grzegorczyk, M. (2010): An Introduction to Gaussian Bayesian Networks. In: Yan Qing (Ed.): Systems Biology in Drug Discovery and Development (Springer Series: Methods and Protocols: Methods in Molecular Biology, Vol. 662). Humana Press. ISBN 978-1-60761-799-0. [book contents]
  • Ickstadt, K., Bornkamp, B., Grzegorczyk, M., Wieczorek, J., Sheriff, M.R., Grecco, H.E. and Zamir, E. (2010): Nonparametric Bayesian Networks. In: Bernardo, Bayarri, Berger, Dawid,  Heckerman, Smith and West (eds.): Bayesian Statistics 9, Oxford University Press, 283-316. [online version] 
  • Lohr, M., Godoy, P., Hengstler, J.G., Rahnenführer, J. and Grzegorczyk, M. (2010): In: Nykter, Ruusuvuori, Carlberg and Yli-Harja (eds.) Extracting differential regulatory sub-networks from genome-wide microarray expression data. Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB 2010, Luxembourg, 63-66.[proceedings available here]
  • Grzegorczyk, M., Husmeier, D. and Rahnenführer, J. (2010): Modelling Non-Stationary Gene Regulatory Processes. Advances in Bioinformatics, Volume 2010, Article ID 749848 [available here
  • Grzegorczyk, M. and Husmeier, D. (2009): Non-stationary continuous dynamic Bayesian networks. In Bengio, Schuurmans, Lafferty, Williams and Culotta (editors) Proceedings of the Twenty-Third Annual Conference on Neural Information Processing Systems (NIPS 2009), Curran Associates, ISBN 9781605603520, 682-690. [available here] [zip folder with supplement]
  • Grzegorczyk, M. and Husmeier, D. (2009): Avoiding Spurious Feedback Loops in the Reconstruction of Gene Regulatory Networks with Dynamic Bayesian Networks. In: V. Kadirkamanathan et al. (eds.): Pattern Recognition in Bioinformatics, Lecture Notes in Bioinformatics, Springer-Verlag Berlin Heidelberg, 113-124. [abstract]
  • Grzegorczyk, M. and Husmeier, D. (2009): Modelling non-stationary gene regulatory processes with a non-homogeneous dynamic Bayesian network and the change point process. In: Manninen et al. (eds.): Proceedings of the Sixth International Workshop on Computational Systems Biology, WCSB 2009, Aarhus, Denmark, 51-54. [proceedings available here
  • Grzegorczyk, M., Husmeier, D., Edwards, D.E., Ghazal, P. and Millar, A.J. (2008): Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler. Bioinformatics, 24 (18), 2071-2078 [available here] [supplement]
  • Grzegorczyk, M. and Husmeier, D. (2008): Improving the structure MCMC sampler for Bayesian networks by introducing a new edge reversal move. Machine Learning, 71 (2-3), 265-305. [available here]
  • Grzegorczyk, M. (2008): Comparison of two different stochastic models for extracting protein regulatory pathways with Bayesian networks. Journal of Toxicology and Environmental Health, Part A, 71, 780–787. [abstract]
  • Grzegorczyk, M., Husmeier, D. and Werhli, A.V. (2008) Reverse Engineering Gene Regulatory Networks with various Machine Learning Methods. In Emmert-Streib and Dehmer (eds.): Analysis of Microarray Data. A Network-Based Approach, Wiley-WCH. [book contents
  • Grzegorczyk, M. (2007): Extracting protein regulatory networks with graphical models. Proteomics, 7, 51-59. [abstract]
  • Grzegorczyk, M. (2006): Comparative evaluation of different Graphical Models for the Analysis of Gene Expression Data. Doctoral Thesis, Department of Statistics, University of Dortmund. [thesis available here
  • Urfer, W., Grzegorczyk, M. and Jung, K. (2006): Statistics for Proteomics: A review of tools for analyzing experimental data. Proteomics, 6, 48-55.  [abstract
  • Werhli, A.V., Grzegorczyk, M. and Husmeier, D. (2006): Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical Gaussian models and Bayesian networks. Bioinformatics, 22 (20), 2523-2531. [available here
  • Sievers, S., Fritsch, C., Grzegorczyk, M., Kuhnen, C. and Müller, O. (2006): Absolute ß-catenin concentrations in Wnt pathway stimulated and non-stimulated cells. Biomarkers, 11 (3), 270-278. [abstract]
  • Werhli, A.V., Grzegorczyk, M., Chiang, M.T. and Husmeier, D. (2006): Improved Gibbs sampling for detecting mosaic structures in DNA sequence alignments In: Urfer and Turkman (eds.) Statistics in Genomics and Proteomics, Centro Internacional de Matematica, Coimbra. [proceedings available here
  • Kutzner, N., Hoffmann, I., Linke, C., Thienel, T., Grzegorczyk, M., Urfer, W., Martin, D., Winde, G., Traska, T., Hohlbach, G., Müller, K.-M., Kuhnen, C. and Müller, O. (2005): Non-invasive detection of colorectal tumours by the combined application of molecular diagnosis and the faecal occult blood test. Cancer Letters, 1, 33-41. [abstract

 

Videolectures

  • Grzegorczyk, M. (2007) Reverse engineering gene and protein regulatory networks using graphical models: A comparative evaluation study.  Talk at PASCAL workshop on Probabilistic Modelling of Biological Networks and Pathways. 04-05 September 2007, Sheffield, Videolecture and slides available from [videolectures.net
  •  

Lectures at TU Dortmund University

  • Genetische Netzwerke WS12/13 (2V+1Ü) [slides]
  • Genetische Netzwerke SS2010 (2V+1Ü) [slides]
  • Genetische Netzwerke SS2009 (2V+1Ü) [slides 
  •  

Lecturs at Oldenburg University

  • Mathematical Statistics SS2011 (3V+1Ü)
  • Linear Models SS2011 (3V+1Ü)
  • Generalised Regression Models SS2011 (3V+1Ü)

 

Attended conferences with contributions ([P]oster/[T]alk)

  • [T] Complex Stochastic Systems in Biology and Medicine (Munich, Germany, 7-8 October, 2004) [webpage]
  • [P] Workshop on Statistics in Genomics and Proteomics (Monte Estoril, Portugal, 5-8 October, 2005) [webpage]
  • [T] Mathematical and Statistical Aspects of Molecular Biology (Dublin, Ireland, 10-11 April, 2006) [webpage]
  • [P] German Conference on Bioinformatics (Tübingen, Germany, 20-22 September, 2006) [webpage]
  • [T] Environmental Toxicology in North Rhine-Westphalia (Dortmund, Germany, 10-11 May, 2007) [webpage]
  • [T] Probabilistic Modelling of Networks and Pathways (Sheffield, England, 4-5 September, 2007) [webpage]
  • [T] 55. Biometrisches Kolloquium (Hannover, Germany, 17-19 March, 2009) [webpage]
  • [T] 6th Workshop on Computational Systems Biology (Aarhus, Denmark, 10-12 June, 2009) [webpage]
  • [T] Statistical Computing (Schloss Reisensburg, Germany, 28 June - 1 Juli, 2009) [webpage]
  • [T] Pattern Recognition in Bioinformatics (Sheffield, England, 7-9 September, 2009) [webpage]
  • [T] Kolloquium der Deutschen Arbeitsgemeinschaft Statistik (Dortmund, Germany, 23-26 March, 2010) [webpage]
  • [T] Statistical Computing (Schloss Reisensburg, Germany, 20-23 June, 2010) [webpage] [Tutorial zipped download]
  • [T] 9th Workshop on Computational Systems Biology (Ulm, Germany, 4-6 June, 2012) [webpage]
  • [T] Workshop on Statistical and Dynamical models in Medicine and Biology (Stuttgart, Germany, 11-12 October, 2012) [webpage]

 

Poster presentations - Yearly colloquium of the Graduate School "Statistical Modelling"

Conferences with contributions as co-author  ([P]oster/[T]alk)

  • [P] Annual International Conference on Intelligent Systems for Molecular Biology (Fortaleza, Brazil, 6-10 August, 2006)  [webpage]
  • [T] Mathematical and Statistical Aspects of Molecular Biology (London, England, 2-3 April, 2009) [webpage]
  • [P] 23rd Annual Conference on Neural Information Processing Systems (Vancouver, B.C., Canada, 7-10 December, 2009) [webpage]
  • [T] 7th Workshop on Computational Systems Biology (Luxembourg, 16-18 June, 2010) [webpage]
  • [T] 9th Valencia International Meeting on Bayesian statistics (Valencia, Spain, 3-8 June 2010) [webpage] 
  • [T] 26th International Workshop on Statistical Modelling (IWSM), (Valencia, Spain, 11-15 July, 2011) [webpage]
  • [P] 15th conference on Artifical Intelligence and Statistics (La Palma, Canary Islands, 21-23 April, 2012) [webpage] [poster]
  • [P] 10th Workshop on Computational Systems Biology (Tampere, Finland, 10-12 June, 2013) [webpage]

Technical Reports

  • Grzegorczyk, M. and Urfer, W. (2004) Determination of interacting genes in kidney tissues using Bayesian networks, Forschungsbericht 2004/3, Fachbereich Statistik, Universität Dortmund. [available here
  • Grzegorczyk, M. and Urfer, W. (2003) Statistical aspects of Bayesian networks used for gene expression data. Forschungsbericht 2003/5, Fachbereich Statistik, Universität Dortmund.

 

Supervised theses

  • Title: "Statistische Modelle und Methoden zur Analyse prognostischer Risikofaktoren beim Prostatakarzinom und Evaluierung zweier Diagnoseverfahren", Bachelor thesis, Department of Statistics, TU Dortmund University, by Laura Holtmann
  • Title: "Netzwerkanalysen von Brustkrebsdaten", Diplom thesis, Department of Statistics, TU Dortmund University, by Miriam Lohr in 2010.
  • Title: "Population Markov Chain Monte Carlo for Structure Learning with Bayesian networks", Master thesis, Department of Statistics, TU Dortmund University, by Xiaoli Wei in 2012.
  • Title: "Untersuchung des Konvergenzverhaltens des Structure-MCMC Samplers für Bayessche Netzwerke", Bachelor thesis, Department of Statistics, TU Dortmund University, by Irina Gulinina in 2013