2013

Grzegorczyk, M., and Husmeier, D. (2013) Regularization of non-homogeneous dynamic Bayesian networks with global information-coupling based on hierarchical Bayesian models. Machine Learning, 91 (1). pp. 105-154. ISSN 0885-6125 (doi:10.1007/s10994-012-5326-3)

Dondelinger, F., Filippone, M., Rogers, S., and Husmeier, D. (2013) ODE parameter inference using adaptive gradient matching with Gaussian processes. In: Sixteenth International Conference on Artificial Intelligence and Statistics, 29 Apr - 1 May 2013, Scottsdale, AZ, USA. (In Press)

Dondelinger, F., Lèbre, S., and Husmeier, D. (2013) Non-homogeneous dynamic Bayesian networks with Bayesian regularization for inferring gene regulatory networks with gradually time-varying structure. Machine Learning . ISSN 1573-0565 (doi:10.1007/s10994-012-5311-x) (In Press)

2012

Aderhold, A., Husmeier, D., Lennon, J.J., Beale, C.M., and Smith, V.A. (2012) Hierarchical Bayesian models in ecology: Reconstructing species interaction networks from non-homogeneous species abundance data. Ecological Informatics, 11 . pp. 55-64. ISSN 1574-9541 (doi:10.1016/j.ecoinf.2012.05.002)

Grzegorczyk, M., and Husmeier, D. (2012) A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology. Statistical Applications in Genetics and Molecular Biology, 11 (4). Art. 7. ISSN 2194-6302 (doi:10.1515/1544-6115.1761)

Dondelinger, F., Rogers, S., Filippone, M., Cretella, R., Palmer, T., Smith, R., Millar, A., and Husmeier, D. (2012) Parameter inference in mechanistic models of cellular regulation and signalling pathways using gradient matching. In: WCSB2012 - 9th International Workshop on Computational Systems Biology, 4-6 Jun 2012, Ulm, Germany.

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, 22 . pp. 467-476. ISSN 1938-7228

Ji, R., and Husmeier, D. (2012) Warped Gaussian process modelling of transcriptional regulation. In: 9th International Workshop on Computational Systems Biology, 4-6 Jun 2012, Ulm, Germany.

Dondelinger, F., Husmeier, D., and Lebre, S. (2012) Dynamic Bayesian networks in molecular plant science: inferring gene regulatory networks from multiple gene expression time series. Euphytica, 183 (3). pp. 361-377. ISSN 0014-2336 (doi:10.1007/s10681-011-0538-3)

Lebre, S., Dondelinger, F., and Husmeier, D. (2012) Nonhomogeneous dynamic Bayesian networks in systems biology. In: Wang, J., Tan, A.C. and Tian, T. (eds.) Next Generation Microarray Bioinformatics. Humana Press, New York, NYC, USA, pp. 199-213. ISBN 9781617793998

2011

Dondelinger, F., Aderhold, A., Lebre, S., Grzegorczyk, M., and Husmeier, D. (2011) A Bayesian regression and multiple changepoint model for systems biology. In: Conesa, D., Forte, A., Lopez-Quilez, A. and Munoz, F. (eds.) International Workshop on Statistical Modelling. Copiformes S.L., Valencia, Spain, pp. 189-194. ISBN 9788469451298

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). pp. 693-699. ISSN 1367-4803 (doi:10.1093/bioinformatics/btq711)

Grzegorczyk, M., and Husmeier, D. (2011) Non-homogeneous dynamic Bayesian networks for continuous data. Machine Learning, 83 (3). pp. 355-419. ISSN 0885-6125 (doi:10.1007/s10994-010-5230-7)

Grzegorczyk, M., Husmeier, D., and Rahnenführer, J. (2011) Modelling non-stationary dynamic gene regulatory processes with the BGM model. Computational Statistics, 26 (2). pp. 199-218. ISSN 0943-4062 (doi:10.1007/s00180-010-0201-9)

Husmeier, D., Werhli, A.V., and Grzegorczyk, M. (2011) Advanced applications of Bayesian networks in systems biology. In: Stumpf, M.P.H., Balding, D.J. and Girolami, M. (eds.) Handbook of Statistical Systems Biology. Wiley, Chichester, UK, pp. 270-289. ISBN 9780470710869

2010

Dondelinger, F., Lebre, S., and Husmeier, D. (2010) Heterogeneous continuous dynamic Bayesian networks with flexible structure and inter-time segment information sharing. In: Furnkranz, J. and Joachims, T. (eds.) International Conference on Machine Learning (ICML). Omnipress, Haifa, Israel, pp. 303-310. ISBN 9781605589077

Faisal, A., Dondelinger, F., Husmeier, D., and Beale, C.M. (2010) Inferring species interaction networks from species abundance data: a comparative evaluation of various statistical and machine learning methods. Ecological Informatics, 5 (6). pp. 451-464. ISSN 1574-9541 (doi:10.1016/j.ecoinf.2010.06.005)

Grzegorcyzk, M., Husmeier, D., and Rahnenführer, J. (2010) Modelling nonstationary gene regulatory processes. Advances in Bioinformatics, 2010 . pp. 1-17. ISSN 1687-8027 (doi:10.1155/2010/749848)

Husmeier, D., Dondelinger, F., and Lebre, S. (2010) Inter-time segment information sharing for non-homogeneous dynamic Bayesian networks. In: Advances in Neural Information Processing Systems. Series: Advances in neural information processing systems, 23 (23). Curran Associates, La Jolla, CA, USA, pp. 901-909. ISBN 9781617823800

Lin, K., and Husmeier, D. (2010) Mixtures of factor analyzers for modeling transcriptional regulation. In: Lawrence, N., Girolami, M., Rattray, M. and Sanguinetti, G. (eds.) Learning and Inference in Computational Systems Biology. Series: Computational molecular biology . MIT Press, Cambridge, MA, USA, pp. 153-200. ISBN 9780262013864

Lin, K., Husmeier, D., Dondelinger, F., Mayer, C.D., Liu, H., Prichard, L., Salmond, G.P.C., Toth, I.K., and Birch, P.R.J. (2010) Reverse engineering gene regulatory networks related to Quorum sensing in the plant pathogen Pectobacterium Atrosepticum. In: Fenyo, David (ed.) Computational Biology. Series: Methods in Molecular Biology (673). Humana Press, New York, NYC, USA, pp. 253-281. ISBN 9781607618416

2009

Lehrach, W.P., and Husmeier, D. (2009) Segmenting bacterial and viral DNA sequence alignments with a trans-dimensional phylogenetic factorial hidden Markov model. Journal of the Royal Statistical Society: Series C (Applied Statistics), 58 (3). pp. 307-327. ISSN 0035-9254 (doi:10.1111/j.1467-9876.2008.00648.x)

Grzegorczyk, M., and Husmeier, D. (2009) Avoiding spurious feedback loops in the reconstruction of gene regulatory networks with dynamic bayesian networks. Lecture Notes in Computer Science , 5780 . pp. 113-124. ISSN 0302-9743 (doi:10.1007/978-3-642-04031-3_11)

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, T., Wiuf , C., Lahdesmaki, H., Grzegorczyk, M., Rahnenfuhrer, J., Ahdesmaki, M., Linne, M.L. and Yli-Harja, O. (eds.) Proceedings of the Sixth International Workshop on Computational Systems Biology (WCSB). Tampere International Centre for Signal Processing. ISBN 9789521521607

Grzegorczyk, M., and Husmeier, D. (2009) Non-stationary continuous dynamic Bayesian networks. In: Bengio, Y., Schuurmans, D., Laftery, J., Williams, C.K.I. and Culotta, A. (eds.) Advances in Neural Information Processing Systems. Series: Advances in neural information processing systems (22). Curran Associates, La Jolla, CA, USA, pp. 682-690. ISBN 9781615679119

Lin, K., and Husmeier, D. (2009) Modelling transcriptional regulation with a mixture of factor analyzers and variational Bayesian expectation maximization. EURASIP Journal on Bioinformatics and Systems Biology, 2009 (601068). ISSN 1687-4145

Mantzaris, A.V., and Husmeier, D. (2009) Distinguishing regional from within-codon rate heterogeneity in DNA sequence alignments. Lecture Notes in Computer Science, 5780 . pp. 187-198. ISSN 0302-9743 (doi:10.1007/978-3-642-04031-3_17)