Magnus Rattray

Professor Magnus Rattray

Collaborative Chair in Neuro- and Computer Science

Department of Computer Science
Regent Court
211 Portobello Street
University of Sheffield
Sheffield S1 4DP

The Sheffield Institute for Translational Neuroscience
385A Glossop Road
Sheffield S10 2HQ
Phone: +44 114 222 2240

email: M.Rattray@sheffield.ac.uk

News

  • New paper on Identifying differentially expressed transcripts from RNA-seq data with biological variation is now accepted for publication in Bioinformatics.

  • I gave an invited talk at Machine Learning in Systems Biology describing our group's recent work on Bayesian non-parametric models for gene expression time-series analysis.

  • A paper describing the tigre bioconductor package for transcription factor activity reconstruction and target inference has been published (work with Antti Honkela and Neil Lawrence) implementing a model-based method for transcription factor target identification with limited data which was published in the Proceedings of the National Academy of Sciences USA.

    Research

    I co-lead a Computational Biology research group located in the Sheffield Institute for Translational Neuroscience with Neil Lawrence.

    I carry out research in Computational Biology, Probabilistic Modelling and Machine Learning. I am an investigator on the following projects:

    • SYNERGY: Systems approach to gene regulation biology through nuclear receptors.

    • TIGRE: Transcription factor inference through Gaussian process reconstruction of expression.

    • PUMA: developing probabilistic models for investigating gene expression and for propagating measurement uncertainty in microarray data analysis.

    and these completed projects:
    • e-Fungi: using methods from comparative and functional genomics to learn about fungal pathogenicity.

    • PHASE: developing methods for Bayesian phylogenetic inference with specialised evolutionary models for RNA genes with conserved secondary structure.

    Research opportunities

    If you would like to carry out research in one of the above areas then you can apply to the department for PhD study. Students with an excellent undergraduate record will be considered for funding. Contact me for news of any post-doctoral research opportunities.

    Current PhD students

    Departed PhD students

    Research Papers

    Preprints

  • P.Glaus, A. Honkela, M. Rattray "Identifying differentially expressed transcripts from RNA-seq data with biological variation" arXiv:1109.0863v1 [q-bio.GN]. Accepted for publication in Bioinformatics.

    Journal Publications

  • I.J. Donaldson, S. Amin, J.J. Hensman, E. Kutejova, M. Rattray, N.D. Lawrence, A. Hayes, C.M. Ward and N. Bobola "Genome-wide occupancy links Hoxa2 to Wnt-beta-catenin signaling in mouse embryonic development" Nucleic Acids Research, doi: 10.1093/nar/gkr1240 (2012).
  • A. Honkela, P. Gao, J. Ropponen, M. Rattray and N.D. Lawrence "tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression for Bioconductor" Bioinformatics 27(7): 1026-1027 (2011).
  • X. Liu and M. Rattray "Including Probe-Level Measurement Error in Robust Mixture Clustering of Replicated Microarray Gene Expression" Statistical Applications in Genetics and Molecular Biology 9(1), Article 42 (2010).
  • H.M.S. Asif, M.D. Rolfe, J. Green, N.D. Lawrence, M. Rattray and G. Sanguinetti "TFInfer: A Tool for Probabilistic Inference of Transcription Factor Activities" Bioinformatics 26(20): 2635-2636 (2010).
  • M. Barton, D. Delneri, S.G. Oliver, M. Rattray and C.M. Bergman "Evolutionary systems biology of amino acid biosynthetic cost in yeast" PLoS ONE 5(8), e11935 (2010).
  • A. Honkela, C Girardot, E.H. Gustafson, Y.-H. Liu, E.E.M. Furlong, N.D. Lawrence and M. Rattray "Model-based method for transcription factor target identification with limited data" Proc. Natl. Acad. Sci. USA 107(17), 7793-7798 (2010).
  • R. Pearson, X. Liu, G. Sanguinetti, M. Milo, N.D. Lawrence, M. Rattray "puma: a Bioconductor package for Propagating Uncertainty in Microarray Analysis" BMC Bioinformatics 10, 211 (2009).
  • P. Gao, A. Honkela, M. Rattray, N.D. Lawrence "Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities" Bioinformatics 24(16), i70-i75 (2008).
  • D.M. Soanes, I. Alam, M. Cornell, H.-M. Wong, C. Hedeler, N.W. Paton, M. Rattray, S.J. Hubbard, S.G. Oliver, N.J. Talbot "Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis" PLoS ONE 3(6), e2300 (2008).
  • B. Jayawardhana, D.B. Kell, M. Rattray "Bayesian Inference of the Sites of Perturbations in Metabolic Pathways via Markov chain Monte Carlo" Bioinformatics 24(9), 1191-1197 (2008). (on-line version)
  • J. Pinney, G. Amoutzias, M. Rattray and D. Robertson "Reconstruction of ancestral protein interaction networks for the bZIP transcription factors" Proc. Natl. Acad. Sci. USA 104 (51): 20449 (2007). (on-line version)
  • M.J. Cornell, I. Alam, D.M. Soanes, H.-M. Wong, C. Hedeler, N.W. Paton, M. Rattray, S.J. Hubbard, N.J. Talbot, and S.G. Oliver "Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi" Genome Research, DOI: 10.1101/gr.6531807 (2007). (on-line version)
  • C. Hedeler, H.-M. Wong, M. Cornell, I. Alam, D. M. Soanes, M. Rattray, S. J. Hubbard, N. J. Talbot, S. G. Oliver and N. W. Paton "e-Fungi: A Data Resource for Comparative Analysis of Fungal Genomes" BMC Genomics 8,426 (2007). (on-line version)
  • J. Chen, V. Agrawal, M. Rattray, M.A.L. West, D.A. St.Clair, R.W. Michelmore, S.J. Coughlan and B.C. Meyers "A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis" BMC Genomics 8,414 (2007). (on-line version)
  • I. Alam, M. Cornell, D.M. Soanes, C. Hedeler, H. M. Wong, M. Rattray, S.J. Hubbard, N.J. Talbot, S.G. Oliver and N.W. Paton. "A Methodology for Comparative Functional Genomics" J. Integrative Bioinformatics 4(3), 69 (2007).
  • V. Gowri-Shankar and M. Rattray "A reversible jump method for Bayesian phylogenetic inference with a non-homogeneous substitution model" Molecular Biology and Evolution 24, 1286-1299 (2007) (on-line version)
  • I. Alam, S.J. Hubbard, S.G. Oliver and M. Rattray "A kingdom-specific protein domain HMM library for improved annotation of fungal genomes" BMC Genomics 8:97 (2007) (on-line version).
  • X. Liu, K.K. Lin, B. Andersen and M. Rattray "Including probe-level uncertainty in model-based gene expression clustering" BMC Bioinformatics 8:98 (2007) (on-line version).
  • D.C. Hoyle and M. Rattray "Statistical mechanics of learning multiple orthogonal signals: Asymptotic theory and fluctuation effects" Physical Review E 75, 016101 (2007). (on-line version).
  • G. Sanguinetti, N.D. Lawrence and M. Rattray "Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities" Bioinformatics 22, 2775-2781 (2006) (on-line version, errata are listed here).
  • T. C. Poon, N. Wong, P. B. Lai, M. Rattray, P. J. Johnson, J. J. Sung "A tumor progression model for hepatocellular carcinoma: bioinformatic analysis of genomic data" Gastroenterology 131, 1262-1270 (2006).
  • X. Liu, M. Milo, N.D. Lawrence and M. Rattray "Probe-level measurement error improves accuracy in detecting differential gene expression" Bioinformatics 22, 2107-2113 (2006) (on-line version).
  • G. Sanguinetti, M. Rattray and N.D. Lawrence "A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription" Bioinformatics 22, 1753-1759 (2006). (on-line version).
  • J. Chen and M. Rattray "Analysis of Tag-position Bias in MPSS Technology" BMC Genomics 7,77 (2006). (on-line version).
  • M. Rattray, X. Liu, G. Sanguinetti, M. Milo and N.D. Lawrence "Propagating Uncertainty in Microarray Data Analysis" Briefings in Bioinformatics 7(1), 37-47 (2006). (on-line version).
  • V. Gowri-Shankar and M. Rattray "On the correlation between composition and site-specific evolutionary rate: implications for phylogenetic inference" Molecular Biology and Evolution 23, 352-364 (2006). (on-line version).
  • G. Sanguinetti, M. Milo, M. Rattray and N.D. Lawrence, "Accounting for probe-level noise in principal component analysis of microarray data" Bioinformatics 21, 3748-3754 (2005). (on-line version).
  • X. Liu, M. Milo, N.D. Lawrence and M. Rattray "A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips" Bioinformatics 21, 3637-3644 (2005). (on-line version).
  • A. Gibson, V. Gowri-Shankar, P.G. Higgs and M. Rattray "A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods" Molecular Biology and Evolution 22, 251-264 (2005). (on-line version).
  • D.C. Hoyle and M. Rattray "Principal component analysis eigenvalue spectra from data with symmetry breaking structure" Physical Review E 69, 026124 (2004). (pdf preprint)
  • Y. Fang, A. Brass, D.C. Hoyle, A. Hayes, A. Bashein, S.G. Oliver. D. Waddington, M. Rattray "A model-based analysis of microarray experimental error and normalisation" Nucleic Acids Research (methods) 31(16) e96 (2003).
  • G. Basalyga and M. Rattray "Statistical dynamics of on-line independent component analysis" Journal of Machine Learning Research (special issue on ICA) 4, 1393-1410 (2003). (preliminary version available as e-print )
  • P. G. Higgs, D. Jameson, H. Jow and M. Rattray "The evolution of tRNA-Leu genes in animal mitochondrial genomes" Journal of Molecular Evolution 57, 435-445 (2003). (journal link).
  • C. Hudelot, V. Gowri-Shankar, H. Jow, M. Rattray and P. Higgs "RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences" Molecular Phylogenetics and Evolution 28, 241-252 (2003). (preliminary version available as pdf )
  • D.C. Hoyle and M. Rattray "PCA learning for sparse high-dimensional data" Europhysics Letters 62(1), 117-123 (2003). (available as pdf )
  • H. Jow, C. Hudelot, M. Rattray and P. Higgs "Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution" Molecular Biology and Evolution 19(9), 1591-1601 (2002). (on-line version).
  • D. C. Hoyle, M. Rattray, R. Jupp and A. Brass "Making sense of microarray data distributions," Bioinformatics 18, 576-584 (2002). (on-line version).
  • M. Rattray "Stochastic trapping in a solvable model of on-line independent component analysis," Neural Computation 14, 421-435 (2002). (preliminary version available as e-print )
  • M. Rattray and J. L. Shapiro "Cumulant dynamics of a population under multiplicative selection, mutation and drift," Theoretical Population Biology 60, 17--32 (2001) (preliminary version available as e-print )
  • M. Brutsche, I. Brutsche, P. Wood, A. Brass, N. Morrison, M. Rattray, N. Mogulkoc, N. Simler, M. Craven, A. Custovic, J. Egan, A. Woodcock, "Apoptosis signals in atopy and asthma measured with cDNA arrays," Clin. Exp. Immunology 123, 181--187 (2001).
  • S. Scarpetta, M. Rattray and D. Saad, "Matrix momentum for practical natural gradient learning," Journal of Physics A 32, 4047-4059 (1999).( compressed postscript )
  • M. Rattray, D. Saad, "Analysis of Natural Gradient Descent for Multilayer Neural Networks," Physical Review E 59(4), 4523-4532 (1999). ( compressed postscript )
  • M. Rattray, D. Saad and S. Amari, "Natural Gradient Descent for On-line Learning," Physical Review Letters 81, 5461-5464 (1998). ( compressed postscript )
  • M. Rattray and D. Saad, "Analysis of On-line Training with Optimal Learning Rates," Physical Review E 58(5), 6379-6391 (1998). ( compressed postscript )
  • D. Saad and M. Rattray, "Learning with Regularizers in Multilayer Neural Networks," Physical Review E 57(2), 2170-2176 (1998). ( compressed postscript )
  • M. Rattray and D. Saad, "Globally Optimal On-line Learning Rules for Multilayer Neural Networks," Journal of Physics A 30, L771-L776 (1997). ( compressed postscript )
  • D. Saad and M. Rattray, "Globally Optimal Parameters for On-line Learning in Multilayer Neural Networks," Physical Review Letters 79, 2578-2581 (1997). ( compressed postscript )
  • M. Rattray and J. L. Shapiro, "The Dynamics of a Genetic Algorithm for a Simple Learning Problem," Journal of Physics A 29, 7451-7473 (1996). ( compressed postscript )
  • M. Rattray, "The Dynamics of a Genetic Algorithm under Stabilizing Selection, "Complex Systems 9, 213-234 (1995). ( abstract )

    Conference proceedings and book chapters

  • N.D. Lawrence, M. Rattray, A. Honkela, M. Titsias "Gaussian Process Inference for Differential Equation Models of Transcriptional Regulation" in M.P.H. Stumpf, D.J. Balding, M. Girolami (eds) Handbook of Statistical Systems Biology (Wiley, 2011).
  • M. Titsias, N.D. Lawrence and M. Rattray "Markov Chain Monte Carlo Algorithms for Gaussian Processes" in D. Barber, A. T. Cemgil and S. Chiapp (eds) Inference and Estimation in Probabilistic Time-Series Models (Cambridge University Press, 2011).
  • A. Honkela, M. Milo, M. Holley, M. Rattray and N.D. Lawrence "Ranking of gene regulators through differential equations and Gaussian processes" in Proc. of IEEE workshop on Machine Learning for Signal Processing (MLSP 2010), Kittilä, Finland, September 1, 2010.
  • K. Sharp and M. Rattray "Dense Message Passing for Sparse Principal Component Analysis" in Y.W. Teh and M. Titterington (Eds.), Proceedings of The Thirteenth International Conference on Artificial Intelligence and Statistics (AISTATS 2010), JMLR: W & CP 9, pp 725-732, Chia Laguna, Sardinia, Italy, May 13-15, 2010.
  • N. D. Lawrence, M. Rattray, P. Gao and M. K. Titsias. (2010) "Gaussian processes for missing species in biochemical systems" in N. D. Lawrence, M. Girolami, M. Rattray and G. Sanguinetti (eds) Learning and Inference in Computational Systems Biology, MIT Press, Cambridge, MA.
  • N. D. Lawrence and M. Rattray. (2010) "A brief introduction to Bayesian inference" in N. D. Lawrence, M. Girolami, M. Rattray and G. Sanguinetti (eds) Learning and Inference in Computational Systems Biology, MIT Press, Cambridge, MA.
  • M. Rattray, O. Stegle, K. Sharp and J. Winn "Inference algorithms and learning theory for Bayesian sparse factor analysis" in Proceedings of the International Workshop on Statistical-Mechanical Informatics (Kyoto 2009), Journal of Physics A Conf. Series 197, 012002 (2009).
  • M. Titsias, N.D. Lawrence and M. Rattray "Efficient Sampling for Gaussian Process Inference using Control Variables" to appear in Advances in Neural Information Processing Systems (NIPS 22), 2009. (available as pdf)
  • G. Englebienne, T.F. Cootes and M. Rattray "A probabilistic model for generating realistic lip movements from speech" Advances in Neural Information Processing Systems (NIPS 21), 2008. (available as pdf and here is the associated dataset)
  • N.D. Lawrence, G. Sanguinetti and M. Rattray "Modelling transcriptional regulation using Gaussian processes" Advances in Neural Information Processing Systems (NIPS 20), 2007. (available as pdf).
  • G. Sanguinetti, M. Rattray and N.D. Lawrence "Identifying submodules of cellular regulatory networks" Computational Methods in Systerms Biology (CMSB 2006; Trento, Italy) (pre-print pdf ).
  • J. Pinney, M. Rattray and D.L. Robertson "Understanding the evolution of protein interaction networks" in S. Barber, P.D. Baxter, K.V.Mardia, & R.E. Walls (Eds.), Interdisciplinary Statistics and Bioinformatics, pp. 153-156. (Leeds University Press, 2006) (available as pdf ).
  • M. Cornell, I. Alam, D. Soanes, H.-M. Wong, M. Rattray, S. Hubbard, N.J. Talbot, B. Lings, D. Hoyle, S.G. Oliver and N.W. Paton. "e-Fungi: An e-Science Infrastructure for Comparative Functional Genomics in Fungal Species" BBSRC All-hands meeting (Nottingham, 2005). (available as pdf )
  • M. Rattray and P.G. Higgs "RNA-based phylogenetic methods" in Probabilistic Modeling in Bioinformatics and Medical Informatics, edited by D. Husmeier, R. Dybowski and S. Roberts (Springer, 2005).
  • D. C. Hoyle and M. Rattray "A Statistical Mechanics Analysis of Gram Matrix Eigenvalue Spectra" to appear in Proceedings of COLT 2004. (available as pdf )
  • D. C. Hoyle and M. Rattray "Limiting form of the sample covariance matrix eigenspectrum in PCA and kernel PCA" Advances in Neural Information Processing Systems (NIPS 16), 2003. (available as pdf )
  • G. Basalyga and M. Rattray "Dynamics of ICA for high-dimensional data," Proceedings of ICANN 2002, Madrid, August 25-27, 2002 ( compressed postscript ).
  • M. Rattray and G. Basalyga "Scaling laws and local minima in Hebbian ICA," Advances in Neural Information Processing Systems (NIPS 14), Vancouver, Dec. 8, 2001. ( compressed postscript )
  • M. Rattray, "A model-based distance for clustering," Proceedings of IJCNN 2000 (short paper , slides , related MSc thesis applying method to mixtures of PPCA models)
  • S. Scarpetta, M. Rattray and D. Saad, "Natural Gradient Matrix Momentum," Proceedings of ICANN 99 (Edinburgh, 7--10 September, 1999).
  • M. Rattray and D. Saad, "Transients and Asymptotics of Natural Gradient Learning," in Proceeding of ICANN 98, edited by L. Niklasson, M. Boden and T. Ziemke (Springer, 1998).
  • M. Rattray and D. Saad, "The Dynamics of Matrix Momentum," in Proceeding of ICANN 98, edited by L. Niklasson, M. Boden and T. Ziemke (Springer, 1998). ( compressed postscript )
  • M. Rattray and D. Saad, "Incorporating Curvature Information into On-line Learning," in On-line Learning in Neural Networks, edited by D. Saad (Cambridge University Press, 1998).
  • D. Saad and M. Rattray, "Optimal On-line Learning in Multilayer Neural Networks," in On-line Learning in Neural Networks, edited by D. Saad (Cambridge University Press, 1998).
  • M. Rattray and D. Saad, "Globally Optimal On-line Learning Rules," in NIPS 10, edited by M. I. Jordan, M. J. Kearns and S. A. Solla, 322-328 (1998).
  • D. Saad and M. Rattray, "Globally Optimal Learning Rates for Multilayer Neural Networks," in Proc. of the Minerva Workshop on Mesoscopics, Fractals and Neural Networks (Eilat, Israel, 1997), Philosophical Magazine B 77(5), 1523--1530 (1998).
  • M. Rattray and J. L. Shapiro, "Noisy Fitness Evaluation in Genetic Algorithms and the Dynamics of Learning," Foundations of Genetic Algorithms 4, 117-139 (1997). ( compressed postscript )
  • J. L. Shapiro, A. Prügel-Bennett and M. Rattray, "A Statistical Mechanics Analysis of Genetic Algorithms for Search and Learning," in Mathematics of Neural Networks (Kluwer Academic Publishers, 1997).
  • J. L. Shapiro, M. Rattray and A. Prügel-Bennett, "The Statistical Mechanics Approach to the Study of Genetic Algorithm Dynamics," in Proc. of the 1st Int. Conf. of Evolutionary Computing Algorithms (Moscow, 1996).
  • J. L. Shapiro, A. Prügel-Bennett and M. Rattray, "A Statistical Mechanics Formulation of the Dynamics of Genetic Algorithms," Lecture Notes in Computer Science 865, 17-27 (1994). ( abstract , compressed postscript )

    PhD Thesis

  • M. Rattray, "Modelling the Dynamics of Genetic Algorithms using Statistical Mechanics," University of Manchester (1996). (pdf of thesis) .