Statistical Bioinformatics
Electrophorectic gel with annotated landmarks (see for
example Green and Mardia, 2006)
“The lack of real contact between mathematics and
biology is either a tragedy, a scandal or a challenge,
it is hard to decide which”.
Gian-Carlo Rota, Discrete Thoughts (1986)
The increasing understanding of the human genome has been one of the great success stories in biology over the past 50 years. DNA in the genome contains "genes" which contain the information needed to build proteins, which in turn carry out the functions of life.
Many deep questions remain, and statistical ideas will play a key role in understanding genes and proteins. Some of the key problems in bioinformatics are:-
(i) measuring when different genes are expressed at different stages in a life cycle
(ii) measuring the differences between genes for different species.
The shape of a protein is one of the key properties which determines how a protein works. The advances in geometric statistics and particularly shape analysis from the LASR workshops enables us to explore new ways of modelling protein structure.
A key challenge in adapting shape analysis to protein bioinformatics is the lack of natural labelling on the proteins.
“At the end of last year, representatives from around
30 university research departments, supported by the BBSRC, met to discuss this
issue *. They concluded that action is
needed urgently to prevent the
* (Mathematical skill for biosciences students).
“Data Rich but Maths Poor”, Julia M. Goodfellow CBE, LASR Proceedings 2006, p99.
Bioinformatics of matching active sites through Bayesian
hierarchical model, Bayesian refinement, high-dimensional directional
distributions for Ramachandran plots, and, directional hidden Markov models for
synthetic proteins.
Edited Volumes:
2003 Stochastic Geometry,
Biological Structure and Images, co-editors R. G. Aykroyd and M. J.
Langdon. LASR Proceedings:
2004 Bioinformatics, Images, and Wavelets, co-editors R. G. Aykroyd and
S. Barber. LASR Proceedings:
2005 Quantitative Biology, Shape Analysis, and Wavelets, co-editors S.
Barber, P. D. Baxter and R.E. Walls. LASR Proceedings:
2006 Interdisciplinary Statistics and Bioinformatics, co-editors S.
Barber, P.D. Baxter and R.E. Walls. LASR Proceedings:
2007 Systems Biology & Statistical
Bioinformatics, co-editors S. Barber and P.D. Baxter. LASR Proceedings:
2008 The Art & Science of Statistical Bioinformatics, co-editors S. Barber, P.D. Baxter and A. Gusnanto. LASR Proceedings: Leeds University Press.
Papers in Journals:
2006 Bayesian alignment using hierarchical models, with applications in
protein bioinformatics (with P.J. Green). Biometrika 93,
235-254.
2007 Protein bioinformatics and mixtures of bivariate von Mises distributions
for angular data (with C. C. Taylor and M. Subramaniam).
Biometrics 63,
505-512.
2007 Bayesian
refinement of protein functional site matching (with V. B. Nyirongo,
P. J. Green, N. G. Gold, and D. R. Westhead). BMC Bioinformatics
http://www.biomedcentral.com/1471-2105/8/257.
2007 The Poisson index: A new probabilistic model for protein-ligand
binding site similarity. (with J. R. Davies, R. M. Jackson, and C. C. Taylor). Bioinformatics,
23, 3001-3008.
2008 A multivariate von Mises distribution with applications to
bioinformatics. (with Hughes, G.,
2008 Matching unlabelled configurations and protein bioinformatics
(with J. T. Kent and C. C. Taylor). Submitted as a read paper
for the half-day research meeting of the Royal
Statistical Society on “Inference Methods for Complex and
High-Dimensional Structural Systems”.
2008 A generative, probabilistic model of
local protein structure”. (with Boomsma, W.,
2008 Simulating virtual protein $C_\alpha$ traces with applications (with Nyirongo, V.B.). Journal of Computational Biology, 15, pp1209-1220.
2008 Protein structure
prediction using a probabilistic model of local structure”. (with Boomsma, W., Borg, M., Frellsen, J., Harder, T., Stovgaard,
K., Ferkinghoof-Borg, J., Krogh, A., and Hamelryck,
T.). 8th Community Wide
Experiment on the Critical Assessment of Techniques for Protein Structure
Prediction Cagliari, Sardinia, Italy December 3-7, 2008, pp82-83.
Papers in Edited Volumes:
2001 Statistics and molecular structure of biological
macromolecules (with
2003 Structural bioinformatics revisited (with C.C. Taylor and D.R.
Westhead). LASR2003 Proceedings. (Editors: R. G. Aykroyd, K. V. Mardia & M.
J. Langdon),
2005 A vision of statistical
bioinformatics. LASR2005 Proceedings. (Editors: S. Barber, P. D. Baxter, K.V.
Mardia & R.E. Walls),
2005 Protein gels matching
(with V. Patrangenaru, and
2006 Modeling protein folds with a trivariate von Mises distribution (with G. Hughes, K. V. Mardia, and C. C. Taylor). LASR2006 Proceedings. (Editors: S. Barber, P. D. Baxter, K. V. Mardia and R. E. Walls), Leeds University Press, pp120-123.
2006 Matching pesticides to proteins to predict toxicity (with E.M. Petty, C. C. Taylor, and Q. Chaudhry). LASR2006 Proceedings. (Editors: S. Barber, P.D. Baxter, K.V. Mardia and R.E. Walls), Leeds University Press, pp150-153.
2006 Graphical models and
directional statistics capture protein structure” (with
2007 Statistical modelling of
globular proteins. (with V.B. Nyirongo). LASR2007
Proceedings. (Editors: S. Barber, P. D. Baxter, and K. V. Mardia),
2007 On some recent advancements
in applied shape analysis and directional statistics. LASR2007 Proceedings.
(Editors: S. Barber, P. D. Baxter, and K. V. Mardia),