Recent Publications
General bioinformatics
Phylogenetics
- Walter R. Gilks and Chinying Wang.
A non-parametric method for detecting specificity determining sites in protein sequence alignments.
Statistical Applications in Genetics and Molecular Biology, 2011, 10, Art. 20, 1-31.
- Walter R. Gilks, Tom M. W. Nye and Pietro Liò.
A variance-components model for distance-matrix phylogenetic reconstruction.
Statistical Applications in Genetics and Molecular Biology, 2011, 10, Art. 16, 1-33.
- Kerstin Hommola, Judith E. Smith, Yang Qiu and Walter R. Gilks.
A permutation test of host-parasite cospeciation.
Molecular Biology and Evolution, 2009, 26(7), 1457-1468.
- Tom M. W. Nye, Brad J.C. Baxter and Walter R. Gilks.
A covariance matrix inversion problem arising from the construction of phylogenetic trees.
London Mathematical Society Journal of Computation and Mathematics, 2007, 10, 119-131.
- Tom M. W. Nye, Pietro Liò, and Walter R. Gilks.
A novel algorithm and web-based tool for comparing two alternative phylogenetic trees.
Bioinformatics, 2006, 22, 117-119.
Protein structure
Protein interactions
- Tom M. W. Nye, Carlo Berzuini, Walter R. Gilks, M. Madan Babu and Sarah Teichmann.
Predicting the strongest domain-domain contact in interacting protein pairs.
Statistical Applications in Genetics and Molecular Biology, 2006, 5, Art. 5, 1-17.
- Tom M. W. Nye, Carlo Berzuini, Walter R. Gilks, M. Madan Babu and Sarah A. Teichmann.
Statistical analysis of domains in interacting protein pairs.
Bioinformatics, 2005, 21, 991-1001.
Highly conserved non-coding DNA
- Irina Abnizova, Klaudia Walter, Rene te Boekhorst, Greg Elgar and Walter R. Gilks.
Statistical information characterization of conserved non-coding elements in vertebrates.
Journal of Bioinformatics and Computational Biology , 2007, 5(2B), 533-547.
- Tanya Vavouri, Klaudia Walter, Walter R. Gilks, Ben Lehner and Greg Elgar.
Parallel evolution of conserved noncoding elements that target a common set of developmental regulatory genes from worms to humans.
Genome Biology, 2007, 8(2), R15.
- Tanya Vavouri, Gayle K. McEwen, Adam Woolfe, Walter R. Gilks and Greg Elgar.
Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key.
Trends in Genetics, 2006, 22, 5-10.
- Klaudia Walter, Irina Abnizova, Greg Elgar and Walter R. Gilks.
Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences..
Trends in Genetics, 2005, 21, 436-440.
Regulatory DNA
- Irina Abnizova and Walter R. Gilks.
Studying statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the eukaryotic genomes.
Briefings in Bioinformatics, 2006, 7, 48-54.
- Irina Abnizova, Alistair G. Rust, Mark Robinson, Rene te Boekhorst and Walter R. Gilks.
Transcription binding site prediction using Markov models.
Journal of Bioinformatics and Computational Biology, 2006, 4, 425-441.
- Irina Abnizova, Rene te Boekhorst, Klaudia Walter and Walter R. Gilks.
Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.
BMC Bioinformatics , 2005, 6, 109.
Database annotation errors
- Walter R. Gilks, Benjamin Audit, Daniela de Angelis, Sophia Tsoka, Christos A. Ouzounis.
Percolation of annotation errors through hierarchically structured protein sequence databases.
Mathematical Biosciences , 2005, 193, 223-234.
- Emmanuel D. Levy, Christos A. Ouzounis, Walter R. Gilks and Benjamin Audit.
Probabilistic annotation of protein sequences based on functional classifications.
BMC Bioinformatics , 2005, 6, 302.
Microarrays
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