Old Projects
The following section contains old project proposals. These are typically proposals that have already been the basis of one or more student projects. The questions involved do evidently interest us, so if you believe you have a new angle on the proposal please feel free to contact us to discuss the possibility of doing it as a project.
Modelling Evolution, Genome annotation and Comparative Biology
Evolving Dynamical Systems – case study: Cell Cycle Collaboration with Bela Novak Summary
RNA, Stochastic Context Free Grammars and Classifiers Summary
Comparative Annotation of Metabolic Pathways Summary
Evolving Language Grammars: “Evolving English” Collaboration with Stephen Clark Summary
Evolving Biological Grammars Summary
Fine Scale Regulatory Annotation of a Gene Summary
Evolving Dynamical Systems – case study: Cell Cycle Summary
Algorithms for finding Autocatalytic SystemsSummary
Evolutionary Models for Combined Regulation-Metabolism Graphs Collaboration with Gail Preston Summary
Evolutionary Analysis of Molecular Movements Collaboration with Thomas Darden & Mark SansomSummary
Parallelising pairwise-statistical alignment Summary
MCMC Integration over Evolutionary Histories of Metabolic Networks Collaboration with Tom Snijders Summary
Modelling evolution of protein secondary structure topologies Summary
Extending the Domain of Comparative Genomics Collaboration with Kay DaviesSummary
Modelling the dynamics and evolution of nitrogen assimilation in plant pathogenic Pseudomonas Collaboration with Gail Preston Summary
Choice of parameter set for use with a mathematical model of mechanical force generation in the heart Summary
Evolutionary Pattern Formation Summary
Measurement of Selection on RNA molecules Summary
Fitting Genome Models To Known Virus Structures Summary
Virus evolution simulation Summary
Population Genetics, Mapping and Genealogical Structures
Population Pedigree Inference from Genomic Data Collaboration with Steffen Lauritzen Summary
Mapping and Arabidopsis Collaboration with Richard Mott Summary
Statistical Alignment via k-Restricted Steiner Trees Summary
Counting Pedigrees up to Isomorphism Summary
Networks and Association mapping SummaryCollaboration with Andrew Rzhetsky
A Gibbs Sampler of the ancestral recombination graph Summary
User Interface for Recombination Analysis Summary
From exact marginals to good importance sampling Summary
“Corner Cutting” approaches to the Ethier-Griffiths-Tavare Recursions Summary
Counting Ancestral Recombination Graph (ARG) Topologies Summary
Workbench for Ancestral Recombination Graph Summation Summary
Somatic Cell Genealogies and Differentiation Collaboration with Kevin Talbot Summary
Systems Biology
Identifiability of a Simple Biological System Summary
Difficult Concepts in Systems Biology: Emergence Collaboration with Carsten Wiuf Summary
Parameter and Sensitivity Analysis for Large System of ODEs Collaboration with Dagmar IberSummary
Algorithmic, Probabilistic and Modelling Challenges
Gaussian Processes and Gene Regulation Summary
Efficient sampling of ancestral states in the infinite site model Summary
A Constraint Optimization Problem in Phylogenetics Collaboration with Raphael Hauser Summary
Stochastic Turing Patterns Summary
How many transcripts does it take to reconstruct the Splice Graph? Summary
Combining Stochastic Grammars Summary
Pseudoknots in RNA secondary structure Summary
Combining RNA energy minimisation with microscopy informationSummary
Parallelisation of Recombination Analysis Summary
Temporal Multiple Statistical Alignment Collaboration with Gerton Lunter Summary
Collaborative Data Analysis
Computational Promoter Analysis of Metazoan α-Globins Collaboration with Doug Higgs Summary
Reconstruction of an Ancestral Protein: Sequence, Function, Motion and Structure Collaboration with Lee Pedersen and Mark Sansom Summary
Computational Promoter Analysis of non-Coding RNAs Collaboration with Kay Davies Summary
Analysis of single-molecule FRET trajectories of transcription complexes based on Hidden-Markov Modelling Collaboration with Achilles Kapanides Summary
Phylogenetic Analysis of “New” Homeobox in the Lineage Leading to Humans Collaboration with Peter W H Holland Summary
Cataloguing sequences homologous to the Rhodobacter flagellar motorCollaboration with Judith Armitage Summary
Annotate 12 Drosophila genomes for regulatory signals Collaboration with Lior Pachter & Vasile Palade Summary
Structural Analysis of Aptamers Collaboration with William James Summary
Fine Scale Regulatory Annotation of Cancer Genes Collaboration with Thorunn Rafnar Summary
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