Present Project Proposals
These project proposals are drafts or suggestions about someting that could be interesting to investigate. Anyone can place one here if it is of appropriate content. Proposals that have the opportunity to be done will be modified to contain considerably more detail and will be subject to discussion to ensure their realism. About 10-15 projects get done every year.
Modelling Evolution, Genome Annotation and Comparative Biology
- Correlated Alignment Summary
- Evolutionary Models for Complex Signals Summary
- Analysing Multiple Functionalities in Proteins Summary
- Metabolic Random Fields Summary
- Stochastic Models Combining Alignment and Annotation Summary
- Fine Scale Regulatory Annotation of a Gene Summary
- A Unified Approach to Signal Detection Summary
- Local Pairwise Statistical Alignment Summary
- Evolutionary Docking of Proteins Summary
- Quantifying the Structural Value of Evolution Summary
Population Genetics, Mapping and Genealogical Structures
These projects are all motivated by the wide use of population variation data. The major genealogical structures are phylogenies, pedigrees and ancestral graphs (ARG). A central use of variation data is mapping - making statements about the positions in the genome that is causal for individual phenotypes, such as disease. New sequencing techniques creates new opportunities for research, such as pedigree and somatic tree inference, but also changes the nature of more traditional problems, such as phylogeny, alignment and recombination analysis, due to the large quantity of data.
Systems Biology
These projectsare all motivated by the present rise of systems biology. Systems biology poses many questions, both in terms of modelling on a large scale, how feasible it is to infer biological systems and the use of concepts in this field. Networks are central to many systems biology models and the role of evolution also needs to be explored.
- Difficult Concepts in Systems Biology II: Levels and Reduction Summary
- Difficult Concepts in Systems Biology III: Function and Purpose Summary
Algorithmic, Probability, Modeling and Software Development Challenges
Computational Biology leads to a series of technical problems that could be undertaken by someone with a more pure interest in combinatorics, statistics, mathematics, algorithms, modeling or software development. Some of these might have biological terms in them, but the biological component is minimal (or could be minimized).
- Path Sampling in Continuous Time Markov Chains
- Dealing with Large, Sparse Continuous Time Markov Chains
- Error Correcting Codes, Lumpability and Sequence Evolution
- Incorporating RNA secondary structure prediction into StatAlign
- Kinetic and Co-Transcriptional Folding of RNA
- Combinatorics of Biological Networks Collaboration with Alex Scott Summary
- Multiple Alignment Using Guide Networks Summary
- Automatic Code Generation for Probabilistic Inference in Computational Biology Collaboration with Oege de Moor Summary
- Combinatorics Problems in Genome Rearrangement Summary
- Artifacts from Combining Hidden Markov Models Summary
Collaborative Data Analysis
We are extremely keen to launch larger collaborative projects by starting a pilot student project under joint supervision of our more methodological group and experimental person or laboratory. These are a few examples.
- Recombination analysis in Arabidopsis Thaliana
- Testing the Biogeographical Hypotheses Collaboration with Finn Borchsenius & Anders Barfod
- Molecular Evolution of Selected Families of Human Endogenous Retroviruses Collaboration with Palle Villesen & Hugo Martins
- Phylogenomic Analysis of Algae Collaboration with Tom Cavalier-Smith Summary
- Stochastic Models of Leaf Shape Evolutiion Collaboration with Nick Jones and Miltos Tsiantis Summary
- Footprinting with additional knowledge Collaboration with Richard Mott Summary
RNA Structure and Evolution Modelling
- Evaluation of SCFGs Summary
- Evolution Grammar Search Summary
- Practical Implications of Grammar Ambiguity on RNA Secondary Structure Prediction Summary
- Boltzmann Weighted Combinatorics of RNA Secondary Structures Summary
Computational Origin of Life Models
- Mass Action Equations for Autocatalytic Systems
- Autocatalytic Sets of RNAs Collaboration with Wim Hordijk & Mike Steel Summary
- Proposal for the Development of a Software Package for Simulating and Studying Catalytic Reaction Systems and Autocatalytic Sets Summary
High School Projects
- RNA Secondary Structure (Algorithms)Summary
- Signals in Single Genomes (Computer Science)Summary
- Counting in Phylogenetics (Combinatorics)Summary
- Pairwise Alignment (Algorithms) Summary
- Sequence Evolution (Probability Theory) Summary
Oxford Summer School in Computational Biology 2011
Oxford Summer School in Computational Biology 2012
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