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Project Sketches

Examples of earlier projects:

Potential students or supervisors could use the course to test an idea, make a minor literature study or develop a plan for a data study in more detail. Some examples are listed here:

Crossover and Gene Conversion Discovery using Local Phasing (Stefania Bjarney Olafsdottir, 2013)

Maximum Entropy Model for Alternative Splicing Starting Pattern (Qianyun Guo, 2013)

Endogenous retrovirus (Trine Line Hauge Okholm & Carina Tangsgaard, 2013)

Inference of Population History in an Isolation-with-Migration Model (Jade Yu Cheng, 2013)

Classification of Non-Ribosomal Peptide Syntheses with Feed-Forward Neural Networks (Dan A. Søndergaard, Torben M. Andersen & Henrik Schmidt-Møller, 2013)

Paths in Continuous-Time Markov Chains with Applications to Studies of Protein Tertiary
Structure Evolution
(Andreas Sand, 2009)

RNA, SCFGs and Classifiers (Zsuzsanna Sükösd & Paula Tataru, 2009)

A profile-Hidden Markov Model approach for detecting endoretroviral LTR sequences in the Platypus genome (Hugo M. Martins & Yu Qian, 2009)

Inference of signal transduction pathways (Silvio Waschina, 2009)

Virtual Docking using General Purpose Graphic Processing Units (Martin Simonsen, 2009)

Using HMMs for eukaryotic promoter elements prediction (Shengting Li)

Computational Analysis of ChIP-Seq Data (Jinjie Duan, 2010)

Implementation of a MSA-based method for detecting Coevolution (Vikas Gupta & Oleg Sitsel, 2010)

Different Representations of Multi-Domain Proteins; Principal Component Analysis (Iwona Siuda, 2010)

 

Examples of present project proposals:

Anybody can place a project draft on this page. Clearly, the more detailed and "thought-through"the project draft, the easier it will be for a student to make progress. It is only advantageous if students work in groups on a common project.

Simultaneous Genome Annotation for Multiple Levels (Jotun Hein)

Alignment of large RNA viral genomes (Zsuzsanna Sükösd & Jørgen Kjems)

Fast Stem Finder (Jotun Hein & Jakob Skou Pedersen)

Identification of tertiary structure interactions from evolutionary analysis (Jakob Skou Pedersen)

Molecular evolution of selected families of human endogenous retroviruses (with Palle Villesen & Hugo Martins)

Using the molecular clock to test biogeographical hypotheses (Jotun Hein, Anders Barfod & Finn Borchsenius)

Inverse RNA Folding (Anders Okholm, Rune Lyngsø, Jørgen Kjems & Jotun Hein)

For further examples of projects see:

www.stats.ox.ac.uk/research/genome/projects