Projects with some reports
This section contains past projects carried out by students in our group. Where we have been given permission, reports on the projects are made available. The projects have been categorised according to the project programme the student was working under.
|
MSc in Applied Statistics
Project Title |
Student |
Year |
|
Stochastic Modes of Pedigree Generation |
Laura McLelland |
2011 |
|
Evolutionary Models and Machine Learning Patterns |
Man Tang |
2011 |
|
Assembly of Multiple Genomes from Fragments |
Cheuk Yiu |
2011 |
|
Incremental Pedigree Likelihood Calculation |
Shou Zhang |
Sep 2007 |
|
Using Probabilistic Models to Infer Infection Rates in Viral Outbreaks |
Claire Simons |
Feb 2007 |
ComLab MSc
|
Project Title |
Student |
Date |
|
|
Andrey Kravchenko |
Sept 2009 |
|
|
Jose Angel Riarola |
Sept 2009 |
|
|
Markus Gerstel |
Sept 2008 |
|
|
Waqar Ali |
Aug 2007 |
|
Annotation of 12 drosophila genomes using multiple neural networks and evolutionary history |
Ulf Schafer |
Sept 2006 |
|
|
Charles Lin |
Sept 2006 |
|
Algorithms for haplotype inference from genotypes in the presence of recombination |
Syedur Rahman |
Sept 2006 |
|
Graphical programming interface for an XML-based hidden Markov model compile |
Ahmad Chugtai |
Sept 2005 |
|
Automatic code generation for recursions involving stochastic context-free grammars |
Jonathan Churchill |
Sept 2005 |
|
4th Year Mathematics Project Title |
Student |
Year |
|
James Wood Ashley Brooks |
Sep 2010 Feb 2006 |
Summer Students
| Project Title | Student | Year |
| Ina Trolle Andersen, Lin Nan & Maiken Ina Siegismund Kjaersgaard | Aug 2010 | |
| Modelling coupled evolution of gene regulatory and metabolic networks | Hong Noh | Aug 2010 |
| Ancestral recombination histories for error detection in genome sequencing | Chris Campbell, Zi Wang & Qian Yu | Aug 2010 |
| A genetic algorithm for evolving stochastic context-free grammars | James Anderson, Joe Staines & Paula Tataru | Aug 2010 |
| Stefan Hansen, Rita Pancsa & Marcus Webb | Aug 2010 | |
| Artemisa Labi & Chris Campbell | Oct 2009 | |
| Computational analysis of the regulatory region of vertebrate GSX1 | Syazana Ebil | Oct 2009 |
| Gabor Boross, Cathleen Heil, Andras Gyorgy & Nanette Coetzer | Aug 2009 | |
| Difficult concepts in Systems Biology II: the concept of reduction in systems biology | Nick Tasker & Andrew Stephenson | Aug 2009 |
| Difficult concepts in Systems Biology III: function and purpose | Nick Tasker | Aug 2009 |
| Miklos Zoltan Racz | Aug 2009 | |
| James Anderson & Chris Choy | Aug 2009 | |
| Paths in Markov Chains with applications to protein evolution | Tomas Fabsic & Andreas Sand Pedersen | Aug 2009 |
| Jon Ingi Sveinbjornsson & Eirikur Fannar Torfason | Aug 2009 | |
| Katalin Orosz | Aug 2008 | |
| Angela Matthies, Andrew Stephenson & Nick Tasker | Aug 2008 | |
| Anders Okholm & Camilla Mondrup Andreassen | Aug 2008 | |
| Corner cutting approaches to the Either-Griffiths Tavare recursions | Stephen O'Keeffe & Ferenc Huszar | Aug 2008 |
| Jesper Nielsen | Aug 2007 | |
| Lu Gram | Aug 2007 | |
| Lu Gram | Aug 2007 | |
| On recombination induced multiple coalescent events Published in Genetics | Joanna Davies & Frantisek Simancik | Oct 2006 |
| Evolving turing patterns | Maria Demidova | Octo 2006 |
| Max Leung | Sep 2006 | |
| Tong Chen | Oct 2006 | |
| Combining different grammars to make multiple annotations of a single sequence | Joanna Davies | Feb 2005 |
| Naila Mimouni | 2004 |
High School Summer Students
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DPhil Reports
Joe Herman Stochastic Models of Structure Evolution 2013 James Anderson Gaussian Processes and Gene Regulation 2013 Luke Cartey Advance Software for Generating HMM Code 2011 Marton Munz Comparative Analysis of Molecular Motion 2011 Joanna Davies Genetic Heterogeneity and Mapping 2010 Rahul Satija Statistical Alignment and Footprinting 2009 Aziz Mithani Evolutionary Modelling and Analysis of Metabolic Networks 2009 Ben Holtom A Paralogy Based Strategy for Identifying Regulatory Elements in Mammalian Genomes 2008 Naila Mimouni An Investigation of Section Constraints on Non-Coding RNAs and Reliability of Alignments 2008 Saskia de Groot Genome Annotation and Selectional Analysis of Viral Evolution 2007 Lizhong Hao Analysis of Global Gene Expression during the Epithelium Differentiation 2007 Stephen McCauley The Annotation and Evolutionary analysis of Overlapping CDS in ssRNA Viral Genomes 2006
| DTC Projects | ||
| Modelling coupled evolution of gene regulatory and metabolic networks | Hong Noh | 2010 |
| Integrating prior knowledge to reverse-engineer simple biological systems | Martin Munz | 2008 |
| Hidden Markov modelling of single molecular FRET trajectories | Brian Cheung |
|
| Richard Mann | 2008 | |
| Nicolas Wu | 2006 | |
| Robin Ryder | 2006 | |
| Eleni Giannoulatou | 2006 | |
| How many transcripts does it take to reconstruct the splice graph? | Paul Jenkins | 2006 |
| Identifying gene clusters and regulatory themes using time course expression data, hidden Markov models and transcription factor information | Karen Lees | 2004 |
| Naila Mimouni | 2004 | |
| The hunt for genomic dark matter: aligning non-coding functional DNA | Naila Mimouni | 2004 |
| An analysis of the relative efficacy of the Nussinov-Felenstein and the Knudsen-Hein RNA Secondary structure prediction algorithms | Stephen McCauley | 2004 |
Some of Jotun Hein's earlier students who still work in this field are Carsten Wiuf, Bjarne Knudsen, Jakob Skou Pedersen, Rune Lyngsoe, Christian Storm Pedersen, Roald Forsberg and Rasmus Nielsen.
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