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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.

Challenges in Bioinformatics

Crossover & Gene Conversion Discovery Using Local Phasing

Stefania Olafsdottir

Oct 2013

Classification of Non-Ribosomal Peptide Syntheses with Feed-Forward Neural Networks

Dan Sondergaard, Torben Andersen & Henrik Schmidt-Moller

Oct 2013

Inference of Population History in an Isolation-with-Migration Model

Jade Y Cheng

Oct 2013

Maximum Entropy Model for Alternative Splicing Starting Pattern

Qianyun Guo

Oct 2013

Endogenous Retrovirus

Trune Line Okholm & Carina Tansgaard

Oct 2013

Modelling the Contribution of SNP Variation in HSD11B2 to the Risk of Schizophrenia in Individuals Exposed to Pre and Postnatal Stress

Jean-Christophe Debost


Bioinformatic Studies of Bacterial Ca2+ Transporting P-type ATPases

Mateus Dyla

Oct 2012

Assembly in Theory and Practice

Jesper Jensen Bjerg

Oct 2012

Is a Specific Type of Endogenous Retrovirus a Cause of Leukemia?

Karen Jessen

Oct 2012

Classification of Non-Ribosomal Peptides Using Support Vector Machines

Hannah Acheson-Field & Eric Chu

Dec 2013

RNA Secondary Structure Prediction

Mads Krogh Jensen


For earlier projects from this course, see also Project Sketches at Bioinformatics Research Centre, Aarhus, Denmark

 

MSc in Applied Statistics


Project Title

Student

Year

Approximation Sequence Evolution by Stepping Stones by using Codes and Lumpability

Yu Mu

2013

The Relationship Between Genealogical and Genetic Ancestry: Extending the Matsen-Evans Model to k-gene Chromosomes

Farah Colchester

2012

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

 

Predicting RNA Secondary Structures Including Pseudoknots

 

Andrey Kravchenko

 

Sept 2009

 

Reconstruction of Ancestral Metabolisms

 

Jose Angel Riarola

 

Sept 2009

 

Evolving Language Grammar

 

Markus Gerstel

 

Sept 2008

 

Large-scale comparative annotation of bacterial genomes

 

Waqar Ali

 

Aug 2007

 

Annotation of 12 drosophila genomes using multiple neural networks and evolutionary history

 

Ulf Schafer

 

Sept 2006

 

User interface for recombination analysis

 

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

Improved ncRNA prediction

Katsuya Noguchi

Sept 2001


4th Year Mathematics

 

Project Title

 

Student

 

Year

Likelihood Maximizationylogenic Trees

 

James Wood

Sep 2010

Evolving Turing Patterns

Ashley Brooks

Feb 2006


Summer Students

Project Title

Student

Year

Search for life in catalytic reactiion systems

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

Spannoid alignment   

Stefan Hansen, Rita Pancsa & Marcus Webb

Aug 2010

Metabolic random fields 

Artemisa Labi & Chris Campbell

Oct 2009

Computational analysis of the regulatory region of vertebrate GSX1 

Syazana Ebil

Oct 2009

Fine scale regulatory annotation of cancer genes 

 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

MCMC and the infinite set model

Miklos Zoltan Racz  

Aug 2009

Gaussian Processes and Gene Regulation

James Anderson & Chris Choy

Aug 2009

Paths in Markov Chains with applications to protein evolution  

Tomas Fabsic & Andreas Sand Pedersen

Aug 2009

Population pedigree inference from genomic data 

Jon Ingi Sveinbjornsson & Eirikur Fannar Torfason

Aug 2009

Fine scale regulatory annotation of ORMDL3

Katalin Orosz

Aug 2008

The concept of emergence in systems biology

Angela Matthies, Andrew Stephenson & Nick Tasker

Aug 2008

From exact marginals to better importance sampling

Anders Okholm & Camilla Mondrup Andreassen

Aug 2008

Corner cutting approaches to the Either-Griffiths Tavare recursions

Stephen O'Keeffe & Ferenc Huszar

Aug 2008

Corner cutting in statistical alignment

Jesper Nielsen

Aug 2007

Random drift on probability distributions

Lu Gram

Aug 2007

On the Monotonicity of HIPP

Lu Gram

Aug 2007

On recombination induced multiple coalescent events - published in Genetics

Joanna Davies & Frantisek Simancik

Oct 2006

Evolving turing patterns

Maria Demidova

Oct 2006

Protein Secondary Structures Enumeration

Max Leung

Sep 2006

Counting pedigrees up to isomorphism

Tong Chen

Oct 2006 

Combining different grammars to make multiple annotations of a single sequence

Joanna Davies 

Feb 2005

Gap Attraction: A new measure for whole-genomealignment

Naila Mimouni

2004

 

High School Summer Students


   

Conrad Godfrey

Aug 2010

RNA secondary structure prediction: the co-transcriptional effect on RNA folding

Fiona Rust

Aug 2010

Investigation of the number of possible secondary RNA structures with refernece to theoretical expressions

Abigail Linton

Oct 2009

Pattern searching in a single genome

Michelle Parker

Oct 2009

Pattern search in a single genome

Ken Mawhinney

Artemisa Labi

Oct 2008

Aug 2007

Basic models of nucleotide evolution

Counting in Phylogenetics

   

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




Evolving and primitive embryotic cell cycle model

Malte Luecken

2013

Real chemical systems, RAFs and the Origin of Life

Lukas Hutter

2013

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


A phylogenetic model for the prediction of quantitative characteristics and applications to cardiac modelling

Richard Mann

2008

Applications of process algebra in systems biology

Nicolas Wu

2006

Grammar and phylogenies

Robin Ryder

2006

Evolution of metabolic networks

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

Hidden Markov models for protein sequence alignment

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.