Previous projects

Present project proposals

Here we provide a bit of background for ongoing or proposed projects and also a description of work completed earlier by students in Oxford.

Summer school projects

2013

Coalescent inference from serially sampled, next-generation sequencing data from HIV patients – Lasse Maretty, Jonas Sibbesen and Kevin Dialdestoro (report, presentation, poster)
MCMC and spannoids – Kasper Nielsen, Aldo Pacchiano, Preeyan Parmar (report, presentation, poster)
RAF application – Edward Rolls, Eli Bingham, Laurence Hutton-Smith (report, presentation, poster)
RAF theory – Jie Gao, Leonard Hasenclever, Dilyana Mincheva (report, presentation, poster)
Genealogical and Genetic Ancestry – Philip Arathoon, Farah Colchester, Rachel Moore (report, presentation, poster)
Importance Sampling under the Coalescent with Times and Variable Population – Martin Ye, Svend Nielsen and Michael Nicholson (report, presentation)
eQTL effects on gene co-expression network structure – Naomi Cannell, Andrew P. Morgan, Ran Li (presentation, poster)

2012

Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information – Pierre A. Haas, Leigh-Anne Mathieson, Vladimir Volynkin (report, presentation, poster)
StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction – Preeti Arunapuram, Ingolfur Edvardsson, Michael Golden (report, presentation)
Regulatory Annotation of the Human Genome – Mauricio Barrientos, Yingchao Zhong (report, presentation, poster)
HMMingbird: tree extension – Alexander Wood, Balazs Koszegi, Dmitrii Bychkov (report, presentation, poster)
Path sampling – Surojit Biswas, Jeffrey Chan, Jie Xiong (report, presentation, poster)
Gene Co-expression Network Design from RNA-seq data in Arabidopsis thaliana – Ximena Contreras, Daniel Nichol, Michelle Parker (report, presentation)
Correlated evolution of autoinhibitory proteins – A. Cumberworth, A. M. Grigore, N. M. D. Niezink (report, presentation, poster)
Inverse RNA – C. Lake, W. Weir, A. Teufel (report, presentation, poster)

2011

Modelling leaf shape evolution – Nomenjanahary Alexia Raharinirina, Liutauras Rusaitis, Henry Jackson (report, presentation, poster)
Advanced Software Design for StatAlign (report, poster)
Solving the Inverse RNA Folding Using a Genetic Algorithm – Elena Sizikova, Amarendra Badugu, Tomas Hyland (report, presentation, poster)
A Mathematical Model of Correlated Evolution – Patrick Fried, Marie-Hélène Descary, Chris Lester (presentation, poster)
Comparison of Parallel Solution Techniques for the Eikonal Equation – T. Prince, P. Crowley, O. Thomas (presentation, poster)

Project Title	Student	Year
Search for life in catalytic reaction 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-genome alignment	Naila Mimouni	2004

DTC projects

Probing Prebiotic Toy-Chemical Reaction Systems for Autocatalytic Sets	Federico Paoletti	2015
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 Chuang
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

Old project proposals

Modelling Evolution, Genome annotation and Comparative Biology
A Stochastic Model of Gene Duplication and Loss (March 15)
Statistical Model for the Evolution of Directions (March 15)
The Origin of Life and Toy Chemistries (Jotun Hein) (Dec 14)
Understanding the evolution of assembly specificity in protein oligomers (March 15)
Molecular Evolution of Primate Retroelements (Aris Katzourakis and Jotun Hein) (Dec 14)
Investigating the Miklos-Lunter-Holmes (2004) Model of Insertion-deletion (Jotun Hein) (Dec 14)
Markov Random Fields on Biological Networks (Jotun Hein and George Deligiannidis) (Dec 14)
Metrics on RNA Secondary Structure Ensembles (Jotun Hein) (Dec 14)
Algorithms for finding Autocatalytic Systems (June 10)
Virus evolution simulation (June 10)
Measurement of Selection on RNA molecules (June 10)
Evolving Dynamical Systems – case study: Cell Cycle Collaboration with Bela Novak (Feb 10)
Evolutionary Models for Complex Signals (Feb 10)
RNA, Stochastic Context Free Grammars and Classifiers Summary (June 09)
Fine Scale Regulatory Annotation of a Gene (May 08)
A Unified Approach to Signal Detection (May 08)
Evolving Language Grammars: “Evolving English” Collaboration with Stephen Clark (Jan 07)
Evolving Biological Grammars (June 07)
Evolutionary Docking of Proteins (May 07)
Evolutionary Analysis of Molecular Movements Collaboration with Thomas Darden Mark Sansom (Jan 07)
Extending the Domain of Comparative Genomics Collaboration with Kay Davies

Population Genetics, Mapping and Genealogical Structures

The following project proposals 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 create 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.

Genetic and Genealogical Ancestors (April 2011)
Population Pedigree Inference from Genomic Data Collaboration with Steffen Lauritzen (Jan 08)
Counting Pedigrees up to Isomorphism (June 07)
User Interface for Recombination Analysis (Dec 05)

Systems Biology

These projects are 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 III: Function and Purpose (Jan 09)
Identifiability of a Simple Biological System (Jan 08)
Difficult Concepts in Systems Biology: Emergence Collaboration with Carsten Wiuf (Jan 08)
Parameter and Sensitivity Analysis for Large System of ODEs Collaboration with Dagmar Iber (Nov 07)

Algorithmic, Probabilistic and Modelling 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).
Dealing with Large, Sparse Continuous Time Markov Chains (Dec 11)
Combinatorics of Biological Networks Collaboration with Alex Scott (Oct 08)
Combinatorics Problems in Genome Rearrangement (March 08)
Artifacts from Combining Hidden Markov Models (March 07)
Stochastic Turing Patterns (April 06)
Parallelisation of Recombination Analysis (Feb 06)

Collaborative Data Analysis
Testing the Biogeographical Hypotheses Collaboration with Finn Borchsenius & Anders Barfod
Footprinting with additional knowledge Collaboration with Richard Mott (Feb 10)
Computational Promoter Analysis of Metazoan α-Globins Collaboration with Doug Higgs (June 07)
Annotate 12 Drosophila genomes for regulatory signals Collaboration with Lior Pachter & Vasile Palade(June 07)
Structural Analysis of Aptamers Collaboration with William James (Dec 05)

RNA Structure and Evolution Modelling
Evaluation of SCFGs (May 11)
Evolution Grammar Search (April 11)
Practical Implications of Grammar Ambiguity on RNA Secondary Structure Prediction (April 11)

Computational Origin of Life Models
Mass Action Equations for Autocatalytic Systems (April 11)