The following Theses by PhD students of the EBI are available online. They are arranged in the order they were submitted, with the most recent submissions first.

 

2014

Title: Differential Drug Response as a Function of Age

Rita Santos, 3 September 2014

Supervisor:  John Overington

 

Title: to be advised

Sarah Parks, 20 August 2014

Supervisor:  Nick Goldman

 

Title: Genome Analysis In Three Dimensions: Functional Analysis of HI-C Derived Datasets

Robert Sugar, 11 August 2014

Supervisor:  Nick Luscombe

 

The Chemistry and Evolution of Enzyme Function: Isomerases as a Case Study

Sergio Martinez-Cuesta, 31 July 2014

Supervisor: Janet Thornton

 

Cheminformatics for Genome-Scale Metabolic Reconstructions

John May, 10 June 2014

Supervisor: Christoph Steinbeck

 

Title: to be advised

Benedetta Baldi, 28 May 2014

Supervisor: Nicolas Le Novere

 

Title: to be advised

Jean-Baptiste Pettit, 27 May 2014

Supervisor: John Marioni

 

RNA sequencing for the study of splicing

Mar Gonzalez-Porta, 25 April 2014

Supervisor: Alvis Brazma

 

Informatics for tandem mass spectrometry-based metabolomics

Stephan Beisken, 10 April 2014

Supervisor: Christoph Steinbeck

 

Biological network evaluation and relation discovery from scientific literature

Chen Li, 31 March 2014

Supervisor: Dietrich Rebholz-Schuhmann

 

Drug repositioning and indication discovery using description logics

Samuel Croset, 18 March 2014

Supervisor: Dietrich Rebholz-Schuhmann

 

Modelling high content proteomics data in a signalling context

Camille Terfve, 12 March 2014

Supervisor: Julio Saez-Rodriguez

 

Title: to be advised

Ying Yan, 3 January 2014

Supervisor:  Dietrich Rebholz-Schuhmann

 

Spatial and Stochastic Modeling of TrkB Mediated Signaling Pathways Involved in Long Term Potentation in the Dendritic Spine

Christine Seeliger, 1 January 2014

Supervisor: Nicolas Le Novere

 

2013

Analysis of the Haematopoietic Transcriptome in Development

Myrto Kostadima, 2 December 2013

Supervisor:  Paul Bertone

 

A genomic study of regulation of transcription by chromatin

Filipe Cadete, 18 November 2013

Supervisor: Nick Luscombe

 

Understanding the epigenome using system genetics

Sander Timmer, 30 October 2013

Supervisor:  Ewan Birney

 

Transcriptome sequencing analysis with application to embryonic stem cell self-renewal

Tamara Steijger, 4 October 2013

Supervisor: Paul Bertone

 

Integration and analysis of protein evolutionary relationships and small molecule bioactivity data

Felix Kruger, 4 October 2013

Supervisor:  John Overington

 

Computational biology of longevity in model organisms

Matthias Ziehm, 4 October 2013

Supervisor:  Janet Thornton

 

On key modulators of higher-order chromatin structure

Andre Faure, 2 September 2013

Supervisor:  Paul Flicek

 

Methods for the Investigation of Protein-Ligand Complexes

Ben Stauch, 24 June 2013

Supervisor:  John Overington

 

2012

Computational studies on the biogenesis and function of small non-coding RNAs

Nenad Bartonicek, 30 November 2012

Supervisor: Anton Enright

Using natural language processing methods to support curation of a chemical ontology

Adam Bernard, 13 November 2012

Supervisor: Dietrich Rebholz-Schuhmann

Evolutionary analysis of animal microRNAs

José Afonso Guerra Martins dos Santos Assunção, 8 October 2012

Supervisor: Anton Enright

Supporting disease candidate gene discovery based on phenotype mining

Anika Oellrich, 22 August 2012

Supervisor: Dietrich Rebholz-Schuhmann

Bioinformatic methods for species-specific metabolome inference

Pablo Moreno, 14 August 2012

Supervisor: Christoph Steinbeck

RNA sequencing for the study of gene expression regulation

Angela Goncalves, 18 July 2012

Supervisor: Alvis Brazma

Transomics: Integrating core `omics' concepts.

Joe Foster, 25 May 2012

Supervisor: Rolf Apweiler

Genome-scale strategies controlling the impact of deleterious mutations

Inigo Martincorena, 21 May 2012

Supervisor: Nick Luscombe

Genome-wide analyses of transcriptional regulation across multiple tissues and species

Petra Schwalie, 29 March 2012

Supervisor: Paul Flicek

2011

Transcriptional characterization of glioma neural stem cells

Diva Tommei, 23 December 2011

Supervisor: Paul Bertone

Analysis of alignment error and sitewise constraint in mammalian comparative genomics.

Gregory Jordan, 30 November 2011

Supervisor: Nick Goldman

Exploiting high throughput DNA sequencing data for genomic analysis.

Markus Fritz, 14 October 2011

Supervisor: Ewan Birney

Multi scale modelling in neuroscience: integration of computer simulations of biochemical and electrical signalling in the medium spiny neuron of the striatum.

Michele Mattioni, 29 July 2011

Supervisor: Nicolas Le Novère

A computational study of promoter structure and transcriptional regulation in yeast on a genomic scale

Judith Zaugg, 12 May 2011

Supervisor: Nick Luscombe

Characterisation, Classification and Conformational Variability of Organic Enzyme Cofactors

Julia Fischer, 11 April 2011

Supervisor: Janet Thornton

Large Scale Genomic Association Studies in Fruit Fly and Human

Dace Ruklisa, 4 January 2011

Supervisor: Ewan Birney

2010

A computational study of transcriptional regulation in eukaryotes on a genomic scale

Florence Cavalli, 24 December 2010

Supervisor: Nick Luscombe

Evolution of Transcription Factor Repertoires in the Saccharomycotin

Jacky Hess, 17 December 2010

Supervisor: Nick Goldman

Time-resolved analysis of transcription factor induction and cell differentiation

Heidi Dvinge, 11 October 2010

Supervisor: Paul Bertone

Visualization and Exploration of Transcriptomics Data

Nils Gehlenborg, 14 September 2010

Supervisor: Alvis Brazma

Mathematical and Statistical Models for the Analysis of Protein Interactions

Tony Chiang, 21 June 2010

Supervisor: Wolfgang Huber

A statistical model relating transcription factor concentrations to positional information in the early Drosophila embryo

Garth Ilsley, 14 June 2010

Supervisor: Rolf Apweiler

Analysis of large-scale RNAi screens in the search for genetic interactions

Elin Axelsson, 11 June 2010

Supervisor: Wolfgang Huber

Modelling dopamine and glutamate signal integration

Lu Li, 30 March 2010

Supervisor: Nicolas Le Novère

2009

Transcriptional and Post-transcriptional Regulation of Gene Expression: Computational Analysis of Microarray Studies in Fungal Species

Katherine Lawler, 3 November 2009

Supervisor: Alvis Brazma

Function and evolution of regulatory elements in vertebrates

Alison Meynert, 28 July 2009

Supervisor: Ewan Birney

A computational study of bacterial gene regulation and adaptation on a genomic scale

Aswin Sai Narain Seshasayee, 30 June 2009

Supervisor: Nick Luscombe

On the function of calcium-regulated allosteric devices in synaptic plasticity

Melanie Stefan, 31 March 2009

Supervisor: Nicolas Le Novère

Genome assembly and comparison

Daniel Zerbino, 31 March 2009

Supervisor: Ewan Birney

Integrated analysis of proteomics data to assess and improve the scope of mass spectrometry based genome annotation

Michael Mueller, 30 March 2009

Supervisor: Rolf Apweiler

Algorithms on Phylogenetic Trees

Fabio Pardi, 25 February 2009

Supervisor: Nick Goldman

Investigating the Consequences of AMPA Receptor Diffusion on Long-term Potentiation using Single-Particle Modelling Approaches

Dominic Tolle, 20 February 2009

Supervisor: Nicolas Le Novère

The Geometry and Physicochemistry of Protein Binding

Abdullah Kahraman, 6 February 2009

Supervisor: Janet Thornton

Automatic functional annotation of predicted active sites: combining PDB and literature mining

Kevin Nagel, 1 January 2009

Supervisor: Dietrich Rebholz-Schuhmann

2008

Comprehensive analysis of high-throughput experiments for investigating transcription and transcriptional regulation

Joern Toedling, 29 August 2008

Supervisor: Wolfgang Huber

Quantifying evolution and natural selection in vertebrate noncoding sequence

Michael Hoffman, 20 March 2008

Supervisor: Ewan Birney

2007

The geometry and evolution of catalytic sites and metal binding sites

James Torrance, 24 September 2007

Supervisor: Janet Thornton

Annotation of Gene Products based on the Biomedical Literature

not available online; click here for further details

Sylvain Gaudan, 17 September 2007

Supervisor: Dietrich Rebholz-Schuhmann

2006

Large-scale multiple alignment and transcriptionally-associated pattern discovery in vertebrate genomes

not available online; click here for further details

Ben Paten, 29 August 2006

Supervisor: Ewan Birney

Towards Relating the Evolution of the Gene Repertoire in Mammals to Tissue Specialisation

Shiri Freilich, 13 August 2006

Supervisor: Janet Thornton

The Causes and Consequences of Variation in Evolutionary Processes Acting on DNA Sequences

Lee Bofkin, 6 March 2006

Supervisor: Nick Goldman

Markov Models for Protein Sequence Evolution

Carolin Kosiol, 3 March 2006

Supervisor: Nick Goldman

2005

Prediction of gene expression in embryonic structures of Drosophila melanogaster 

not available online; click here for further details

Anastassia Samsonova, 12 December 2005

Supervisor: Alvis Brazma

Understanding the Relationship Between Enzyme Structure and Catalysis

Alex Gutteridge, 26 August 2005

Supervisor: Janet Thornton

Applications of Combinatorial Pattern Discovery in Computational Genomics

Nikos Darzentas, 4 July 2005

Supervisor: Christos Ouzounis

2004

Computational analysis of complete proteomes by clustering and analysis of alternative splicing impact on proteome diversity

Evgenia Kriventseva, 2004

Supervisor: Rolf Apweiler

Evolution and function of protein families in complete genomes 

not available online; click here for further details

Victor Kunin, 2004

Supervisor: Christos Ouzounis

Computational Investigations into cis-Regulation in Eukaryotes

Laurence Ettwiler, June 2004

Supervisor: Ewan Birney

2003

Computational analysis of gene regulatory sites in two yeasts

not available online; click here for further details

Katja Kivinen, 2003

Supervisor: Alvis Brazma

Towards reverse engineering gene regulatory networks

not available online; click here for further details

Thomas Schlitt, 2003

Supervisor: Alan Robinson

DNA Phonology: Investigating the Codon Space

Giuseppe Insana, November 2003

Supervisor: Heikki Lehväslaiho

Novel Algorithms for Protein Interaction Networks

Michael Lappe, November 2003

Supervisor: Liisa Holm

Sex determination in Drosophila melanogaster : a theoretical model for the regulation of the Sex-lethal gene

*not available online; click here for further details*

Matthieu Louis, 1 September 2003

Supervisor: Liisa Holm

2002

Protein sequence database searching

not available online; click here for further details

Caleb Webber, 2002

Supervisor: Geoff Barton

Hierarchical clustering of sequence space

not available online; click here for further details

Andreas Heger, 2002

Supervisor: Liisa Holm

Computational Analysis of Protein Function within Complete Genomes

Anton Enright, March 2002

Supervisor: Christos Ouzounis

A CORBA-based mediation system for the integration of wrapped molecular biology data sources

not available online; click here for further details

Anastassia Spiridou, 2002

Supervisor: Patricia Rodriguez-Tomé

2001

An environment for consistent sequence annotation and its application to transmembrane proteins

Steffen Möller, June 2001

Supervisor: Rolf Apweiler

2000

From general scientific workflows to specific sequence analysis applications: the study of compositionally biased proteins 

not available online; click here for further details

David Kreil, 2000

Supervisor: Thure Etzold

Semi-automatic generation of CORBA interfaces for databases in molecular biology 

not available online; click here for further details

Kim Jungfer, 2000

Supervisor: Tom Flores

1999

Protein structure prediction

not available online; click here for further details

James Cuff, 1999

Supervisor: Geoff Barton

< h1>1998

Using genetic algorithms to analyse biological sequences

Cedric Notredame, 1998

Supervisor: Des Higgins