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. 



Computational discovery and modelling of tandem domain repeats in proteins

Aleix Lafita Masip, 25 February 2021

Supervisor: Alex Bateman


Insights into transcriptional regulation from natural and induced variation in closely related species

Elissavet Kentepozidou, 18 January 2021

Supervisor: Paul Flicek



Understanding the genetics and function of complex human retinal phenotypes

Hannah Currant, 4 November 2020

Supervisor: Ewan Birney


Computational Tools for Characterising the Effects of Genomic Organisation and Activity on Mutagenesis 

Harald Vöhringer, 30 September 2020

Supervisor: Moritz Gerstung


Using single-cell RNA-seq to assess the effect of common genetic variants on gene expression during development

Anna Cuomo, 30 September 2020

Supervisor: Oliver Stegle / John Marioni


Statistical methods for the integrative analysis of single-cell multi-omics data

Ricard Argelaguet, 25 September 2020

Supervisor: John Marioni / Oliver Stegle


The Influence of Structural Constraints on Protein Evolution

Umberto Perron, 18 May 2020

Supervisor: Nick Goldman


Computational studies on ageing and age-related diseases

Melike Dönertas, 17 April 2020

Supervisor: Janet Thornton


Statistical methods to infer kinase activities and kinase-substrate interactions using phosphoproteomic data

Claudia Ivonne Hernández Armenta, 9 January 2020

Supervisor: Pedro Beltrao



Computational Analysis of Transcriptional Regulation

Jack Monahan, 18 October 2019

Supervisor: Anton Enright / Ewan Birney


Quantifying the pro- and antimutagenic roles of DNA damage and repair

Nadezda Volkova, 30 September 2019

Supervisor: Moritz Gerstung


The evolutionary genomics of CTCF binding and functional signatures in mouse

Dhoyazan Azazi, 28 September 2019

Supervisor: Paul Flicek


Structural analysis of phosphorylation hotspots and kinase target preferences

Marta Strumillo, 26 July 2019

Supervisor: Pedro Beltrao


Leveraging genomic and molecular variations to understand the regulatory landscape in human cancers and differentiating stem cells

Lara Urban, 30 May 2019

Supervisor: Oliver Stegle


On the epigenetic ageing clock in humans

Daniel Elias Martin Herranz, 10 April 2019

Supervisor: Janet Thornton



Statistical Methods for the Analysis of Contextual Gene Expression Data

Damien Arnol, 26 September 2018

Supervisor: Julio Saez-Rodriguez, Oliver Stegle


The evolution of protein kinase specificity

David Bradley, 12 September 2018

Supervisor: Pedro Beltrao


Fit for purpose? A metascientific analysis of metabolomics data in public repositories

Rachel Spicer, 31 July 2018

Supervisors: Christopher Steinbeck



Elucidating the mechanistic impact of single nucleotide variants in model organisms

Omar Wagih, 26 October 2017

Supervisor:  Pedro Beltrao


A genetic analysis of molecular traits in skeletal muscle

D Leland Taylor, 28 September 2017

Supervisor:  Ewan Birney


Elucidating the function and biogenesis of small non-coding RNAs using novel computational methods & machine learning

Dimitrios Vitsios, 15 August 2017

Supervisor:  Anton Enright


The evolution, modifications and interactions of proteins and RNAs

Ananth Prakash Surappa-Narayanappa, 01 August 2017

Supervisor:  Alex Bateman


Probabilistic modelling of cellular development from single-cell gene expression

Valentine Svensson, 23 June 2017

Supervisor:  Sarah Teichmann


Deep neural networks and statistical models for studying single-cell DNA methylation

Christof Angermuller, 29 March 2017

Supervisor:  Oliver Stegle



Structural and functional determinants of protein evolution

Grzegorz Slodkowicz, 15 December 2016

Supervisor:  Nick Goldman


Multivariate linear mixed models for statistical genetics

Francesco Paolo Casale, 04 October 2016

Supervisor:  Oliver Stegle


Insights into the function of non-coding RNSs

Tommaso Leonardi, 29 September 2016

Supervisor:  Anton Enright


Gene expression signatures for cancer cell line drug sensitivity and patient outcome

Michael Schubert, 18 August 2016

Supervisor:  Julio Saez-Rodriguez


Modelling regulatory interactions between metabolism and signalling

Emanuel Goncalves, 30 June 2016

Supervisor:  Julio Saez-Rodriguez


Applications for ChIP-sequencing data reusability

Tom Rensch, 17 February 2016

Supervisor:  Paul Flicek

Clustering approaches for incongruent phylogenies

Kevin Gori, 11 February 2016

Supervisor:  Nick Goldman




An evaluation of cancer subtypes and glioma stem cell characterisation

Ewan Johnstone, 22 October 2015

Supervisor:  Paul Bertone


Quantitative genetics of gene expression during fruit fly development 

Nils Kölling, 12 August 2015

Supervisor:  Ewan Birney


In silico  models of drug response in cancer cell lines based on various molecular descriptors

Michael Menden, 12 August 2015

Supervisor:  Julio Saez-Rodriguez


Investigating the link between tRNA and mRNA abundance in mammals

Konrad Rudolph, 14 May 2015

Supervisor:  John Marioni



Differential Drug Response as a Function of Age

Rita Santos, 3 September 2014

Supervisor:  John Overington


Mathematical Models and Statistics for Evolutionary Inference

Sarah Parks, 20 August 2014

Supervisor:  Nick Goldman


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


Modelling at the Mesoscale: a Novel Approach to Protein-Protein Interaction and Multicomplex Formation

Benedetta Baldi, 28 May 2014

Supervisor: Nicolas Le Novere


Spatial analysis of complex biological tissues from single cell gene expression data

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


Identifying bioactivity events of small molecules from the scientific literature

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



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



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


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


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


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


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


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


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


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


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


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


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


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

Steffen Möller, June 2001

Supervisor: Rolf Apweiler


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


Protein structure prediction

not available online; click here for further details

James Cuff, 1999

Supervisor: Geoff Barton


Using genetic algorithms to analyse biological sequences

Cedric Notredame, 1998

Supervisor: Des Higgins