EMBL-EBI PhD Theses
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.
2012
Computational studies on the biogenesis and function of small non-coding RNAs
Nenad Bartonicek, 30 November 2012
Supervisor: Anton Enright
Evolutionary analysis of animal microRNAs
José Afonso Guerra Martins dos Santos Assunção, 8 October 2012
Supervisor: Anton Enright
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
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Using genetic algorithms to analyse biological sequences
Cedric Notredame, 1998
Supervisor: Des Higgins