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EBITrainingPhD StudiesEMBL International PhD Programme

EMBL International PhD Programme

Completed PhD Theses' of Students for the EBI

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.

Michele Mattioni
Thesis Title Multi scale modelling in neuroscience: integration of computer simulations of biochemical and electrical signalling in the medium spiny neuron of the striatum.
Thesis Submission Date 29 July 2011
Supervisor Name Nicolas Le Novère
Judith Zaugg
Thesis Title A computational study of promoter structure and transcriptional regulation in yeast on a genomic scale
Thesis Submission Date 12 May 2011
Supervisor Name Nick Luscombe
Julia Fischer
Thesis Title Characterisation, Classification and Conformational Variability of Organic Enzyme Cofactors
Thesis Submission Date 11 April 2011
Supervisor Name Janet Thornton
Dace Ruklisa
Thesis Title Large Scale Genomic Association Studies in Fruit Fly and Human
Thesis Submission Date 4 January 2011
Supervisor Name Ewan Birney
Florence Cavalli
Thesis Title A computational study of transcriptional regulation in eukaryotes on a genomic scale
Thesis Submission Date 24 December 2010
Supervisor Name Nick Luscombe
Jacky Hess
Thesis Title Evolution of Transcription Factor Repertoires in the Saccharomycotin
Thesis Submission Date 17 December 2010
Supervisor Name Nick Goldman
Heidi Dvinge
Thesis Title Time-resolved analysis of transcription factor induction and cell differentiation
Thesis Submission Date 11 October 2010
Supervisor Name Paul Bertone
Nils Gehlenborg
Thesis Title Visualization and Exploration of Transcriptomics Data
Thesis Submission Date 14 September 2010
Supervisor Name Alvis Brazma
Tony Chiang
Thesis Title Mathematical and Statistical Models for the Analysis of Protein Interactions
Thesis Submission Date 21 June 2010
Supervisor Name Wolfgang Huber
Garth Ilsley
Thesis Title A statistical model relating transcription factor concentrations to positional information in the early Drosophila embryo
Thesis Submission Date 14 June 2010
Supervisor Name Rolf Apweiler
Elin Axelsson
Thesis Title Analysis of large-scale RNAi screens in the search for genetic interactions
Thesis Submission Date 11 June 2010
Supervisor Name Wolfgang Huber
Lu Li
Thesis Title Modelling dopamine and glutamate signal integration
Thesis Submission Date 30 March 2010
Supervisor Name Nicolas Le Novère
Katherine Lawler
Thesis TitleTranscriptional and Post-transcriptional Regulation of Gene Expression: Computational Analysis of Microarray Studies in Fungal Species
Thesis Submission Date 3 November 2009
Supervisor Name Alvis Brazma
Alison Meynert
Thesis TitleFunction and evolution of regulatory elements in vertebrates
Thesis Submission Date 28 July 2009
Supervisor Name Ewan Birney
Aswin Sai Narain Seshasayee
Thesis TitleA computational study of bacterial gene regulation and adaptation on a genomic scale
Thesis Submission Date 30 June 2009
Supervisor Name Nick Luscombe
Melanie Stefan
Thesis TitleOn the function of calcium-regulated allosteric devices in synaptic plasticity
Thesis Submission Date 31 March 2009
Supervisor Name Nicolas Le Novère
Daniel Zerbino
Thesis TitleGenome assembly and comparison
Thesis Submission Date 31 March 2009
Supervisor Name Ewan Birney
Michael Mueller
Thesis TitleIntegrated analysis of proteomics data to assess and improve the scope of mass spectrometry based genome annotation
Thesis Submission Date 30 March 2009
Supervisor Name Rolf Apweiler
Fabio Pardi
Thesis TitleAlgorithms on Phylogenetic Trees
Thesis Submission Date 25 February 2009
Supervisor Name

Nick Goldman
Dominic Tolle
Thesis Title Investigating the Consequences of AMPA Receptor Diffusion on Long-term Potentiation using Single-Particle Modelling Approaches
Thesis Submission Date 20 February 2009
Supervisor Name Nicolas Le Novere
Abdullah Kahraman
Thesis TitleThe Geometry and Physicochemistry of Protein Binding
Thesis Submission Date 6 February 2009
Supervisor Name Janet Thornton
Kevin Nagel
Thesis TitleAutomatic functional annotation of predicted active sites: combining PDB and literature mining
Thesis Submission Date 1 January 2009
Supervisor Name Dietrich Rebholz-Schuhmann
Joern Toedling
Thesis Title Comprehensive analysis of high-throughput experiments for investigating transcription and transcriptional regulation
Thesis Submission Date 29 August 2008
Supervisor Name Wolfgang Huber
Michael Hoffman
Thesis Title Quantifying evolution and natural selection in vertebrate noncoding sequence
Thesis Submission Date 20 March 2008
Supervisor Name Ewan Birney
James Torrance
Thesis Title The geometry and evolution of catalytic sites and metal binding sites
Thesis Submission Date 24 September 2007
Supervisor Name Janet Thornton
Sylvain Gaudan
Thesis Title Annotation of Gene Products based on the Biomedical Literature
*not available online; click here for further details*
Thesis Submission Date 17 September 2007
Supervisor Name Dietrich Rebholz-Schuhmann
Ben Paten
Thesis Title Large-scale multiple alignment and transcriptionally-associated pattern discovery in vertebrate genomes
*not available online; click here for further details*
Thesis Submission Date 29 August 2006
Supervisor Name Ewan Birney
Shiri Freilich
Thesis Title Towards Relating the Evolution of the Gene Repertoire in Mammals to Tissue Specialisation
Thesis Submission Date 13 August 2006
Supervisor Name Janet Thornton
Lee Bofkin
Thesis Title The Causes and Consequences of Variation in Evolutionary Processes Acting on DNA Sequences
Thesis Submission Date 6 March 2006
Supervisor Name Nick Goldman
Carolin Kosiol
Thesis Title Markov Models for Protein Sequence Evolution
Thesis Submission Date 3 March 2006
Supervisor Name Nick Goldman
Anastassia Samsonova
Thesis Title Prediction of gene expression in embryonic structures of Drosophila melanogaster
*not available online; click here for further details*
Thesis Submission Date 12 December 2005
Supervisor Name Alvis Brazma
Alex Gutteridge
Thesis Title Understanding the Relationship Between Enzyme Structure and Catalysis
Thesis Submission Date 26 August 2005
Supervisor Name Janet Thornton
Nikos Darzentas
Thesis Title Applications of Combinatorial Pattern Discovery in Computational Genomics
Thesis Submission Date 4 July 2005
Supervisor Name Christos Ouzounis
Evgenia Kriventseva
Thesis TitleComputational analysis of complete proteomes by clustering and analysis of alternative splicing impact on proteome diversity
Thesis Submission Date 2004
Supervisor Name Rolf Apweiler
Victor Kunin
Thesis Title Evolution and function of protein families in complete genomes
*not available online; click here for further details*
Thesis Submission Date 2004
Supervisor Name Christos Ouzounis
Laurence Ettwiler
Thesis Title Computational Investigations into cis-Regulation in Eukaryotes
Thesis Submission Date June 2004
Supervisor Name Ewan Birney
Katja Kivinen
Thesis Title Computational analysis of gene regulatory sites in two yeasts
*not available online; click here for further details*
Thesis Submission Date 2003
Supervisor Name Alvis Brazma
Thomas Schlitt
Thesis Title Towards reverse engineering gene regulatory networks
*not available online; click here for further details*
Thesis Submission Date 2003
Supervisor Name Alan Robinson
Giuseppe Insana
Thesis Title DNA Phonology: Investigating the Codon Space
Thesis Submission Date November 2003
Supervisor Name Heikki Lehväslaiho
Michael Lappe
Thesis Title Novel Algorithms for Protein Interaction Networks
Thesis Submission Date November 2003
Supervisor Name Liisa Holm
Matthieu Louis
Thesis Title Sex determination in Drosophila melanogaster : a theoretical model for the regulation of the Sex-lethal gene
*not available online; click here for further details*
Thesis Submission Date 1 September 2003
Supervisor Name Liisa Holm
Caleb Webber
Thesis Title Protein sequence database searching
*not available online; click here for further details*
Thesis Submission Date 2002
Supervisor Name Geoff Barton
Andreas Heger
Thesis Title Hierarchical clustering of sequence space
*not available online; click here for further details*
Thesis Submission Date 2002
Supervisor Name Liisa Holm
Anton Enright
Thesis Title Computational Analysis of Protein Function within Complete Genomes
Thesis Submission Date March 2002
Supervisor Name Christos Ouzounis
Anastassia Spiridou
Thesis Title A CORBA-based mediation system for the integration of wrapped molecular biology data sources
*not available online; click here for further details*
Thesis Submission Date 2002
Supervisor Name Patricia Rodriguez-Tomé
Steffen Möller
Thesis Title An environment for consistent sequence annotation and its application to transmembrane proteins
Thesis Submission Date June 2001
Supervisor Name Rolf Apweiler
David Kreil
Thesis Title From general scientific workflows to specific sequence analysis applications: the study of compositionally biased proteins
*not available online; click here for further details*
Thesis Submission Date 2000
Supervisor Name Thure Etzold
Kim Jungfer
Thesis Title Semi-automatic generation of CORBA interfaces for databases in molecular biology
*not available online; click here for further details*
Thesis Submission Date 2000
Supervisor Name Tom Flores
James Cuff
Thesis Title Protein structure prediction
*not available online; click here for further details
Thesis Submission Date 1999
Supervisor Name Geoff Barton
Cedric Notredame
Thesis Title Using genetic algorithms to analyse biological sequences
Thesis Submission Date 1998
Supervisor Name Des Higgins

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