The following theses by PhD students of EMBL-EBI are available online. They are arranged in the order they were submitted, with the most recent submissions displayed first.
Cancer Cartography: Mapping cancer evolution in tissue space
Artem Lomakin
February 2024
Supervisor: Moritz Gerstung
Inferring context-specific essentiality networks using large-scale CRISPR-KO screens
Paula Helena Weidemuller
February 2024
Supervisor: Evangelia Petsalaki
Computational discovery of bacterial fibrillar adhesins and adhesive domains
Vivian Monzon
February 2024
Supervisor: Alex Bateman
Synthetic ground truth of biological shapes — Simulating variable Nuclear Pore Complexes for Microscopy
Maria Theiss
January 2024
Supervisor: Alvis Brazma
Computational optimisation strategies for targeted DNA sequencing using nanopores
Lukas Weilguny
January 2024
Supervisor: Nick Goldman
Structural studies on enzyme active sites
Ioannis G. Riziotis
November 2023
Supervisor: Janet Thornton
The skin microbiome in health and atopic dermatitis
Sara Saheb Kashaf
May 2023
Supervisor: Rob Finn
Japanese courage: a genetic analysis of complex traits in medaka fish and humans
Birney
2022
Supervisor: Ian Brettell
Network approaches for data-driven reconstruction of intracellular signalling
Charlie Barker
2022
Supervisor: Petsalaki
Genome-graph based genotyping with applications to highly variable genes in p. falciparum
Brice Letcher
September 2022
Supervisor: Zam Iqbal
Network approaches for data-driven reconstruction of intracellular signalling
Alexander Jung
September 2022
Supervisor: Moritz Gerstung
Recovery and quality estimation of metagenomic assembled genomes of eukaryotes
Paul Julian Saary
7 June 2022
Supervisor: Robert D. Finn
Computational analyses of blood cells: somatic evolution and morphology
Jose Guilherme Coelho Peres de Almeida
30 May 2022
Supervisor: Moritz Gerstung
Multiomic investigation of the human gut toward insight into childhood inflammatory bowel disease pathogenisis
Rachel Edgar
April 2022
Supervisor: Daniel Zerbino
Prognostic biomarker discovery from omics data using machine learning approaches
Manik Garg
February 2022
Supervisor: Alvis Brazma
Examining bacterial variation with genome graphs and nanopore sequencing
Michael Benjamin Hall
October 2021
Supervisor: Zamin Iqbal
Statistical Analysis of short template switch mutations in human genomes
Conor Reece Walker
October 2021
Supervisor: Nick Goldman
Modelling the structural functional and phenotypic consequences of protein coding mutations
Alistair S. Dunham
September 2021
Supervisor: Pedro Beltrao
Analysis of the understudied parts of the phospho-signalome using machine learning methods
Borgþór Petursson
August 2021
Supervisor: Petsalaki
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
Supervisor: 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
1 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
4 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