About us

We are the Pathogen Informatics and Modelling group at EMBL-EBI (also known as the Lees Group). On this page you can find information about current and past group members, who we work with, and some nice pictures.

Lab members

Hsueh-Chien (Raymond) Cheng is a visiting PhD student (based at the Wellcome Sanger Institute)

I am a PhD student at the Wellcome Sanger Institute in Prof. Stephen Bentley’s group and also under the supervision of Dr. John Lees at the EBI. My current work is focusing on quantifying the invasiveness of Streptococcus pneumoniae with different genetic backgrounds by using the WGS data among populations. I am also interested in studying various modes of evolution in pathogenic bacteria and how they shape different population structures.

Languages: Python, R

raymond at ebi dot ac dot uk

Joel Hellewell is an EIPOD fellow

My background is in transmission modelling and statistics. I did my PhD at Imperial College London in the Malaria group with Tom Churcher and Azra Ghani. I then did a post-doc at the London School of Hygiene and Tropical Medicine in Sebastian Funk’s group. I contributed towards models that performed routine short-term forecasts of COVID-19 deaths, hospitalisations, and reported cases in the United Kingdom. I also worked on reproduction number estimates and modelling the sensitivity of PCR tests over the course of a COVID-19 infection.

I am now interested in integrating genetic and epidemiological models and data to see if this improves the answers to key questions that were repeatedly asking during the COVID-19 pandemic. For example, how early can we tell that the number of infections is increasing? Does this novel variant have a transmission advantage? Does this novel variant cause infections with more serious outcomes?

Languages and tools: R, stan

joel at ebi dot ac dot uk

Samuel Horsfield is a postdoctoral fellow

My PhD focused on pangenome evolution in pathogenic bacteria. I designed and developed ggcaller, a new annotation tool for bacterial pangenomes that works on pangenome graphs. In my Postdoc, I’m working on graph methods to improve Nanopore sequencing for enrichment of the accessory genome, using large population datasets to understand pangenome evolution, and developing large language models to simulate bacterial populations.

Languages and tools: C++, Rython, R

Organisms: Bacteria (S. pneumoniae, E. coli and many more) and viruses (polio).

shorsfield at ebi dot ac dot uk

John Lees is a research group leader

My previous work has attempted to understand the pathogenesis and transmission of infectious diseases. I primarily work on statistical genetics, genomic epidemiology and genome evolution of pathogenic bacteria. I have also worked on infectious disease modelling, GPU algorithms, and visualisation. I write methods and software to scale these analyses and make them more accessible to others in attempts to democratise bioinformatics.

Languages and tools: C++, CUDA, python, R, rust, stan

Organisms: Any microbe, but especially Streptococcal bacteria.

My personal website is www.johnlees.me and you can find my papers here.

jlees at ebi dot ac dot uk

Leonie Lorenz is a PhD student

In my PhD, I will focus on jointly using epidemiological and genomic data for developing mathematical models of pathogen transmission. While the spreading and evolution of pathogens are often analysed separately, exploiting both data streams together as input for epidemiological models could increase the models’ predictive power and result in new insights.

I studied biomathematics at the University of Greifswald, Germany. For my master thesis, I developed a Boolean model for the regulation of apoptosis at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association.

Languages and tools: python, R

llorenz at ebi dot ac dot uk

Víctor Rodríguez Bouza is a Postdoctoral Fellow.

After high school, I started a BSc in Bioinformatics, but I decided to change after a year to Mathematics and Physics, both in the Universidad de Oviedo (Asturias, Spain). After a MSc in High Energy Physics (in the UAB in Barcelona, Spain), I did my PhD thesis in the same field in the Universidad de Oviedo, as a member of the CMS Collaboration at CERN. Now I have returned to the bio-sciences and started as a postdoctoral fellow in the Lees Group.

Languages, tools: Python, C++, R, ROOT.

~~Organisms~~ Quarks: I have worked mainly in top quark physics.

vrbouza at ebi dot ac dot uk

Matt Russell is a postdoctoral fellow.

Currently, I’m working on a project to catalogue and characterise bacterial capsules, which are important for both infection and as vaccination targets, across all sequenced bacteria. In addition to this, I am improving the GPU backend of the dust stochastic simulation package. The idea is that we can exploit the dependency structure of the underlying model to automatically produce a more efficient set of GPU kernels.

My background is in applied mathematics, mathematical biology, and computer science. My PhD was supervised by Oliver Jensen and Tobias Galla at the University of Manchester and focussed on mathematical models of transport processes in spatially disordered media. After that, I was a postdoc at the University of Nottingham working with Bindi Brook on models of chemokine gradient formation and immune cell migration.

Languages and tools: C++, CUDA, Mathematica, R, Rust, Stan

mjrussell at ebi dot ac dot uk

Ines Sanchez-Hombria is a research intern.

During my internship, I will work on a tool called TOMBOMBADIL, which is based on the GenomegaMap model designed to track adaptive mutations in bacteria. My work will involve applying TOMBOMBADIL to detect selection signals in two common gut commensals, P. vulgatus and B. uniformis. Additionally, I will reimplement the tool in Python and convert it into JAX code, a machine learning framework. This model has the potential to predict bacterial mutations and evolutionary patterns.

Prior to this internship, I studied BSc Biomedical Science at Anglia Ruskin University and MRes Neurotechnology at Imperial College London. My master’s thesis explored the interpretability of neural networks, often perceived as “black boxes” in machine learning. Employing response-weighted averaging, a technique inspired by neuroscience, the research examined the mechanisms underpinning neural networks, focusing on a robotic arm’s control in goal-oriented tasks. A key aim was to investigate how proprioception—the body’s sense of spatial position—could emerge solely from visual inputs.

Languages and tools: Python

sanchezh at ebi dot ac dot uk

Alireza Tajmirriahi is a research intern.

During my internship, I will develop a database and an AI-driven tool for analyzing pneumococcal capsular biosynthetic loci, the primary target of Pneumococcal Conjugate Vaccines (PCVs). Additionally, I will have the opportunity to deploy both tools on a web-based platform utilizing WebAssembly.

I am currently pursuing my MSc in Bioinformatics at Aalto University in Finland. Previously, I earned my Bachelor’s degree in Computer Engineering, during which my thesis focused on multi-omics integration for discovering novel cancer biomarkers.

tajmirri at ebi dot ac dot uk

Jacqueline Toussaint is a PhD student

I’m broadly focused on developing more efficient and accurate methods for performing genome-wide association studies (GWAS) in bacteria, with a particular focus on antibiotic resistance and the possibility of expanding to real-time analysis. I’m also working on developing methods to improve the speed and consistency of bacterial genome annotation.

I previously studied biochemistry and microbiology at Montana State University, USA, with my Bachelor’s thesis research focused on generating and analyzing multi-omics datasets. I’m excited to further my education in the lab of Dr. John Lees at EMBL-EBI and the University of Cambridge, UK.

Languages and tools: python, R, Rust, Stan

Organisms: I work with a diverse set of microbes, including Streptococcus, Klebsiella, and Neisseria.

lilyjacqueline at ebi dot ac dot uk

Johanna von Wachsmann is a PhD student (based in Rob Finn’s lab).

I did my master’s degree in bioinformatics with a focus on advanced algorithms at the Freie Universität Berlin. I wrote my master’s thesis under the supervision of Dr. John Lees.

I am now working on developing tools and algorithms for the analysis of large metagenomic datasets.

Languages: C++, Python, R

wachsmannj at ebi dot ac dot uk

Alumni

Oluwaremilekun Grace Ajakaye (2024) was a visiting scientist (based at Adekunle Ajasin University).

Lale Maouloud (2024) was a master’s student from the University of Rouen Normandy.

Antoine Andréoletti (2024) was a master’s student from the Ecole Polytechnique in Paris.

Berk Gonenc (2023) was an intern.

Oladipo Omotosho (2023) was a visiting scientist on an EMBL training fellowship (based at the University of Ibidan).

Tendai Washaya (2023) was a visiting PhD student (based at the University of Zimbabwe).

Tommi Mäklin (2023) was a visiting postdoc on the Theory@EMBL visitor scheme (based at the University of Helsinki).

Timothy Russell (2023) was a visiting scientist (based at London School of Hygiene and Tropical Medicine).

Gherard Batisti Biffignandi (2022) was a visiting PhD student (based at the University of Pavia). Now at the University of Cambridge (Kate Baker’s lab) and still a visitor at PIM.

Bruhad Dave (2022) was an intern, now at the Wellcome Sanger Institute.