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

Berk Gonenc is a Master’s student

My background includes wet-lab as well as bioinformatics. I have a BSc in Molecular Biology and Genetics from the respected Bogazici University and worked in a NGS analysis bioinformatics company (Genomize) for nearly 2 years. I am now doing my MSc in “Biosciences and Bioengineering Innovations for Precision Medicine (BeInPM)” at the University Grenoble Alpes.

My internship will focus on developing a bayesian model of bacterial populations. I’m motivated to expand my knowledge on statistics and data analysis under Dr. John Lees supervision at EMBL-EBI.

Languages and tools: R, Python, Bash

berk 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 visiting PhD student (based at Imperial College London)

My PhD focuses on pangenome evolution in pathogenic bacteria. I have designed and developed ggcaller, a new annotation tool for bacterial pangenomes that works on genome graphs. Other projects include using graph methods to improve adaptive sequencing of the accessory genome, and using large population datasets to compare rates of core and accessory genome evolution.

Languages and tools: C++, python

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 works 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

Tommi Mäklin is a visiting postdoc

Tommi is currently visiting from Jukka Corander’s group at the University of Helsinki. He has previously developed the tools mSWEEP and mGEMS for strain deconvolution and genomic epidemiology from metagenomic sequencing data. While here, he will be working on a Theory@EMBL project to combine modelling with metagenomics methods and investigate competition dynamics between strains during carriage and infection.

Languages and tools: C++, R, Stan, bash

Organisms: Gut microbes, E. coli.

tommi at ebi dot ac dot uk

Tim Russell is a visiting postdoc

My background is primarily in mathematical biology. I did my PhD at Royal Holloway University, supervised by Vincent Jansen, studying mathematical aspects of models from theoretical population genetics. I then started a postdoc at London School of Hygiene and Tropical Medicine in Adam Kucharski’s group, originally to work on modelling antibody dynamics for influenza. The COVID-19 pandemic began shortly after I started (!), so I ended up working intensely on several aspects of the pandemic. These included: transmission dynamics, severity estimates, global estimates of infections, the sensitivity of PCR and LFT tests, within-host viral kinetics, within-host antibody dynamics, etc. We have have recently started a long-term project in collaboration with The Francis Crick Institute, setting up a data generating and analysis pipeline, with a large modelling component, studying how antibody levels for COVID-19 vary between different regions and over time.

I aim to use my time at EBI learning more about genomics. Specifically, thinking about whether it is possible to combine models of within-host responses to infection with genomic data data to arrive at detailed estimates of how hosts and pathogens coevolve.

Languages and tools: C++, R, Stan, bash

Organisms: SARS-CoV-2, Influenza, MPX

thimotei 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