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

John Lees is a research group leader

Outside of my main role of running the group, I also keep our software updated and running, and make occasional additions to our newer packages (e.g. sketchlib.rust).

I also develop our resources, including training materials and reusable code. I am currently co-running the AllTheBacteria initiative with Zam Iqbal.

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

jlees at ebi dot ac dot uk

github: https://github.com/johnlees

Leonie Lorenz is a PhD student

I combine mathematical models and bioinformatics to increase our understanding of microbial evolution and selection. In a recent project, I investigated how negative frequency-dependent selection (NFDS) drives replacement dynamics in Streptococcus pneumoniae after vaccine introductions. This model has also been published in form of an R package, Stubentiger. Currently, I am developing a new method to estimate diversifying selection using dN/dS in large bacterial datasets.

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.

Languages and tools: python, R

llorenz at ebi dot ac dot uk

github: https://github.com/LeonieLorenz

Neil MacAlasdair is an EIPOD fellow

My fellowship project studies speciation in microbes – particularly in two genera of upper respiratory tract bacteria, Neisseria and Haemophilus – using large collections of whole-genome sequence data. These are opportune genera for this research because each contains well-sampled disease causing species, they inhabit the same niche (the human nasopharynx) and have similar life histories, but are distantly related. To advance this work, I use and develop pangenomic methods to cope with the scale and diversity of genus-wide data.

Previously, I was a Scientia Fellow with Jukka Corander at the University of Oslo, where I primarily studied the global population structure of Haemophilus influenzae and developed methods to infer recombination-free phylogenies from core genome alignments derived from pangenome methods such as panaroo. Prior to that I was a PhD student at the Wellcome Sanger Institute with Stephen Bentley, during which I studied the global population strucure and pangenome of Neisseria meningitidis.

macalasdair at ebi dot ac dot uk

github: https://github.com/nzmacalasdair

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.

vrbouza at ebi dot ac dot uk

github: https://github.com/vrbouza

Matt Russell is an ARISE2 postdoctoral fellow.

My fellowship project is to develop and implement GPU-accelerated bioinformatics algorithms, and deploy them in user-facing services.

I’m also part of a project on bacterial capsules. We are searching across all sequenced bacterial genomes to identify capsule production systems by looking for both sequence and structural homologues of known capsule-associated proteins. We will then use this to investigate broader questions about capsule diversity and evolution.

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.

mjrussell at ebi dot ac dot uk

github: https://github.com/mtrsl

Jackie Toussaint is a postdoctoral fellow.

I develop bacterial GWAS and pangenome graphing methods; more broadly, I’m interested in Bayesian and machine learning models for bacterial population genomics with an emphasis on big data. I joined the Lees group as a PhD student in 2022, and have continued my work as a postdoctoral fellow this year.

lilyjacqueline at ebi dot ac dot uk

github: https://github.com/qtoussaint

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.

wachsmannj at ebi dot ac dot uk

github: https://github.com/johannahelene

Ouli Xie is an ESPOD fellow

I am an infectious diseases physician-researcher with an interest in applied bacterial genomics to understand how pathogens evolve and spread. I completed my PhD at the Doherty Institute, Australia, with Steven Tong and Mark Davies. In my PhD I examined the clinical and evolutionary intersection between pathogenic streptococci integrating large-scale pathogen genomics, clinical, and surveillance data.

In my fellowship, I work across the Lees Group, Bateman Group and Harrison Group at EMBL-EBI and the Wellcome Sanger Institute to study determinants of Staphylococcus aureus carriage. In particular, I examine co-evolution and competition between Staphylococcus aureus and the nasal microbiome during carriage integrating large-scale pathogen, microbiome, and host data.

oxie at ebi dot ac dot uk

github: https://github.com/oulixie

Jose Fierro Bustos is a Trainee

I have a bachelor’s degree in Molecular Biotechnology and am currently a master’s student in Bioinformatics. After an undergraduate background focused on wet-lab work, I transitioned into bioinformatics, specialising in metagenomics from extreme environments and the research and annotation of horizontal transference genes (HTGs) in environmental and clinical samples. I have now joined the Lees Group as a Trainee, where I’m working on promoter identification and characterisation in Streptococcus pneumoniae.

fierro at ebi dot ac dot uk

github: https://github.com/JoseFierroB

Varunika Savla is a Visiting Intern

I completed my MSc in Bioinformatics at Univeristy of Michigan, where I worked on projects involving virtual screening, protein-ligand interactions, and machine learning approaches for drug discovery. Before that, I earned a BSc in Biochemistry and Chemical Biology from Wayne State University, where I worked on a project involving molecular dynamics.

My research interests lie in structural biology and machine learning approaches for studying proteins. My project is in collaboration with the Wellcome Sanger Institute and involves evaluating and benchmarking protein structure search methods to identify structural homologs of bacterial capsular synthesis proteins.

savla at ebi dot ac dot uk

github: https://github.com/vmsavla

Clara Rehmann is a postdoctoral fellow

I’m interested in how geographic and genomic data can inform control of vector-borne disease. I’m working with the Lees group at EBI and the Lawniczak group at Sanger to develop methods that can realistically model how gene drive (modified genes with non-Mendilian inheritance patterns) will spread through Anopheles malaria vectors and suppress population sizes. The goal of these methods is to identify what will maximize the success of gene drive release efforts, and understanding how genetic variation moves through geographically-structured populations is critical for this.

My background is in spatial population genetics, and I completed my PhD at the University of Oregon in the Kern Ralph co-lab using simulation-based methods to inform analysis of geographically-structured populations. My research included using machine learning methods for identifying co-geography between vectors and pathogens and finding positively-selected variation using geographic population structure.

rehmann at ebi dot ac dot uk

github: https://github.com/clararehmann

Marie Becker is a PhD student

I completed my Master’s degree in Bioinformatics at ETH Zurich, working in the groups of Tanja Stadler and Richard Neher. During this time, I worked on several projects, including estimating the fitness of SARS-CoV-2 variants, investigating how coalescent prior assumptions influence node height estimation in time-resolved phylogenetic trees, and using bacterial pangenome graphs to study the evolutionary dynamics of accessory genome hotspots.

In autumn 2026, I joined the Lees group as a PhD student, where I continue to work on bacterial phylogenetics. My current research focuses on bacterial capsule evolution, leveraging the AllTheBacteria database.

marie dot becker at ebi dot ac dot uk

github: https://github.com/marie3003

Alumni

Ina Campan (2026) was an intern from ENSAE Paris.

Ela Sauerborn (2026) was a visiting PhD student from the Technical University of Munich.

Alice Magnoni (2026) was a visiting PhD student from the University of Ferrara.

Anlei Peng (2025-2026) was an intern from the University of Cambridge.

Ines Ngoh Atuh (2024-2025) was a visting scientist (based at the University of Bamenda, Cameroon)

Sam Horsfield (2022-2026) was a PhD student (the first), then postdoc, and founding group member.

Nikki Cannon (2024, 2025) was a PhD student from Jordi van Gestel’s lab in EMBL Heidelberg.

Daria Frolova (2024-2025) was a rehomed PhD student, supervised by Zam Iqbal.

Daniel Anderson (2024-2025) was a rehomed PhD student, supervised by Zam Iqbal.

Raymond Cheng (2022-2025) was a visiting PhD student, co-supervised with Stephen Bentley at the Wellcome Sanger Institute.

Joel Hellewell (2022-2025) was a postdoc, then EIPOD fellow, and founding group member.

Alireza Tajmirriahi (2025) was a research intern from Aalto University.

Aya Ben Taghaline (2025) was a master’s student from Université Paris-Saclay.

Ines Sanchez-Hombria (2025) was an intern.

Andrea Sanchez Serrano (2025) was a visiting PhD student from the University of Valencia.

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

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).

Bruhad Dave (2022) was an intern.

Social and photos

2026

Group Retreat, Kingham. October 2026

Summer events

Ely away day, April 2026

2025

Xmas 2025

LEGEND conference, Aussois. December 2025

Group retreat, Center Parcs. October 2025

EMBO course: Genomics and Modelling. Sept 2025

Group away day, Cambridge/Bury St Edmunds. February 2025

2024

Winter 2024

Public engagement. Oct 2024

Group retreat, Colchester. August 2024

Microbiology society conference

Group away day, Cambridge. April 2024

2023

Xmas dinner 2023

Group retreat, Suffolk. July 2023

Pub bike May 2023 – the hailstorm

2022