About
A microbiologist going computational!
As a microbiologist with a passion for data-driven research, I'm exploring the intersection of microbiology and computing to unlock the power of genomic data. Specifically, I'm interested in modeling bacterial populations to identify evolutionary signatures and transmission determinants, utilizing genomic sequences to track emerging and pathogenic lineages, and developing robust between-host transmission models. Through my work, I hope to gain valuable insights into the factors that drive the spread of infectious diseases and identify strategies for mitigating their impact on public health.
Interest: Microbial Ecology and Evolution, Computational Biology, Genomic Epidemiology
- Degree: PhD
- Email: judit.burgaya@gmail.com
- ResearchGate: Click HERE
- ORCID: Click HERE
- GitHub: Click HERE
Resume
Here is a brief overview of my career to date.
Education
Doctor of Phylosophy (PhD)
Aug 2021 - June 2025
Infection Biology & Dynamics of Host-Pathogen Interactions PhD program, Hannover Medical School (MHH), Hannover, DE
Dissertation: On the use of bacterial genome sequencing in studying pathogenicity and transmission in clinical settings (summa cum laude)
Supervisor: Prof. Dr. Marco Galardini
Co-supervisors: Prof. Dr. Susanne Häußler, Prof. Dr. Davide Sassera
Master of Science (MSc) Applied Microbiology
Sep 2020 - Jun 2021
Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
Dissertation: Cancer immunotherapy based on bacteria
Supervisor: Esther Julián
Bachelor of Science (BSc) Biology
Sep 2015 - Jun 2020
Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
Dissertation: The microbiota-gut-brain axis implications in Alzheimer’s disease
Professional Experience
Postdoctoral Researcher
July 2025 - present
TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, DE
- Implementing a method to investigate strain relatedness and identify strain sharing across individuals within hospital settings
- Investigating within host evolution of specific lineages under similar selective pressures such as antibiotic treatment
Doctoral Researcher
Aug 2021 - June 2025
TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, DE
- Identification of the genetic determinants of E. coli capacity to cause bloodstream infections in humans
- Developed microGWAS, a computational pipeline to facilitate the use of genome-wide association studies by the microbial genomics community
- Implemented a method to investigate strain relatedness and identify strain sharing across individuals within hospital settings
- Investigated within host evolution of specific lineages under similar selective pressures such as antibiotic treatment
Research Assistant
Sep 2020 - Aug 2021
Tuberculosis Research Group, Animal Health Research Center (IRTA-CReSA), Bellaterra, Spain
- Worked on an experimental infection model in laboratory voles to study the pathogenesis and transmission of tuberculosis caused by Mycobacterium microti
- Conducted a project studying adiaspiramycosis in wild rodents using histopathological analysis and measurement of adiaspore diameter with ImageJ software
- Conducted epidemiological research to assess the burden of animal tuberculosis in Catalunya, including statistical analysis of data
- Contributed to an ongoing project evaluating the efficacy of a tuberuclosis autovaccine for goats
Bachelor's internship
Jun 2019 - Sep 2019
Microbiology Clinical Laboratory, Vic Hospital Consortium (CHV), Vic, Spain
Research Projects
My research moves towards leveraging high-throughput technology and interdisciplinary apporaches to study the transmission and evolution of infectious disease pathogens.
Microbiology, Microbial Genomics, Computational Modeling, Genomic Epidemiology, Antimicrobial Resistance
Studying transmission dynamics of bacterial pathogens using a large-scale genomics surveillance dataset
Under supervison of Prof. Dr. Marco Galardini (TWINCORE | Cluster of Excellence RESIST), Prof. Dr. Susanne Häußler (TWINCORE | Cluster of Excellence RESIST | HZI), and Prof. Dr. Davide Sassera (epartment of Biology and Biotechnology, Università di Pavia)
genomic epidemiology
phylodynamics
network graph sampling
transmission modeling
Use of bacterial genomic sequences to identify evolutionary signatures and transmission determinants to improve bacterial pathogen surveillance and mitigatin strategies, and reduce their overall spread. Identify which genetics factors influence the capacity of certain strains to transmit within clinical settings. Identify the trade-offs of transmissibility across bacterial species.
microGWAS: a computational pipeline to perform large-scale bacterial genome-wide association studies
Under the supervision of Prof. Dr. Marco Galardini (TWINCORE | Cluster of Excellence RESIST), as a collaboration with Dr. Bamu Fufor Damaris (TWINCORE | Cluster of Excellence RESIST), and Jenny Fiebig (TWINCORE)
Ecoli
GWAS
machine learning
bacterial genomics
antibiotic resistance
The increase in sequencing data, leads to the need of analyzing large quantity of data. Current GWAS requires the integration of a number of software tools for the pre- and post-processing analyses, leading to a lack of reproducible and robust analyses, or not following the fields best practices. We have developed a pipeline to perform bacterial GWAS from a set of assemblies and annotations, with multiple phenotypes as targets.
The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans
Under the supervision of Prof. Dr. Marco Galardini (TWINCORE | Cluster of Excellence RESIST), as a collaboration with Prof. Dr. Erick Denamur (Université Paris Cité, INSERM, IAME), Prof. Dr. François Blanquart (Center for Interdisciplinary Research in Biology, Collège de France, INSERM), and Assoc. Prof. Dr. Julie Marin (Université Sorbonne Paris Nord, INSERM, IAME)
Ecoli
GWAS
machine learning
bacterial genomics
antibiotic resistance
Explore the genomic determinants of Escherichia coli to cause bloodstream infections vs. commensal isolates comparing their genetic backgrounds for virulence-associated and antimicrobial-resistant genes, performing a GWAS, computing it's heritability, and predicting the pathogenicity over time.
Experimental Mycobacterium microti Infection in Bank Voles (Myodes glareolus)
Under supervision of Dr. Enric Vidal and Dr. Bernat Pérez de Val (CReSA, IRTA-UAB)
tuberculosis
Performed quantitative analyses and computed a pathogenicity score to characterize the disease progression.
Publications
2025
microGWAS: a computational pipeline to perform large scale bacterial genome-wide association studies
Judit Burgaya*, Bamu F. Damaris, Jenny Fiebig, Marco Galardini
Microbial Genomics
Software
2024
microGWAS: a computational pipeline to perform large scale bacterial genome-wide association studies
Judit Burgaya*, Bamu F. Damaris, Jenny Fiebig, Marco Galardini
bioRxiv
Preprint
Adiaspiramycoses in Wild Rodents from the Pyrenees, Northeastern Spain.
Simon Krückemeir, Marco Ramon, Enric Vidal, ..., Judit Burgaya, Bernat Pérez de Val, Oscar Cabezón, Johan Espunyes
Journal of Wildlife Diseases
Original Research
2023
The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans
Judit Burgaya*, Julie Marin*, ..., Erick Denamur, Marco Galardini, François Blanquart
PLOS Genetics
Original Research
The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans
Judit Burgaya*, Julie Marin*, ..., Erick Denamur, Marco Galardini, François Blanquart
bioRxiv
Preprint
2022
Experimental Mycobacterium microti Infection in Bank Voles (Myodes glareolus )
Enric Vidal*, Judit Burgaya, ..., Bernat Pérez de Val
Microorganisms
Original Research
Awards and Grants
2025
Infection Biology PhD Prize
Applied Bioinformatics and Public Health Microbiology bursary award winner
2024
Gesellschaft der Freunde der MHH e.V. conference attendance support
2023
FEMS Meeting Attendance Grant
Applied Bioinformatics and Public Health Microbiology bursary award winner