Team
Joana Pereira, PhD
VIB Group leader and KU Leuven assistant professor as of Feb 2025
Postdoctoral Researcher
Biozentrum, University of Basel, Switzerland 2021-2025
Postdoctoral Researcher
Dept. Protein Evolution, Max Planck Institute for Developmental Biology (MPI-DB), Tübingen, Germany, 2017-2020
PhD in Chemistry
University of Hamburg & EMBL, Germany, 2016
Short bio
Joana Pereira is an expert in computational structural biology and protein evolution, with a focus on structural bioinformatics. She is a biochemist with a doctorate in Chemistry from the University of Hamburg and the European Molecular Biology Laboratory. She has over 7 years of postdoctoral experience in protein evolution and structural bioinformatics, having worked at both the Max Planck Institute for Developmental Biology in Tübingen (Germany) and the Biozentrum of the University of Basel (Switzerland).
Her research interests are focused on applying computer science, complex network analysis, and deep learning to investigate the structure, diversity, and evolution of the 'protein universe'. She led the Protein Universe Atlas project, funded by the Swiss Institute of Bioinformatics. Her research is fundamentally computational, but she also collaborates closely with experimentalists in interdisciplinary projects focused primarily on prokaryotic interactions with the environment, as well as their unknown defense and resistance mechanisms.
Wannes Hermans
PhD student
Wannes holds a Master's in Bioscience Engineering with a major in Bionanotechnology from KU Leuven and an additional Master's in 'General Management: Business Analytics and AI' from Vlerick Business School. After gaining 1.5 years of experience as a Data Analytics Consultant at EpicData, he is excited to join the Pereira Lab at its very beginning and contribute to shaping its research direction. Passionate about bridging the gap between biology and AI, Wannes will focus on developing a novel framework for large-scale protein function prediction, integrating sequence, structure, and graph-based learning. Outside the lab, he has a lifelong love for sports, especially volleyball, which has been a constant in his life since childhood.
Antoine Lambert
PhD student
Antoine Lambert joined the Pereira Lab with a background in Biotechnology Engineering from the European School of Biotechnology of Strasbourg (ESBS), complemented by a Master’s in High-Throughput Analysis in Biology from the University of Strasbourg. Before starting his PhD, he also completed a short Master’s in Business Administration at the Strasbourg Business School. In the lab, Antoine will focus on developing automated approaches to systematically uncover how molecular functions and biological roles evolve, with a particular interest in how protein-protein interactions drive this process through their structural and genomic contexts. He’s excited to be part of a new and dynamic lab environment "where everything still feels possible." Outside of science, Antoine is passionate about cinema and enjoys video editing—a creative outlet he’s put to use helping friends and for school projects.
Arthur Valentin
PhD student
Arthur obtained an MSc in Computational Biology from EPFL. As an associate researcher at Columbia University, he worked on building a dataset for protein function prediction.
Damien Legros
PhD student
Damien obtained a double Masters in AI and Bioinformatics from Sorbonne University. Before joing the Pereira lab as a PhD student, he worked as a Data Scientist at UCB, focusing on optimization of drug compound processes, and leading the technical part of a Bioreactor Digital Twin project. At the Pereira lab he will develop novel segmentation algorithms to discover unknown functions from uncharacterized proteins. In his free time, Damien is passionate about music - he plays guitar and piano - and is quite the latte artist.
Wout Keymis
PhD student
Wout Keymis studied Cellular and Genetic Engineering and Bioinformatics. His research focuses on improving the interpretability of generative protein binder models and developing computational methods for large-scale protein–protein interaction screening. He is particularly interested in the intersection of protein design, machine learning, and structural bioinformatics. Outside the lab, Wout enjoys playing volleyball and spending time at the gym.
Xuanang Li
MSc student
Xuanang is an MSc student in Statistics and Data Science. His project in the Pereira Lab looks at using deep learning methods for protein–DNA binding prediction. He is also interested in how AI can be applied to other areas of molecular biology. In his free time, he enjoys watching football and discovering new places on road trips.
Sakshee Maharaj
MSc student
Sakshee is pursuing a Master’s in Biomedical Sciences at KU Leuven. For her master's thesis, she uses computational approaches to investigate the regulatory mechanisms underlying tumor cell state plasticity in pancreatic ductal adenocarcinoma (PDAC). Using a human PDAC atlas and patient-derived organoids with transcriptomic, genomic, and drug-response data, she aims to reconstruct tumor cell state trajectories and identify candidate regulators that may influence transitions between states. What's so exciting about this project is that it sits at the intersection of computational biology and cancer research. Specifically for pancreatic cancer, it is important to understand how tumors adapt.
Outside the lab, Sakshee enjoys hiking in nature. She's also an avid dancer and enjoy painting.
Zynab Bdour
MSc student
Zynab is pursuing an MSc in Biomedical Sciences at KU Leuven. Her research explores the role of ROC-COR domains in bacteria and archaea. These domains are of particular interest because they are also found in LRRK2, a protein linked to Parkinson's disease. As their functions remain poorly understood, her project investigates what ROC-COR domains do across different organisms and what their evolution can reveal about how they work.
Outside the lab, Zynab is passionate about art and museums, and enjoys sharing that enthusiasm through guided tours. She is also an avid reader, so book recommendations are always welcome.
Anne van Reenen
Alumni
Anne van Reenen, former MSc student in the lab
