Hottopics committee

Anne Kupczok

I am an assistant professor in the Bioinformatics group since August 2020. I am a bioinformatician by training with a particular interest how microbes and viruses evolve and how the interaction with eukaryotic hosts impact their evolution. My research focus is evolutionary (meta-)genomics, that is, the inference of population genetic processes in microorganisms from genomic and metagenomic data. Metagenomes represent the genetic content of community members in a specific environment and contain unprecedented information on the genetic variation that exists within all the community members.

In my research, I infer the diversity within microbial populations from genomes and metagenomes, where I focus on the interaction between organisms, such as phages and bacteria, and the consequences of this interaction on genome evolution. I am interested in understanding how different evolutionary processes (mutation, recombination, and horizontal gene transfer) contribute to viral and microbial evolution.

Zerrin  Işik

I work as an Assistant Professor in the Bioinformatics Group at Vrije Universiteit Amsterdam. I completed my PhD at METU in Turkey and developed an algorithm to score signaling pathways using graph theory and transcriptome data. During my postdoc at the Biotec Research Center, TU Dresden, I applied machine learning approaches that combined transcriptome data with interaction networks to identify biomarkers involved in cancer development.

My expertise spans drug–target identification, drug repositioning, cancer biomarker discovery, multi-omics data analysis, and biomedical image processing. Currently, my research focuses on developing AI models for the integration of multimodal data—including genetic, microbiome, and imaging data—to improve diagnostics and support treatment strategies.

Catherine Chia

Catherine is a PhD candidate at the Dermatology Department of Erasmus Medical Center in Rotterdam and at the Diagnostic Image Analysis Group of the
Radboud University Medical Center in Nijmegen. She studied Biomedical Engineering (neuropathology) at the RWTH Aachen (2014) and later a joint degree in Bioinformatics and Systems Biology at the University of Amsterdam and Vrije Universiteit Amsterdam (2023). Between these two masters programs, she
co-founded and worked in a startup focused on medical image processing and 3D medical printing.

Her current research focuses on cancer prognosis using multimodal AI, integrating imaging data with omics. She is particularly interested in advancing in this field through the incorporation of knowledge graphs to better connect heterogenous biomedical data and improving predictive modelling.

Daniel Tamarit

 

Cunliang Geng

I am a Senior Research Software Engineer at the Netherlands eScience Center in Amsterdam. My work sits at the interface of scientific research, software engineering,

and machine learning, with a focus on designing robust, reusable, and open-source software for life sciences research.

 

I hold a PhD in computational structural biology from Utrecht University, where I applied machine learning methods to study protein interactions — an area that has become increasingly central with the rapid progress of AlphaFold and related approaches for protein structure prediction and design. Since joining the eScience Center, I have played technical and collaborative roles of increasing responsibility in more than a dozen life sciences projects, working closely with research groups in the Netherlands and internationally. These projects span topics such as deep learning for biomolecular science, multi-omics data integration and analysis, federated learning, and scalable research software infrastructure.

In these collaborations, I contribute not only as a developer, but also as a technical lead and scientific partner: helping researchers translate complex biological questions into computational workflows, making architectural decisions, guiding software design, ensuring code quality and sustainability, and supporting research teams in adopting

best practices for reusable and maintainable research software. All of my research software contributions are open source and can be found here: Research Software Directory.

 

Cheers

Cunliang

Sinah Wingert

I am a PhD candidate in the Parasitic Behavioural Manipulation Lab at Utrecht University. I studied Biology at the JGU in Mainz (Germany) and relocated for my masters’ project to the Insect-Symbiosis Department at the MPI for Chemical Ecology in Jena (Germany), where I specialised in symbiotic interactions between insects and microbes.

My current research focuses on the parasitic interaction between fungal entomopathogens and their insect hosts. I am particularly interested in the underlying molecular mechanisms of parasitic behavioural manipulation.

All the best,
Sinah Wingert