Hottopics committee

Anne Kupczok

dr. A (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.

 

Evert Bosdriesz

I’m an Assistant professor in the Integrative Bioinformatics group at the Vrije Universiteit Amsterdam. Previously, I did my PhD in the Systems Biology group of Bas Teusink and Frank Bruggeman, after which I did a postdoc in the Computational Cancer Biology group of Lodewyk Wessels at the Netherlands Cancer Institute.

My research focuses on computational approaches to understand signal transduction networks and the role they play in cancer, and I’m particularly excited about the possibilities of novel single cell technologies. By using a combination of statistical and mechanistic modeling approaches, we aim to bridge the gap between “top down” bioinformatics and “bottom up” systems biology.

 

Nikolaos Strepis

I’m a Postdoc in Medical Microbiology, Erasmus Medical Center, Rotterdam. My background consists of a PhD in Microbial Physiology and Systems and Synthetic Biology, and a MSc in Bioinformatics in Wageningen University and Research. 

For the past three years in Erasmus MC, I have been involved in multiple omics studies including genomics, proteomics, transcriptomics and metagenotyping. My main focus is antimicrobial resistance mechanisms. I study their presence and evolution in prokaryotic genomes, and their expression and translation in the phenotype. I also perform outbreak management and research regarding epidemiological species. Recently, NGS (Illumina and Nanopore platform) was introduced for diagnostic purposes, which I contribute in the supervision and implementation. 

 

Daniel Tamarit

I am an assistant professor at the Theoretical Biology and Bioinformatics group at Utrecht University. After studying Biology at the University of Valencia (Spain), I specialised in molecular evolution during my PhD at Uppsala University (Sweden) and later in ancient evolution and phylogenomics during my postdoc at Wageningen University. In my
 career I have studied diverse topics such as bacteria-animal symbioses and the archaeal ancestry of the eukaryotic cell. 
 
My current research focuses on elucidating evolutionary transitions through genome analysis. I am particularly interested in the evolution of genome architecture in bacteria and archaea, including the characterisation of evolutionary pressures that generate specific, unexplored gene organisations.

 

Swier Garst

I’m a PhD student in the bioinformatics group lead by Marcel Reinders at the Delft University of Technology. I’m mainly focused on federated learning and privacy preserving machine learning, and how we can use that to accelerate research in the biological and life sciences. I’m also a member of the youngCB board, where we try to connect young computational biologists through activities such as networking events and workshops.