Research team
Expertise
Dr. Wim Cuypers is a postdoctoral researcher at the Adrem Data Lab at the University of Antwerp. With a strong background in microbial genomics, transcriptomics and general bioinformatics, his research focuses on employing cutting-edge techniques to understand and combat infectious diseases. Within the branch of the Adrem Data Lab headed by prof. Kris Laukens, Dr. Cuypers' principal objective centers around harnessing the revolutionary capabilities inherent to nanopore sequencing technology for the purpose of pathogen monitoring. After securing a competitive FWO-SB research grant, Wim conducted extensive investigations into microbial genomics, antimicrobial resistance and transcriptomics for his PhD research from 2018 onwards. Key contributions he made during his PhD include a review on fluoroquinolone resistance in Salmonella which has been cited over 100 times after publication in Microbial Genomics, and a large collaborative study on Salmonella Concord, which was published in Nature Communications. In 2023, he defended his PhD thesis entitled: “Genomic adaptation of Salmonella to antimicrobials and the human host”. In addition to his computational expertise, Wim is also proficient in various wet-lab techniques, including cultivating bacteria, performing DNA extractions, and performing library preps fof sequencing. This practical knowledge allows him to seamlessly integrate benchwork experiments with computational analyses, facilitating a holistic and comprehensive approach to research. Through a strong connection with the Institute of Tropical Medicine in Antwerp were he performed part of his doctoral studies, Wim has established a robust partnership that greatly enriches his academic pursuits. His diverse background and scientific network allows him to actively engage with interdisciplinary teams, fostering an environment conducive to inclusive research. Driven by a passion for effective communication, he can explain difficult scientific concepts to audiences with varying levels of technical expertise. As a true evangelist for the field of bioinformatics and computational biology, Wim holds the position of Vice Chair in the Executive Team of the International Society for Computational Biology (ISCB) Student Council. He plays a crucial role in fostering connections and building bridges within a diverse global network of more than 2000 master's students, PhD students, and early-career researchers who share a profound dedication to advancing the frontiers of computational biology. Driven by a strong sense of social responsibility, and through his active involvement in the ISCB Student Council and his current research position, Wim is dedicated to providing equitable access to sequencing capacity and high-quality bioinformatics training, particularly for individuals in low- and middle-income countries who face limited opportunities in this field.
Systems biological analysis of niche adaptation in resistant and virulent Salmonella pathogens.
Abstract
The foodborne pathogen Salmonella poses a significant threat to human health worldwide. This is further complicated by the emergent spread of antibiotic resistant strains. Salmonella serotypes and subtypes can have different niches, from a broad range to a very specific niche, e.g. humans. Such bacteria can become very efficient in infecting humans and will contribute even more to the spread of antibiotic resistance. To combat the emergent spread of multiresistant bacteria, molecular monitoring of bacterial strains that show increased adaptation towards the human host, combined with high resistance and virulence, it is vital. While researchers can relatively accurately predict alarming resistant and virulent phenotypes based on whole genome sequencing data, niche adaptation prediction techniques are lagging behind. I will solve these problems by (i) analysing niche adaptation from a broad perspective and (ii) implementing cutting edge computational technologies to predict niche adaptation in Salmonella. This methodology will be built and tested on a model Salmonella serotype, Salmonella Concord. Salmonella Concord is intrinsically a highly virulent and resistant serotype, and shows geographical restriction (the Horn of Africa). It has been reported in Belgium through adopted children, mainly from Ethiopia. Insights from my research will empower health care innovations, and the predictive model will significantly improve risk assessment of pathogenic bacteria.Researcher(s)
- Promoter: Laukens Kris
- Co-promoter: Meysman Pieter
- Fellow: Cuypers Wim
Research team(s)
Project type(s)
- Research Project