Ludwig Schulte, Mikolaj Czaplejewicz, Dhruv sharma and Jonathon Bird successfully defended master thesis project on "GWAS IE - Information extraction for genome wide association studies". The group developed an LLM-based automated information extraction system to identify key biological entities and their relationships from scientific literature and translate this information in the form of a knowledge graph. The resulting tool aids researchers in rapidly uncovering and organizing genotype–phenotype insights from GWAS papers, demonstrating both high accuracy and strong coverage in a specialized scientific domain. This work was jointly supervised by Prof. Wim Vriezen (Head, Plant Functional Genomics BFFI Maastricht University), Dr. Aki Harma (Assistant Professor DACS, Maastricht University) and myself. Congratulations to the team on their successful defense. Good luck for future scientific adventures.
Selen Pehlivanoglu, Mara Wackermann, Anne Savelkoul, Tereza Stockova and Jerry Overweg presented their project on "Transcriptomics-based profiling of tomato responses against fungal and bacterial infections". The study examined how biosynthetic and signalling pathways are activated in Solanum lycopersicum (tomato plant) during bacterial and fungal infections. RNA sequencing data was analysed to identify differentially expressed genes under stress conditions, focusing on mapping them to key biosynthetic and signalling pathways identified from the literature. Congratulations to the team their successful presentation and final report. Good luck for future scientific adventures.
I am thrilled to share that I have recently joined Maastricht University’s Brightlands Future Farming Institute (BFFI) as an Assistant Professor in the department of Plant Functional Genomics. This marks an exciting new chapter in my academic journey, where I will continue to explore Bioinformatics, multi-omics data integration, and AI-driven approaches to advance sustainable agriculture. I look forward to collaborating with colleagues, students, and researchers worldwide in driving cutting-edge innovations at the interface of computational biology, plant science, and AI. Stay tuned for exciting updates as I embark on this journey. I am open to new collaborations—feel free to reach out!
Erika Castaneda Sastre defended her master dissertation (Master of Science) on the topic "WYtigger - Identifying autosomal and sex-linked contigs using a machine learning-based classifier". This work was jointly supervised by Prof. Dick de Ridder (Bioinformatics, WUR) and myself. Congratulations to Erika on her successful defense and good luck for future scientific adventures.
I am thrilled to announce that, as of March 9, 2024, I have been appointed as an Honorary Senior Research Fellow in the Faculty of Environment, Science, and Economy, University of Exeter, United Kingdom. This appointment, which extends until 2027, will foster new scientific collaborations and research initiatives.
I had a great time attending the Copenhagen Bioscience Conference on Plant-microbe Interactions for enhanced crop resilience. I truly had good discussions on my research and in general on all the topics covered in the conference. I also won a poster prize on my poster that I presented in the conference. Special thanks to all the organizers involved, all the presenters who presented their work and to Novo Nordisk Foundation for organizing such a great workshop.
I have recently participated in the Metabolomics workshop organized by EMBO at the Wageningen University and Research, the Netherlands. This course has provided an overview of key issues that affect metabolomics studies, handling datasets and procedures for the analysis of metabolomics data using bioinformatics tools. It was delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course provided a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification. Special thanks to the organizers Reza Salek (Bruker GmbH, Germany), Jos Hageman (Wageningen University and Research), Ron Wehrens (Wageningen University and Research) and all the trainers.
I recently attended the annual symposium organized by Max Plank society for Checmical Ecology, Jena on their 25th anniversary. It was a great event and I had a chance to meet Sarah O’Connor (Department of Natural Product Biosynthesis), Jonathan Gershenzon (Department of Biochemistry), Jakob Franke (Hannover University), Sandra Irmisch (Leiden University, The Netherland), Eric Schranz (Wageningen University, The Netherlands) and Radhika Venkatesan (Indian Institute of Science, Education and Research, Kolkata, India). I also got a chance to catch up with some old friends. I would like to congratulate Max Plank on their 25th anniversary and also like to thank for organizing such a great event.
I am very excited to share our recently published review article on “Integrative omics approaches for biosynthetic pathway discovery in plants” in Natural Product Reports. We have been working on this review for quite a while but I am very pleased to see how this work has shaped up. Design of the paper was conceived by all co-authors, which literally changed multiple times. Later we recived some constructive comments/feedback from the reviewers due to which it eventually turned out in a very good flow. With this work we have laid the foundation of plant-based integrative omics research to explore metabolic potential of plants and its regulation in the groups of Marnix Medema, Justin Van der Hooft & Saskia van Wees. So watch out for the new products that will be out soon under this research umbrella. Once again I would like to thank them for such an amazing support.
The bioinformatics group at WUR recently organized a two-days retreat at Hapert, The Netherlands. It was a lovely location amidst beautiful country side. The retreat mainly comprised of social events and scientific flash talks. I presented a flash talk on my research as a part of the NWO Groot project and also delivered a workshop on teams/project management in academia. The retreat allowed all the department members to interact closely with their fellow workers and group leaders in an informal way.