Integrative Genomics – The 9th UBC Symposium

We are happy to announce that the 9th UBC symposium will take place at the Princess Máxima Center (Utrecht Science Park) on Wednesday, October 11, 2023. The theme of this years symposium is Integrative Genomics. At this yearly event, we aim to bring the bioinformatics community working at the Utrecht Science Park together to exchange knowledge and expertise and discuss the latest progress in the field of bioinformatics.

We strongly encourage you to register for the symposium (free registration) and submit an abstract for a poster presentation at the symposium, to promote your bioinformatics research, gain more exposure, and win a cash price of 150 euros!

Wednesday, October 11, 2023

6th Floor | Princess Máxima Center for Pediatric Oncology |
Heidelberglaan 25
 | 3584 CS | Utrecht

Final Programme


8:30 – 9:00 Registration


9:00 – 9:15 Welcome by the UBC executive board and Prof. dr. Carl Moons (UMCU, chair of the Data Science and Cohorts board)


9:15 – 10:00 Keynote talk by Prof. dr. Vera van Noort


10:00 – 10:30 Coffee break


10:30 – 12:00 Pitch talks “Biology and Methods”


12:00 – 13:30 Walking lunch and Poster Presentations


13:30 – 14:15 Keynote talk by Dr. Laura Villanueva


14:15 – 15:45 Pitch talks “Methods and Biology”


15:45 – 16:15 Break


16:15 – 17:00 Keynote talk by Prof. dr. Tobias Marschall


17:00 – 18:00 Closing ceremony followed by drinks


Keynote Speakers
Screenshot 2023-08-18 at 09.08.54

Laura Villanueva

Head of the Department of Marine Microbiology and Biogeochemistry,
Royal Netherlands Institute for Sea Research (NIOZ)

Associate Professor, Department of Earth Sciences, Faculty of
Geosciences, Utrecht University

Screenshot 2023-08-18 at 09.09.37

Tobias Marschall

Professor, Director of the Marschall Lab, Institute for Medical Biometry and
Bioinformatics, Heinrich Heine University Düsseldorf


Vera van Noort

Professor, Faculty of Bioscience Engineering, Microbial and Plant Genetics,
KU Leuven

Guest Professor of Computational Biology, Institute for Biology, Leiden

Title: “Microbial membrane lipids: opening pandora’s box under the bioinformatics light”


Membranes are composed by proteins and lipids that separate and protect the cell from the surrounding environment. Membrane lipids from Bacteria and Eukarya are structurally the same while they differ from those of Archaea. This differentiation raises unresolved questions regarding the evolution of all cell forms. Besides, the study of microbial membranes also helps in determining microbial adaptation mechanisms to environmental conditions. Here, we will dive into a journey to the bottom of a breathless sea, by using bioinformatic approaches, to determine the biological sources and evolution of the acquisition of membrane lipids.

Speaker overview:

Laura Villanueva her research fields are Geomicrobiology and Marine Microbiology in which she studies the diversity, metabolism, and evolution of marine microbes and their contribution to biogeochemical cycles. She also focusses on the study of the biological sources of organic biomarkers to make better constraints of the predictive power of these molecules to reconstruct past environmental conditions. This research addresses key questions of different disciplines such as paleoclimatology, paleobiology, (biogeo)chemistry, limnology, microbiology, metagenomics, molecular evolution, among others.

Title: “A draft human pangenome”


Reference genomes are foundational for the life sciences and underly many workflows to analyze omics data, including in genomics, epigenomics, transcriptomics, and proteomics. However, present flat reference genomes, such as GRCh38, are not adequately capturing human diversity and hence introduce reference biases. As part of the Human Pangenome Reference Consortium, we have created 47 phased, reference-quality diploid assemblies from a cohort of genetically diverse individuals. Based on alignments of the assemblies, we generated a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. Using our draft pangenome to analyse short-read data reduces small variant discovery errors by 34% and increases the number of structural variants detected per haplotype by 104% compared with GRCh38-based workfows, which enables the typing of the vast majority of structural variant alleles per sample.

Speaker overview:

Tobias Marschall is a professor at Heinrich Heine University and director of the Institute for Medical Biometry and Bioinformatics at the Medical Department. Prior to that, from 2014 to 2019, he was a professor at the Center for Bioinformatics at Saarland University and a senior researcher at the Max Planck Institute for Informatics, heading the Algorithms for Computational Genomics group. He is broadly interested in algorithms and statistical methods for computational genomics, including variant calling, haplotype phasing, structural variants single-cell genomics, genome assembly, and pangenome analyses. He contributes to a number of large-scale international projects, inluding the Human Pangenome Reference Consortium, the Telomere-to-Telomere Consortium and the Human Genome Structural Variation Consortium, where he acts as a co-chair. Tobias is an associate editor for the journal Bioinformatics.

Title: “Post-translational modifications at the interface of phage-bacteria interactions”


During phage infection, both virus and bacteria attempt to gain and/or maintain control over critical bacterial functions, through a plethora of strategies. These strategies include post-translational modifications (PTMs), as rapid and dynamic regulators of protein behavior. However, to date knowledge on the topic remains scarce and fragmented, while a more systematic investigation lies within reach. The release of AlphaFold2 and the increasing inclusivity and scale of mass spectrometry applications to new PTM types, could significantly accelerate research in the field. To date, acetylation, ADP-ribosylation and phosphorylation remain the predominant PTM-types described during phage infection. They play roles in bacterial defense (e.g. preventing phage adsorption through type IV pili glycosylation) and viral counter-defense (e.g. disarming the CRISPR-Cas system by acetylation of DNA binding residue. I will present an overview of the processes affected by lysine acetylation and our ongoing efforts to characterize the impact of Nε-lysine acetylation on methionine synthase (MetE), the enzyme ultimately in charge of synthesizing methionine in a cobalamin-independent fashion in Pseudomonas aeruginosa.

Speaker overview:

Vera van Noort is professor at the Faculty of Bioscience Engineering, KU Leuven, chair of the Leuven Centre for Bio-Science, Bio-Engineering and Bio-Technolog and program director of the POC Bioinformatics – Faculty of Bioscience Engineering, KU Leuven. Next to this, she is a guest professor of Computational Biology at the Institute for Biology at Leiden University. Her group at KU Leuven, Computational Systems Biology, is interested in understanding biological systems as a whole. They try to achieve this through computational analysis of large-scale data generated by the ever growing number of new technologies that can systematically measure the behaviour of multiple cellular components, such as biochemical activities, biophysical properties, subcellular localization and interaction. They use and develop new methods to integrate, visualize and query the large amounts of information available and in such a way come to new biological discoveries. They apply their expertise in bioinformatics, comparative genomics, proteomics data analysis and structural protein modelling to innovative research projects and relevant questions from society and industry.

Pitch Talks

“Biology and Methods”

Title Speaker PI
Order and chaos in bacterial and archaeal chromosomes Dr. Daniel Tamarit (UU) Dr. Daniel Tamarit
Complex structural variation is prevalent and highly pathogenic in pediatric solid tumors Ianthe van Belzen (PMC) Dr. Jayne Hehir-Kwa
Growing French fries; An interdisciplinary approach to understand potato tuber formation Ir. Bas van den Herik (UU) Prof. dr. Kirsten ten Tusscher
Discovery of novel CSF biomarkers to predict progression in dementia using machine learning Dea Gogishvili (UU) Prof. dr. Sanne Abeln
Dissecting bacterial root colonization strategies using complex synthetic communities on diverse hosts Gijs Selten (UU) Dr. Ronnie de Jonge
Ultra-fast deep-learned CNS tumor classification during surgery
Dr. Carlo Vermeulen (UMCU) Dr. ir. Jeroen de Ridder

“Methods and Biology”

Title Speaker PI
DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model Xiaotong Xu (UU) Prof. dr. Alexandre Bonvin
Base analog recognition in Nanopore assays for DNA replication studies Dr. Soufiane Mourragui (Hubrecht Institute) Prof. dr. ir. Alexander van Oudenaard
Causality-trained deep learning of the regulatory grammar of human promoters
Lucia Barbadilla Martinez (UMCU) Dr. ir. Jeroen de Ridder
Benchmarking Bioinformatic Virus Identification Tools Using Real-World Metagenomic Data across Biomes Lingyi Wu (UU) Prof. dr. Bas E. Dutilh
gplas2: Plasmid reconstruction in short read sequencing data using the assembly graph Jesse Kerkvliet (UMCU) Dr. Anita Schürch
Decoding polar microbial interactions in the Western Antarctic peninsula (WAP) with network modelling of unique molecular identifier (UMI)-tagged long amplicons Dr. Swan Sow (NIOZ) Dr. Julia Engelmann