Microbiome Data Analysis Workshop 2025

16 December 2024 - 17 December 2024
09:00 - 17:00
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About

Unlock the potential of microbiome research with expert-led training and insights into microbiome data analysis! Accurate microbiome data analysis is crucial for understanding the complex interactions between microorganisms and their environments, impacting fields like health, agriculture, and environmental science. However, microbiome data comes with its own challenges, making it different from other -omics data types.

On day 1 of the workshop you will learn about the basics: going from reads to OTU/ASV tables, exploring and visualizing microbiome data, and differential abundance analysis. These take the form of lectures, including hands-on sessions. The second day continues with more advanced and emerging topics, brought to you by top experts who will guide you through cutting-edge techniques to manage and interpret microbiome datasets. Whether you’re a beginner or looking to enhance your skills, this is your opportunity to learn from the best!

This workshop will be of interest to a broad range of profiles, ranging from PhD students, post-docs to experienced professionals who need to work with microbiome data. We target people with backgrounds in biology, biomedical sciences, engineering, environmental sciences, …, but also statisticians and data scientists with an interest in the challenges specific to the microbiome.

Secure your place and register here! Only 50 places are available.

Program

Day 1: Introduction to Microbiome Data Analysis (16/12)

We shall kick-off the workshop with some basics, starting from raw sequence reads to the generation of an ASV (Amplicon Sequence Variant) or OTU (Operational Taxonomic Unit) table, followed by data visualization, and finally differential abundance (DA) analysis. The workshop is designed to guide participants through each stage of microbiome data analysis, providing both theoretical background and practical hands-on experience. Therefore, each session on the first day will consist of two parts: a theoretical introduction to key concepts and methodologies, followed by an interactive hands-on session.

Program

09:00 - 09:30 Registration and welcome coffee

09:30 - 12:30 From reads to ASV table by Stijn Wittouck, Department of Bioscience Engineering, University of Antwerp, Belgium

12:30 - 13:30 Lunch

13:30 - 15:30 Data Visualisation by Thies Gehrmann, Department of Bioscience Engineering, University of Antwerp, Belgium

15:30 - 16:00 Coffee Break

16:00 - 18:00 Differential Abundance Analysis by Olivier Thas, Data Science Institute, Hasselt University, Belgium

Day 2: Advanced Methods in Microbiome Research and Data Integration (17/12)

The second day will focus on additional skills in microbiome research and multi-omics integration. Participants will explore new technologies and bioinformatics tools, such as metagenome assembly, multi-table methods, and covariate-aware testing to gain deeper insights from complex datasets. We will also cover microbial networks and dynamics, integration of data sets, and development of biomarkers, showcasing modern ways of working with microbiome data. Each session will build upon the foundational knowledge from Day 1.

Program

09:00-10:00 Topic TBA by Georg Zeller, European Molecular Biology Laboratory (EMBL), Germany

10:00 - 11:00 Multi-table methods in microbiome data science by Leo Lahti, Department of Computing, University of Turku, Finland

11:00 - 11:30 Coffee Break

11:30 - 12:30 Studying host-microbiota interactions through multi-omics integration by Laura Symul, Institute for Statistics, Biostatistics, and Actuarial Sciences at UCLouvain, Belgium

12:30 - 13:30 Lunch

13:30 - 14:30 Microbial networks and dynamics by Ksenia Guseva, Department of Microbiology and Ecosystem Science, University of Vienna, Switzerland

14:30 - 15:30 TBA

15:30 - 16:00 Coffee break

16:00 - 17:00 Biomarker Development by Ziv Shkedy, Data Science Institute, Hasselt University, Belgium

17:00 Closing

Venue

Holiday Inn Hotel

Kattegatstraat 1

3500 Hasselt

https://www.hihasselt.com/
Accommodation
An overnight stay is possible for the attendees of the workshop at the Holiday Inn Hotel or Holiday Inn Express hotel for a reduced price of  €133 per night. Breakfast is included in the price.
You can book your room via the links below.
Holiday Inn Hotel: Hasselt University_Holiday Inn

Speakers

Olivier Thas


Olivier Thas is a professor of biostatistics with a strong background in nonparametric statistics, genomics, and high-throughput technologies. He is currently affiliated with Hasselt University at the Data Science Institute, where his work focuses on statistical methods applied to life sciences, including microbiome studies and proteomics. He has authored more than 120 scientific papers and two monographs. In addition to his role at Hasselt University, Thas is also a guest professor at Ghent University and an honorary professor at the National Institute for Applied Statistics Research Australia. His research spans various projects in biostatistics, including statistical decision-making and microbiome research, with notable involvement in international collaborations.​

Ziv Shkedy


Ziv Shkedy is a leading expert and a professor in biostatistics and data science at Hasselt University's CenStat and the Data Science Institute. His research interests span statistical modelling, survival analysis, and clinical trials, with a strong focus on biomarker development. Ziv is also the founder of the eR-Biostat initiative, which provides open-access educational materials for learning R, specifically designed for students and professionals globally, including those in developing countries. He is recognized for his contributions to advancing statistical methods in life sciences and his commitment to accessible education in data science.

Stijn Wittouck


Stijn Wittouck is a postdoctoral researcher  in the Department of Bioscience Engineering at the University of Antwerp, where he focuses on the ecology and evolution of lactic acid bacteria by comparative studies of their genome sequences. He develops software to gain new types of insights from such datasets, or to process them on a larger scale. He applies these and existing bioinformatic tools to study how different species of lactic acid bacteria are related to each other, how they adapt to different lifestyles (e.g. free-living vs host-adapted) and how they interact with their viruses and other mobile genetic elements.

Thies Gehrmann


Thies Gehrmann is a senior researcher at the University of Antwerp in the Department of Bioscience Engineering. His work focuses on bioinformatics and statistical analysis within microbiome studies, including the Isala project, which aims to understand the human vaginal microbiome. Gehrmann's background in computer science and statistics, with prior applications to fungal and human genetics and transcriptomics, makes him a valuable contributor to analyzing the diverse data collected in such microbiome research.

Leo Lahti


Leo Lahti is professor in Data Science at the University of Turku, Finland. His research team focuses on computational analysis and modeling of complex natural and social systems. Lahti obtained doctoral degree (DSc) from Aalto University in Finland (2010), developing probabilistic machine learning methods for high-throughput life science data integration. This was followed by subsequent postdoctoral research at EBI/Hinxton (UK), Wageningen University (NL), and VIB/KU Leuven (BE). Lahti has coordinated international networks in data science methods and applications and organizes international data science training events on a regular basis. He is vice chair for the national coordination on open science Finland, executive committee member for the International Science Council Committee on Data (2023-2025), member of the global Bioconductor Community Advisory Board, and founder of the open science work group of Open Knowledge Finland ry.

Laura Symul


Laura Symul is an Assistant Professor of non-clinical biostatistics at UCLouvain's Institute of Statistics, Biostatistics, and Actuarial Sciences (ISBA). Her research focuses on developing statistical methods for women's health, with a particular emphasis on menstrual health, fertility, cycle-related symptoms, and the vaginal microbiome. She utilizes both parametric and non-parametric models to analyze a variety of data, including clinical, self-tracked (from apps), and publicly available datasets. Before joining UCLouvain, Laura was a postdoctoral researcher at Stanford University, where she began her work in this field. She earned her Ph.D. in computational biology from the École Polytechnique Fédérale de Lausanne (EPFL).

Abstract
In humans, several studies have highlighted the associations between the hosts' health and their microbiotas. To understand how microbiotas and their hosts interact, one needs to jointly analyze (omic) data characterizing both the host and the microbiota. This seminar/presentation will focus on the joint statistical analysis of such data. It will first introduce principles and tools for data collection and organization (e.g., the MultiAssayExperiment BioConductor R package), then detail a few statistical methods for unsupervised and supervised multi-omics integration. These methods will be introduced by presenting how well-known multivariate methods, such as PCA, MDS, or PLS, can be extended to a multi-table set-up. Examples drawn from recent vaginal microbiota research will be used for illustration.

Ksenia Guseva

Ksenia Guseva is a postdoctoral researcher at the University of Vienna, working in the Division of Terrestrial Ecosystem Research at the Centre for Microbiology and Environmental Systems Science. Her research focuses on microbial ecology, particularly in soil environments, where she uses modelling and nonlinear dynamics to understand microbial interactions and ecosystem processes. She is involved in projects related to the construction of co-occurrence networks and enzyme production trade-offs during depolymerization.

Registration

Link

https://quetelet.be/mdaw25

Pricing

Type of participant

Price

PhD-student

€40

Other (postdoc, industry,...)

€210

Notice

Please register only if you can attend both days as places are limited.

  • The participation fees are owed upon registration and are payable within 7 days following submission of the registration (but not later than 7 days before the starting day of the event).
  • Participation is not guaranteed until full payment of the registration fee is received.
  • In the event of a "no-show" cancellation, no refund will be issued.

Practical Information

Who?

PhD students, postdocs, researchers, and professionals working in the microbiome field. For PhD students from Uhasselt:  Acknowledged as DS requirement

When?

The workshop will take place from December 16, 2024 to December 17, 2024

Where?

Holiday Inn Hasselt, Kattegatstraat 1, 3500, Hasselt Belgium

Mobility

Holiday Inn Hasselt, an IHG Hotel

Bus or Train: There is a bus stop opposite the hotel. The train station is 1 km (12 minutes walk) away from the hotel.
Car: The hotel offers an excellent base: You are immediately on the E314 direction Brussels/Antwerp/Liège. Parking is available in the underground Q-park parking Molenpoort or underground parking Blauwe Boulevard, for a fee.

Contact

olivier.thas@uhasselt.be

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