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Microbiome Data Analyses Workshop - Online

April 20 - 23, 2021

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The participant team!

2021-edition

The international MDAW workshop brings together leading data scientists to discuss their newest developments, statistical tools, and latest findings in the rapidly expanding field of microbiome data analyses and high-throughput sequencing. MDAW is held to encourage PhD students and Postdocs dealing with large and complicated, highly dimensional microbiome datasets, to get an overview of the current state-of-the art in amplicon sequence data analyses, teached in lectures and hands-on sessions. Of course this workshop also aims to promote scientific networking and international research collaborations!

On behalf of the organizing committee,
Professor Dr. Olivier Thas (Data Sciences Institute, UHasselt),
dr. Sofie Thijs (Center for Environmental Sciences, UHasselt)

 

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Target audience: All Scientists, Biology, Biomedical Sciences, Biostatistics, Bioinformatics

Skills level: Beginner to advanced.
Hands-on sessions are targeted for beginners in R, Linux, python.

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General context (2021 edition)

The following topics are covered in this workshop:

  • We execute a workflow to go from raw fastq files to an OTU-table
  • We use the generated OTU-table for basic data visualisation, data exploration and differential abundance analyses
  • We will identify biomarkers in high-dimensionality microbiome datasets
  • We perform a multidata visualisation using Circos
  • We use the tool manta and anuran to perform a microbial community network analyses
  • We perform a metagenome-wide-association analyes (MWAS) on a microbiome dataset
  • We execute the PEMA pipeline to process 16S, ITS, 18S and COI amplicon data, and visualisation in phyloseq
     

Objectives
In this workshop participants will get a better understanding of how to analyse their amplicon microbiome sequencing data starting from the raw reads (.fastq) to ASV/OTU-table, and a better notion on the downstream biostatistical analyses and associated challenges. Topics that will be critically discussed include: data visualisation, diversity estimation, normalisation prior to differential abundance testing, biomarker discovery, latent variable models of the microbiome, multi-data integration, and ecological network analyses, modelling, stability and multistability, to phylogeny-aware methods in beta-diversity microbiome analyses, concluding with eco-evolutionary modelling and metagenome-wide-association (MWAS) studies. The 4th day will address besides bacterial 16S rRNA gene amplicons, also eukaryotic 18S rRNA, ITS and COI marker gene amplicon datasets. The raw reads will be processed using the pipeline PEMA (Pipeline for Environmental DNA Metabarcoding Analysis), followed by downstream R analyses.

The topics will be introduced in lectures, and virtual hands-on sessions. 

 

Required skills
Basic familiarity with the Illumina sequencing process and FastQ format. Also basic familiarity with R and the package phyloseq. Basic notion of Linux.

 

Softwares and R packages demonstrated:
DADA2
phyloseq and packages
ggplot2, tidyverse, ggpubr
Rmarkdown
Deseq2
Cytoscape
Circos
manta
anuran
PEMA
....

Welcome

09:00 am - 09:15 am CET/GMT+2 (summertime); Lecture hall 2 presentations

09:00 am - 09:00 am

Olivier Thas

Olivier Thas

Olivier Thas

09:00 am - 09:00 am

Sofie Thijs

Sofie Thijs

Sofie Thijs

Hands-on # 1: Raw data to OTU-table

09:15 am - 11:00 am CET/GMT+2 (summertime); Workshop room 2 presentations

09:15 am - 09:15 am

Veronica Llorens-Rico

Veronica Llorens-Rico

Veronica Llorens-Rico

09:15 am - 09:15 am

Sofie Thijs

Sofie Thijs

Sofie Thijs

Coffee break

11:00 am - 11:15 am CET/GMT+2 (summertime); Bar

Data visualisation and exploratory analyses

11:15 am - 12:00 pm CET/GMT+2 (summertime); Lecture hall 1 presentations

11:15 am - 12:00 pm

Olivier Thas

Olivier Thas

Olivier Thas

Lunch break

12:00 pm - 01:00 pm CET/GMT+2 (summertime); Bar

Issue of data normalisations

01:00 pm - 01:45 pm CET/GMT+2 (summertime); Lecture hall 1 presentations

01:00 pm - 01:45 pm

Veronica Llorens-Rico

Veronica Llorens-Rico

Veronica Llorens-Rico

Differential abundance analyses

01:45 pm - 02:30 pm CET/GMT+2 (summertime); Lecture hall 1 presentations

01:45 pm - 02:30 pm

Olivier Thas

Olivier Thas

Olivier Thas

Coffee break

02:30 pm - 02:45 pm CET/GMT+2 (summertime); Bar

Hands-on session #2: Microbiome data visualisation, diversity, differential abundance and normalisations

02:45 pm - 05:00 pm CET/GMT+2 (summertime); Workshop room 2 presentations

02:45 pm - 02:45 pm

Olivier Thas

Olivier Thas

Olivier Thas

02:45 pm - 02:45 pm

Veronica Llorens-Rico

Veronica Llorens-Rico

Veronica Llorens-Rico

The human microbiome from association to modulation

08:30 am - 09:15 am CET/GMT+2 (summertime); Lecture hall 1 presentations

08:30 am - 09:15 am

Thomas Sebastian B. Schmidt

Thomas Sebastian B. Schmidt

Thomas Sebastian B. Schmidt

Latent variable models of the microbiome

09:15 am - 10:00 am CET/GMT+2 (summertime); Lecture hall 1 presentations

09:15 am - 10:00 am

Leo Lahti

Leo Lahti

Leo Lahti

High dimensional biomarkers in intervention studies: an introduction

10:00 am - 10:45 am CET/GMT+2 (summertime); Lecture hall 2 presentations

10:00 am - 10:00 am

Ziv Shkedy

Ziv Shkedy

Ziv Shkedy

10:00 am - 10:00 am

Rudradev Sengupta

Rudradev Sengupta

Rudradev Sengupta

Coffee break

10:45 am - 11:00 am CET/GMT+2 (summertime); Bar

High dimensional microbiome biomarkers: case studies

11:00 am - 12:00 pm CET/GMT+2 (summertime); Lecture hall 2 presentations

11:00 am - 11:00 am

Ziv Shkedy

Ziv Shkedy

Ziv Shkedy

11:00 am - 11:00 am

Rudradev Sengupta

Rudradev Sengupta

Rudradev Sengupta

Multi-domain data integration

12:00 pm - 12:30 pm CET/GMT+2 (summertime); Lecture hall 1 presentations

12:00 pm - 12:30 pm

Rosella Alfano

Rosella Alfano

Rosella Alfano

Lunch break

12:30 pm - 01:30 pm CET/GMT+2 (summertime); Bar

Hands-on session # 3: Methods for biomarker discovery

01:30 pm - 03:15 pm CET/GMT+2 (summertime); Workshop room 3 presentations

01:30 pm - 01:30 pm

Rudradev Sengupta

Rudradev Sengupta

Rudradev Sengupta

01:30 pm - 01:30 pm

Ziv Shkedy

Ziv Shkedy

Ziv Shkedy

01:30 pm - 01:30 pm

Olajumoke Evangelina Owokotomo

Olajumoke Evangelina Owokotomo

Olajumoke Evangelina Owokotomo

Coffee break

03:15 pm - 03:30 pm CET/GMT+2 (summertime); Bar

Hands-on session # 4: Visualisation of multi-omics data

03:30 pm - 05:00 pm CET/GMT+2 (summertime); Workshop room 2 presentations

03:30 pm - 03:30 pm

Leo Lahti

Leo Lahti

Leo Lahti

03:30 pm - 03:30 pm

Rosella Alfano

Rosella Alfano

Rosella Alfano

Modelling microbial communities

09:00 am - 09:45 am CET/GMT+2 (summertime); Lecture hall 1 presentations

09:00 am - 09:45 am

Aisling Daly

Aisling Daly

Aisling Daly

Introduction to microbial network inference and analysis

09:45 am - 10:45 am CET/GMT+2 (summertime); Lecture hall 2 presentations

09:45 am - 09:45 am

Karolien Faust

Karolien Faust

Karolien Faust

09:45 am - 09:45 am

Sam Röttjers

Sam Röttjers

Sam Röttjers

Coffee break

10:45 am - 11:00 am CET/GMT+2 (summertime); Bar

Ecology of microbial systems: Stability, multistability and critical transitions

11:00 am - 11:45 am CET/GMT+2 (summertime); Lecture hall 1 presentations

11:00 am - 11:45 am

Didier Gonzé

Didier Gonzé

Didier Gonzé

Interaction-adjusted indices of community similarity and phylogeny-aware methods in microbiome analyses

11:45 am - 12:30 pm CET/GMT+2 (summertime); Lecture hall 1 presentations

11:45 am - 12:30 pm

Thomas Sebastian B. Schmidt

Thomas Sebastian B. Schmidt

Thomas Sebastian B. Schmidt

Lunch break

12:30 pm - 01:30 pm CET/GMT+2 (summertime); Bar

Hands-on # 5: Network inference and analysis

01:30 pm - 03:15 pm CET/GMT+2 (summertime); Workshop room 2 presentations

01:30 pm - 02:30 pm

Sam Röttjers

Sam Röttjers

Sam Röttjers

02:30 pm - 03:15 pm

Clémence Joseph

Clémence Joseph

Clémence Joseph

Coffee break

03:15 pm - 03:30 pm CET/GMT+2 (summertime); Bar

Hands-on # 6: Metagenome-wide association studies (MWAS) and random forest

03:30 pm - 05:00 pm CET/GMT+2 (summertime); Workshop room 1 presentations

03:30 pm - 05:00 pm

Thomas Sebastian B. Schmidt

Thomas Sebastian B. Schmidt

Thomas Sebastian B. Schmidt

Social networking with online beer tastings (Jessenhofke)

07:30 pm - 11:00 pm CET/GMT+2 (summertime); Beer tasting room upstairs

Introduction to High-Performance Computing and the Flemish Supercomputer Centre (VSC)

08:45 am - 09:15 am CET/GMT+2 (summertime); hall 1 presentations

08:45 am - 09:15 am

Geert-Jan Bex

Geert-Jan Bex

Geert-Jan Bex

Hands-on # 7: PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes.

09:00 am - 10:45 am CET/GMT+2 (summertime); Workshop room 2 presentations

09:00 am - 09:00 am

Haris Zafeiropoulos

Haris Zafeiropoulos

Haris Zafeiropoulos

09:00 am - 09:00 am

Sofie Thijs

Sofie Thijs

Sofie Thijs

Coffee break

10:45 am - 11:00 am CET/GMT+2 (summertime); Bar

Hands-on # 7: PEMA continue

11:00 am - 12:15 pm CET/GMT+2 (summertime); Workshop room 2 presentations

11:00 am - 11:00 am

Haris Zafeiropoulos

Haris Zafeiropoulos

Haris Zafeiropoulos

11:00 am - 11:00 am

Sofie Thijs

Sofie Thijs

Sofie Thijs

Outlook talk: success stories

12:15 pm - 01:00 pm CET/GMT+2 (summertime); Lecture hall 1 presentations

12:15 pm - 01:00 pm

Leo Lahti

Leo Lahti

Leo Lahti

Closure of the workshop

01:00 pm - 01:15 pm CET/GMT+2 (summertime); Lecture hall 2 presentations

01:00 pm - 01:00 pm

Olivier Thas

Olivier Thas

Olivier Thas

01:00 pm - 01:00 pm

Sofie Thijs

Sofie Thijs

Sofie Thijs

Speakers

Olivier Thas Data Sciences Institute, Hasselt University. Expertise: Nonparametric and semi-parametric statistical methods, applied statistical methods for high-throughput technologies
CET/GMT+2 (summertime); Lecture hall
April 20, 2021 01:45 pm - 02:30 pm
Sofie Thijs Postdoctoral research fellow at Center for Environmental Sciences, Hasselt University, Belgium. Studying different aspects of plant-microbe interactions for pollutant remediation, and sustainable agriculture
CET/GMT+2 (summertime); Lecture hall
April 20, 2021 09:00 am - 09:15 am
Veronica Llorens-Rico Postdoctoral researcher at the VIB-KU Leuven Center for Microbiology, Jeroen Raes lab, studying the functionality of the gut microbiota.
CET/GMT+2 (summertime); Workshop room
April 20, 2021 09:15 am - 11:00 am
Vincent Stevens PhD fellow of Research Foundation Flanders in the group of prof dr. Jaco Vangronsveld, CMK, UHasselt. Studying phyllomicrobiome, biochemistry, molecular biology.
Thomas Sebastian B. Schmidt European Molecular Biology Laboratory (EMBL), Heidelberg, German. Expertises: ecology, molecular microbiology, bioinformatics.
CET/GMT+2 (summertime); Lecture hall
April 22, 2021 11:45 am - 12:30 pm
Leo Lahti Computational scientist, Finland. Field of expertise: human microbiome, bioinformatics, Biostatistics, longitudinal analyses, multidata analyses, biomarkers
CET/GMT+2 (summertime); Workshop room
April 21, 2021 03:30 pm - 05:00 pm
Ziv Shkedy Professor for bioinformatics/biostatistics, DSI, Hasselt University, Belgium. Expertise: biostatistics, bioinformatics, epidemiology of infectious diseases
CET/GMT+2 (summertime); Lecture hall
April 21, 2021 11:00 am - 12:00 pm
Rosella Alfano Doctorate Student / Research Assistant under supervision of prof. Michelle Plusquin, CMK, Hasselt University. Studying human microbiome, epidemiology
CET/GMT+2 (summertime); Lecture hall
April 21, 2021 12:00 pm - 12:30 pm
Rudradev Sengupta Scientific Computing at The Janssen Pharmaceutical Companies of Johnson & Johnson
CET/GMT+2 (summertime); Workshop room
April 21, 2021 01:30 pm - 03:15 pm
Aisling Daly Faculty of Bioscience Engineering, Department of Data analysis and mathematical modelling, UGhent, Belgium. Expertise: microbial ecology theories, mathematical modeller, interaction networks, diversity analyses
CET/GMT+2 (summertime); Lecture hall
April 22, 2021 09:00 am - 09:45 am
Sam Röttjers Laboratory of Molecular Bacteriology (Rega Institute), KU Leuven, Belgium. Microbial Systems Biologist.
CET/GMT+2 (summertime); Workshop room
April 22, 2021 01:30 pm - 03:15 pm
Karolien Faust Department of Microbiology and Immunology, University of Leuven, Belgium. Studying immunology and microbiology, human microbiome, bioinformatics, microbial ecology
CET/GMT+2 (summertime); Lecture hall
April 22, 2021 09:45 am - 10:45 am
Haris Zafeiropoulos PhD Student, Institute of Marine Biology, Biotechnology and Aquaculture, lab42open. Expertises: Systems biology, ecology, bioinformatics and computational biology
CET/GMT+2 (summertime); Workshop room
April 23, 2021 11:00 am - 12:15 pm
Didier Gonzé Université libre de Bruxelles, Bruxelles, Belgium. Expertises: Computer biologist, genetic networks and dynamical , microbial ecosystems
CET/GMT+2 (summertime); Lecture hall
April 22, 2021 11:00 am - 11:45 am
Leila Paquay PhD fellow of Research Foundation Flanders at UHasselt, Belgium, group of Jaco Vangronsveld. Expertises: Bio-informatics, microbiology, hemp microbiome, sustainable agriculture
Olajumoke Evangelina Owokotomo PhD researcher at UHasselt, Belgium, DSI. Expertises: Bioinformatics, Biostatistics, Biomarker detection for microbiome experiments. Predictive models based on metabolomic data in cancer patients under treatment.
CET/GMT+2 (summertime); Workshop room
April 21, 2021 01:30 pm - 03:15 pm
Clémence Joseph PhD student, Karolien Faust group and Lisa Röttjers. Department of Microbiology and Immunology, University of Leuven, Belgium.
CET/GMT+2 (summertime); Workshop room
April 22, 2021 01:30 pm - 03:15 pm
Geert-Jan Bex HPC consultant/analist
CET/GMT+2 (summertime); hall
April 23, 2021 08:45 am - 09:15 am

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Live Event

Microbiome Data Analyses Workshop - Online

April 20 - 23, 2021

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