Courses and events

Topics for MSc/PhD theses

We supervise study assignments (BSc/MSc/PhD) on the theory, methods, and applications of data science related to our ongoing research. Welcome to contact us to discuss research/study positions.

Courses and events in 2024

Resistance is Futile: A codeathon to combat antimicrobial resistance (September, 23-27, 2024, Virtual Course)
Metagenomics bioinformatics at MGnify (September, 23-27, 2024, Virtual Course)

Past courses and events

Open science

Conference on Philosophy and History of Open Science (#PHOS16) - digital collection - 2016 University of Helsinki, Finland

Computational science and machine learning

Statistical and Probabilistic Programming (TKO_7097) (5 ECTS; period II; Oct-Dec 2022 - University of Turku, Finland)
Machine Learning and Algorithmics Seminar (TKO_3121) (5 ECTS; period II; with Dr. Matti Ruuskanen; annual course 2020, 2021, 2022 (x2); University of Turku, Finland)
Research seminar on probabilistic machine learning 2018-2020 - University of Turku, Finland
Introduction to probabilistic programming - Lecture slides ODP; PDF - 2018 VIB/KU Leuven, Belgium

Microbiome data science

Nordic Summer School on Computational Microbiome Research; (August 13-15, 2024, Turku, Finland)
Brain, Bacteria and Behaviour: understanding the gut-brain axis (RSS4.06) (2 ECTS; Summer course; 08 July - 12 July 2024 - Radboud University, Nijmegen, Netherlands)
NORBIS: Microbiome data science with R/Bioconductor (Oct 9-12 2023, University of Bergen, Norway)
Summer School: Design and Control of Microbial Communities (Sep 11-13, Leuven, Belgium)
Brain, Bacteria and Behaviour: Understanding the Gut-Brain Axis including microbiome data science with R/Bioconductor (July 10-14, 2023, Nijmegen, The Netherlands)
Microbiome research: analysis and applications including microbiome data science with R/Bioconductor (Feb 21-24, 2023, Pune, India)
Microbiome & Machine Learning: ML4microbiome training school (March 6-8, Utrecht)
Microbiome data science with R/Bioconductor (March 2023, Turku, Finland; weekly meetings)
VLAG Grad School on Intestinal microbiome of humans and animals (Apr 12-14 2023, Wageningen, The Netherlands)
ML4Microbiome Workshop - Advances in the analysis of human microbiome and transcriptomics data (May 24, 2022 - University of Tirana, Albania; Lecture)
Multi-omic data analysis with R/Bioconductor (June 20-23, 2022 - University of Oulu, Finland | Flyer (PDF))
Brain, Bacteria and Behaviour: Understanding the Gut-Brain Axis summer school (July 11-15, 2022 - Radboud University Nijmegen, The Netherlands)
ML4microbiome training school (October 2022 - Barcelona; by Matti Ruuskanen, Tuomas Borman & Chouaib Benchraka)
Microbiome data science with R/Bioconductor (Nov 28 - Dec 1, 2022 - CSC, Finland: virtual course)
Multi-omics Machine Learning workshop. Jan 13-14, 2022 (virtual - H2020/FindingPheno)
Workshop on modeling microbial community time series. November 2021 (virtual)
ML4Microbiome Symposium on Grand Challenges of Data-Intensive Science in microbiome & metagenome data analysis and training. October 2021 (virtual lecture)
Baltic Summer School on Digital Methods in humanities and social sciences, August 2021 (virtual)
ML4Microbiome Training School, September 2021 (virtual)
Brain, Bacteria and Behaviour: Understanding the Gut-Brain Axis online summer school, The Netherlands, July 2021 (virtual)
NORBIS Summer School 2021; National research school in bioinformatics, biostatistics and systems biology, Norway, Aug 2021 (online)
Microbiome Data Analysis Workshop - Hasselt University, Limburg, Belgium, Apr 2021 (online)
Tools and techniques for skin microbiome research - Savitribai Phule Pune University, Pune, India, Jan 2021
Modern statistics for microbiome bioinformatics - Pune, India, Dec 2019
Intestinal microbiome of humans and animals. VLAG Graduate School course - Wageningen University and Research Center, The Netherlands, Oct 2019
Contemporary themes in microbiome data science. - Singapore Centre for Environmental and Life Science Engineering Sep, 2019
Advanced statistical techniques in microbiome bioinformatics - Sep 2019 Nijmegen
International summer school on microbial community modeling - Sep 2019 KU Leuven, Belgium
International spring school on open and reproducible microbiome data analysis - 2018 Wageningen, The Netherlands
International summer school on microbial network analysis - 2017 KU Leuven, Belgium

Computational humanities

Baltic Summer School on Digital Methods in humanities and social sciences. Aug, 2021 (online)

Educational resources

Microbiome data science and multi-omic data integration

Microbiome data science tutorials

Orchestrating microbiome data science with R/Bioconductor (beta version; based on TreeSummarizedExperiment data container)
Introduction to microbiome R package (based on phyloseq data container)

Videos

Playlist on microbiome data science video lectures
Microcosm within us: gut microbiome Science Cafe, Turku, Finland 3/2018

Tutorials