Oulu Summer School

Multi-omic data analysis with R/Bioconductor

June 19-21, 2023

The course is organized by the Health and Biosciences Doctoral Programme (HBS-DP), University of Oulu Graduate School, Research Unit of Translational Medicine, University of Oulu. The Finnish IT Center for Science (CSC) supports the course by providing cloud computing services.

The course is organized in a live format. Preparatory material and video clips, and online support are available before the course. All teaching material will be shared openly.

Venue: University of Oulu. June 19-21, 2023 (Mon-Wed). The course is organized in a live format.

Costs: There is no registration fee for the course. Participants are expected to cover their own travel and accommodation.

Accommodation: Housing tips can be found at https://visitoulu.fi/en/arrival-overnight/.

Schedule: Contact teaching daily between 9am – 4pm, including lectures, demonstrations, hands-on sessions, and breaks.

  • Day 1 Reproducible workflows with R/Bioconductor and Quarto
  • Day 2 Tabular data analysis (working with single ’omics)
  • Day 3 Multi-assay data integration (multi-omics methods)

For a detailed schedule, see Section 2. The course can be extended by an independent assignment (details will be agreed with the main teacher).

For program & schedule, travel tips, registration, and other details, see the course homepage:https://microbiome.github.io/course_2023_oulu

Summer School

Design and Control of Microbial Communities
11 – 13th Sep 2023, Leuven, Belgium

by Karoline Faust, Didier Gonze, Leo Lahti

In this summer school, we want to introduce students at the Master and PhD level to different computational methods to manipulate microbial communities to shift them towards a desired composition or function. In addition, we want to broaden the horizon of our students with a couple of research talks on the latest developments in the field. Beyond educational purposes, we also hope to initiate a scientific exchange between speakers and students.

More information: http://msysbiology.com/microbedesign/


Registration is open for the 4th edition of the ML4Microbiome training school. It is planned to take place on 6-8 March 2023 in Utrecht, The Netherlands. For more details, please check here.



Andrea Mihajlovic is a Mathematician and Data Science researcher, currently a PhD student in Informatics at the Faculty of Sciences, Novi Sad, Serbia.

We are thrilled to announce that thanks to the research work carried out during an ML4Microbiome STSM in Bari, at the Department of Computer Science and under the supervision of Michelangelo Ceci & Gianvito Pio, Andrea won from the Faculty of Sciences, University of Novi Sad, Serbia, the Aleksandar “Saša” Popović Award For Best Student Paper 2022.

A short report of Andrea’s STMS work is available here.

Presentations, papers and photos from the workshop held on 25.11.2022 are available here.


The Department of Computing at the University of Turku is opening a full-time position for a doctoral researcher or research assistant in statistical and computational microbial ecology.

The starting date is 1.3.2023 or later, to be set by mutual agreement. The fixed-term contract will be made for 24 months, after which a possible continuation is agreed upon separately.

The position focuses on the development of Bayesian probabilistic models for analysing spatial and temporal microbial ‘omic data from an ecological perspective. The project aims at advancing our understanding of the assembly and functioning of microbial communities through applications of the developed approaches to environmental and human microbiome data.

For more information go to https://tinyurl.com/2y2c4zdf

ML4Microbiome DREAM Challenge


Can you predict heart failure time-to-event by using clinical and microbiome data? If yes, don’t forget to pre-register(*) here: synapse.org/finrisk




*Note: While ML4Microbiome WG3 members will participate non-competitively, researchers directly associated with the ML4microbiome COST action are not eligible to participate in this DREAM challenge.


ML4Microbiome is glad to announce the publication of the Editorial that concludes and closes the  Frontiers in Microbiology volume Edited by Isabel Moreno-Indias,  Aldert L. Zomer, David Gómez-Cabrero and Marcus J. Claesson on behalf of ML4Microbiome.

Research Topic “Microbiome and Machine Learning”


Front. Microbiol., 05 July 2022
Sec. Evolutionary and Genomic Microbiology


A prestigious INSPIRE Fellowship, which is a Horizon 2020 Marie Sklodowska-Curie co-funded postdoctoral fellowship programme, is available.

The first call will be on the 30th of June and the successful applicant will be based in APC Microbiome Ireland, Cork, one of the world’s leading microbiome institutes.

The successful applicant would carry out a bioinformatics-based project on the role of the microbiome in inflammatory bowel disease under the supervision of Prof. Marcus Claesson.

For details please contact Prof. Marcus Claesson. Contact details at the COST Action website.



Our next training school is now planned at 5-7 October 2022. It will take place in Barcelona, Spain

For more details, please check here: https://www.ml4microbiome.eu/training-schools/ml4microbiome-training-school-2022-barcelona/


The research team of associate prof. Leo Lahti is seeking a researcher willing to support the development and benchmarking of data analysis techniques in human microbiome studies to accomplish the objectives of ML4Microbiome WG2.

The collaboration can be carried out by submitting a request for a Short Term Scientific Mission (STSM) or Virtual Mobility (VM) grant.

Leo Lahti’s team focuses on the development of computational methods for microbial ecology and metagenomics. The timing and content of the STSM or VM activity will be agreed upon together with the candidate.

More information on the research is available at datascience.utu.fi – the interested candidates can contact Leo Lahti | leo.lahti@utu.fi | +358 50 436 4626.”