APC Microbiome Ireland & ML4Microbiome Conference

7-9 June 2023

University College Cork (UCC), Ireland 

The final Conference of ML4Microbiome will be held 7-9 June 2023 at the University College of Cork, Ireland. The event is jointly organised with the APC Microbiome Ireland SFI Research Centre to prompt scientific discussion and collaborations on shared research topics.

June 7th

Next Generation Bioinformatic Tools for Microbiome Research

Aula Maxima, UCC

09.40-10.00     Marcus Claesson, University College Cork, Ireland

Welcome & Introduction

10.00-10.20     Katri Korpela, University of Helsinky, Finland

Impact of data compositionality on detection of microbiota responses

10.20-10.40     Francesca Bottacini, MTU

Making the most of long reads for the analysis of bacteriomes and their mobile genetic elements

10.40-11.00     James Butler, University College Cork, Ireland

Generative AI for Microbiome – Current Progress and Future Potential

11.00-11.30         Coffee Break

11.30-11.50     Kardokh KakaBra, University College Cork, Ireland

SPINGO ver2: Enhancing 16S rRNA taxonomic classification through k-mer counting and native bayesian classification

11.50-12.10     Giorgos Papoutsoglou, University of Crete, Greece

Predictive modelling on microbiome data: the AutoML perspective

12.10-12.30     Thomaz Bastiaansen, University College Cork, Ireland

Kronos: circadian rhythmicity analysis in microbiome and other ‘omics datasets

12.30-13.30     Lunch Break

13.30-13.50     Ines Thiele, University of Galway, Ireland

Microbiome modelling tools for investigation of host-microbiome co-metabolism

13.50-14.10     Tim Hulsthof, University of Galway, Ireland

Opportunities and challenges in using chatGPT for accelerating bioinformatic analysis

14.10-14.30     Leo Lahti, University of Turku, Turku, Finland

Statistical programming techniques for multi-assay data integration in microbiome research

14.30-14.50     Laura Zambrano Marcos, IMDEA Food Institute, Madrid, Spain

Enhancing Metagenomics Analysis with Machine Learning: Available Software and Tools

14.50-15.20     Coffee Break

15.20-15.40     Andrey Shkoporov, University College Cork, Ireland

Metagenomic analysis of viromes

15.40-16.00     Balazs Ligeti, Pázmány Péter Catholic University, Budapest

Harnessing the Power of Genomics Language Models in Microbiome Research

16.00-16.20     Olateju Idowu, University College Dublin, Ireland

A Benchmark Dataset for Evaluating Computational Methods of Detecting Pathogens in Metagenomes

16.20-16.50      Panel discussion – How can we progress microbiome methods development?

18.30-Late…   Pizza & beer at Franciscan Well

June 8th

ML4Microbiome Final Conference

Aula Maxima, UCC

09.00-09.15     Marcus Claesson                               Welcome & Introduction

09.15-09.40     Jaak Truu                                            WG1 Final Report (pdf)

09.40-10.05     Leo Lahti                                             WG2 Final Report (pdf)

10.05-10.30     Giorgos Papoutsoglou                       WG3 Final Report (pdf)

10.30-11.00     Coffee Break

11.00-11.25     Domenica D’Elia/Aldert Zomer          WG4 Final Report (pdf Domenica D’Elia; pdf Aldert Zomer)

11.25-11.50     Alina Nechyporenko/Marcus Frohme

New COST Action application discussion (pdf)

11.50-12.40     Lunch Break

12.40-13.10     Guided Campus Walking Tour

13.10-13.35     Marcus De Goffau

The in utero Microbiome Controversy – Tall tales about the low microbial biomass field

13.35-13.50     Domenica D’Elia/Erik Bongcam-Rudloff/Tatjana Loncar-Turukalo (Grant Awarding Coordinator) (pdf)

Short-Term Scientific Mission Overview (Survey Responses)

STSM Session 1: In-person project summaries

13.50-14.05    Miodrag Cekic

Creating and utilizing ML and Deep Learning models to understand the role of the microbiome in relation to cancer therapeutics and diagnostics

The video was recorded at the hosting Institute (Prof. Osman Ugur SEZERMAN & his research Team)

14.05-14.20   Thomas Klammsteiner

The gut microbiome of black soldier fly larvae – a meta-analysis of available marker gene datasets

14.20-14.35    Mikhail Kolev

Intestinal/Gut microbiome association with bone health – review of literature, machine learning methods and data availability

14.35-14.50   Jamie FitzGerald

Human Teaching, Machine Learning – developing a sharable syllabus from the recommendations generated through ML4Microbiome

14.50-15.20   Coffee Break

STSM Session 2: Video-link project summaries

15.20-15.35    Paul Stefan Popsecu

Exploring the Microbiome-related datasets

15.35-15.50    Malik Yousef

MicroBiomeNet: Machine Learning Analysis of Metagenomics Datasets

15.50-16.05   Eliana Ibrahimi

Generalized linear models with LASSO, and sparse group LASSO regularization to find bacteria associated with colorectal cancer

16.05-16.20   Gianvito Pio

Standardizing the pipeline for the analysis of high dimensional noisy Microbiome data

17.45-19.00     Cork City Walking Tour

19.00-Late…   Dinner at Cornstore Restaurant

June 9th

09.30-11.00     Marcus Claesson/Randi Jacobsen Bertelsen

Final MC meeting, including success stories, post-ML4Microbiome work etc.

11.00-11.30     Coffee Break

11.30-12.30     Writing workshops (separate rooms)

12.30-13.30     Lunch

13.30-15.00     Writing workshops (separate rooms)