We are pleased to announce that three spots are now open for external PhD candidates to attend the upcoming DRomics Online Master Class. This training offers hands-on experience in analyzing omics data in a dose–response framework and is an excellent opportunity to engage with experts in the field.

Application details

Interested PhD students should submit a CV and a motivation letter by December 8, 2025 to pharm-era@inrae.fr.
Priority will be given to candidates working with omics data obtained using a typical dose–response design, especially datasets including a broad range of tested doses (or concentrations) rather than a high number of replicates.
Selected participants will receive an invitation email by December 15, 2025.

Context

Omics methods are increasingly used, especially in ecotoxicology, to explore stressor effects at the molecular scale, to investigate functional responses or to discover new biomarkers. Applied in a dose-response framework, they open new perspectives for mechanistic understanding and risk assessment. But the specificity and the complexity of their responses require a dedicated workflow to properly manage high throughput omics data. DRomics is a freely available tool for dose-response (or concentration-response) characterization from omics data. It is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates to use DRomics). (https://lbbe.univ-lyon1.fr/fr/dromics),or even in-situ data collected on individuals naturally exposed to various doses. It aims to:

• Select monotonic and/or biphasic responsive items (e.g. metabolites, transcripts) ;
• For each selected item, characterize its response by fitting a dose-response (DR) curve and calculating an effect dose/concentration as a benchmark dose/concentration (BMD) ;
• And globally visualize the DR modeling results (shapes of DR curves, BMD values) of all selected items, potentially at different omics levels (e.g. transcriptomics, metabolomics) or in different conditions (e.g. with or without pre-exposition or at different exposure times), and interpret them regarding their biological annotation in a common database (e.g. KEGG or Gene Ontology).

Objectives

Make participants more comfortable and efficient to:

• Understand the bases of the analysis of omics data and the importance of taking into account the nature of measured raw data (e.g. fluorescence for microarray data, counts of reads for RNAseq data, AUCs for metabolomics, ...)
• Understand the bases of dose-response modelling (nonlinear regression, choice of the best-fit model, calculation of a benchmark dose, estimation of uncertainty, …)
• Understand the rationale behind each workflow step to optimize the parameters setting
• Learn how to use the DRomics tools (online shiny applications to begin and the R package to go further)
• Explore the outputs of the tool and exchange about their use in downstream analysis

Prerequisites

No prerequisites except the installation of the following software on your personal laptops:

• A recent version of R (> 4.0.0)
• A recent version of R-Studio (Help / Check for Updates)
• A recent version of the packages that are already installed on your machine (For this purpose go in Tools / Check for Package Updates)

Information regarding the installation of the DRomics package on the participant laptops will be sent be sent to registered particpants prior to the session.

Pedagogical scenario

Introductory presentations of the main theoretical concepts will be followed by practical sessions with both the shiny applications and the functions of the DRomics R package. Omics data examples will be provided to the participants to begin with, but the analysis of their own data will be also possible in a second time.

Training content

• Reminder around omics data analyses and DR modeling ;
• Presentation of the main workflow analysis proposed in the DRomics tool : illustration step by step of the basic functions using the R package and the online Shiny application, keys to interpret the outputs.
• Uptake of the DRomics Shiny application using a training or a personal dataset.
• Presentation of the functions proposed in DRomics to help the biological interpretation of the results of the main workflow analysis (e.g., how to deal with the annotations, how to manage multi-omics data, how to compare omics data obtained in different conditions);
• Discussion with the participants: questions, further needs that DRomics is not yet handling…;
• Evaluation of the skills acquired by the participants at the end of the training.

Information regarding the detailed agenda will be sent to registered particpants prior to the session.

Skills expected to be acquired at the end of the training

• (1) to be able to use the main DRomics workflow using the Shiny application, 
• (2) to understand the statistics and the rationale behind each step of the DRomics workflow so as to be able to interpret the results,
• (3) to have an idea of what types of visualizations are proposed in DRomics to help the interpretation of the main workflow results in conjunction to the biological annotation, especially using multi-omics data.