Stoyan Ivanov and Claudine Blin, LP2M, UMR7370, CNRS, Université Côte d'Azur


Campus Saint Jean d'Angély - Salle 3B48
Bâtiment SJA2

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From December 12 to 16, 2022

International experts will gather in Nice from December 12 to 16, 2022 for a Winter School entitled: Systems Immunology organized by the Graduate School of Life and Health Sciences of Université Côte d'Azur.

The conferences will take place in Nice (exact location to be confirmed).

This Winter School should enable students to acquire the following skills:
  • Understand how to analyze OMICS data
  • Acquire OMICS analysis tools specific to metabolism
  • Know how to apply these analysis tools to immunometabolism
Every day from 9:00 to 17:00

Day 1. Gene expression/RNA-seq approach/Phantasus

Alexey Sergushichev (Washington University/ITMO)
a. General introduction on gene expression analysis and bulk RNA-seq
b. Data exploration (using the web tool Phantasus)
c. Differential expression/pathway analysis (Phantasus)
d. Working with public datasets (Phantasus etc)

Day 2. scRNA-seq from basics to applications, single-nuclei and Cite-seq

Maxim Artyomov and Konstantin Zaitsev (Washington University /LP2M, Nice)
a. General introduction on scRNA-seq approaches
b. Data exploration (using scNavigator)
c. Example of cancer immunology
d. Example of CITE-seq from human scRNA-seq in aging

Day 3. Immunometabolism computational and applications

Alexey Sergushichev (Washington University/ITMO) and Maxim Artyomov (Washington University /LP2M, Nice)
a. Introduction on Immunometabolism
b. Working with network analysis (example of macrophage activation)
c. Metabolic analysis of single-cell RNA-seq data
d. Example of itaconate and immunometabolic regulation

Day 4. Genetics

Nikita Artyomov (Nationwide Childrens Hospital/OSU)
a. Introduction on genetics
b. Introduction on GWAS, exome sequencing, whole genome sequencing
c. Immunological traits seen from human genetics
d. Example of genetic overlap between melanoma and vitiligo

Day 5. Epigenetics – chromatin and DNA methylation

Maxim Artyomov (Washington University /LP2M, Nice)
a. Introduction into chromatin modifications and accessibility (chipseq/atac-seq)
b. Examples of chromatin modification and changes in activated immune cells (atac-seq pipeline)
c. Example of epigenetic regulation of dendritic cell development via specific enhancer
d. Introduction on DNA methylation and example from aging

Download the program

Dr. Maxim Artyomov (Washington University in Saint Louis)
Dr. Alexey Sergushichev (ITMO University/Washington University in Saint Louis)
Dr. Mykyta Artomov (Harvard University)

  • Very good knowledge of english (conferences only in English)
  • Good knowledge of immunometabolism
  • Fundamentals of OMICS analysis
  • Participants must bring a laptop for the practical sessions of the program
Number of participants

The program includes hands-on sessions during which participants will analyze OMICS data. To facilitate interaction between speakers and participants for these sessions, the number should be limited to 25.

Target audience

This Winter School is open to all students (Master, PhD) as well as post-doctoral researchers, researchers or any other person interested in the subject and meeting prerequisites. Master students of the Life Sciences Master of Université Côte d'Azur will be given priority if places are restricted as they will follow the course in the framework of their Master Programme.

The application will be based on a short a short questionnaire at the time of registration.

Modalities of knowledge control

Quizz (only for Master students from Université Côte d'Azur who follow the course in their training curriculum)