On AIRR 16: Deciphering the grammar of immune repertoires with Thierry Mora and Aleksandra Walczak

Dr. Thierry Mora and Dr. Aleksandra Walczak co-lead the Statistical biophysics group within Laboratoire de physique de l'ENS (LPENS) at the Ecole normale supérieure (Paris, France). Physicists by training, Dr. Mora and Dr. Walczak entered the field of the analysis of the immune system in a time when the first AIRR-seq datasets were becoming available. They have applied biophysics, neuroscience, and information theory perspectives to understand V(D)J recombination and quantify diversity. The group has published many software tools for the analysis of immune repertoires, including IGoR (to infer V(D)J recombination related processes from sequencing data), Sonia (infer selection pressures on features of amino acid CDR3 sequences), ALICE (detect TCR involved in immune responses from single RepSeq datasets), and PUBLIC (for analyzing sharing of TCRs, and predict public clones).

In this episode of On AIRR, Dr. Mora and Dr. Walczak discuss the relevance and challenges of quantifying diversity and the questions that remain unanswered. They think of immune repertoire diversity in the same way as one could think of English language sentences, and try to learn the grammar of the combinations and quantify it. They also provide an overview of some of the software tools developed by their group.

Comments are welcome to the inbox of onairr@airr-community.org  or on social media under the tag #onAIRR. Further information can be found here: https://www.antibodysociety.org/the-airr-community/airr-c-podcast.
 
The episode is hosted by Dr. Ulrik Stervbo and Dr. Zhaoqing Ding.

Announcements and links

• Statistical biophysics @ ENS. The website of the group. https://sites.google.com/view/statbiophysens/home
• Tools mentioned:
  • IGoR: https://github.com/statbiophys/IGoR
  • Sonia: https://github.com/statbiophys/SONIA
  • SoNNia: https://github.com/statbiophys/sonnia
  • ALICE: https://github.com/pogorely/ALICE
  • PUBLIC: https://github.com/yuvalel/PUBLIC