On AIRR - Immune receptors in the clinic

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 t...

Dr. Corey Watson is an Associate Professor at the University of Louisville. His work focuses on characterising and cataloguing antibody genetic diversity in human and mouse to better understand disease susceptibility and clinical health outcomes. Dr. William Lees is a researcher at University of London. His work focuses on developing Adaptive Immune Receptor (AIR) reference sets for diverse species and the annotation of experimenta...

Alexander Bernier BCL, JD, LLM, SJD (Candidate) is a Montreal-based lawyer, and a doctoral candidate at the University of Toronto Faculty of Law. His work aims to give scientists a range of compliant data sharing designs that scientists can implement in different situations.

In this episode, we discuss the risk of identifying individuals in a biological data set, how this is approached differently in different countries, and possib...

Maxim Zaslavsky is a computer scientist using machine learning to address problems in immunology. He is currently PhD student at Stanford University.

Scott D. Boyd is a physician-scientist and Professor of Pathology and of Food Allergy and Immunology at Stanford University. His group is focused on using high-throughput DNA sequencing and single-cell experiments to analyse human immune responses to infection and vaccination.

We disc...

Dr. Charlotte Deane is Professor of Structural Bioinformatics in the Department of Statistics in University of Oxford (UK) and heads the Oxford Protein Informatics Group. Prof. Deane’s research merges statistics, immunoinformatics, protein structure and small molecule drug discovery. Her group has published several databases that are widely used by academic researchers and in pharmaceutical drug discovery pipelines. We discuss the ...

Dr. Xenophon Papademetris is Professor of Radiology and Biomedical Imaging, and Biomedical Engineering at Yale University, USA. The research of Prof. Papademetris is in the area of medical image analysis with a focus in the development of medical software.

Dr. Papademetris provides an overview of the typical regulatory process for software classified as a medical device. We draw from his experience in the medical image field to des...

Prof. Dr. Ralf Küppers is the director of Institute of Cell Biology (Tumor Research), University of Duisburg-Essen, Germany. The work of Prof. Küppers revolves around B cell differentiation and function together with pathogenesis of human B cell lymphomas - both Hodgkin and Non-Hodgkin lymphoma.

We discuss how micro-dissection and Sanger sequencing is still the method of choice when analysing Hodgkin lymphoma and the V-gene usage a...

Vadim Nazarov is Co-Founder & CEO of the startup ImmunoMind. The company focuses on improving the design of adoptive T-cell therapies using multi-omics technologies. Vadim's career began at Dr. Dmitry Chudakov’s Laboratory of Adaptive Immunity, where he developed the now discontinued R-package TcR. The replacement package ‘immunarch’ is continuously developed by ImmunoMind.  

The episode is hosted by Dr. Ulrik Stervbo and Dr. Zhaoq...

Dr. Adi Barzel is an associate professor in the department of Biochemistry & Molecular Biology at Tel Aviv University, Tel Aviv, Israel. Adi is President at Israeli Society of Gene and Cell Therapy.

Following Adi’s long standing interest in gene editing, we discuss the therapeutic potential based on Adi’s recent paper “In vivo engineered B cells secrete high titers of broadly neutralizing anti-HIV antibodies in mice” (Nat Biotechno...

Dr. Encarnita Mariotti-Ferrandiz is associate professor in Immunology at Sorbonne Université, Paris, France. Encarnita is Chair-Elect of the AIRR-Community.

The discussion focuses on sample quality and how to assess this. We draw on two papers during the discussion: “Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases” (Nature Biotechnology; 2021; https://doi.org/10.1038/s41587-020-0656-3) a...

Dr. Brian Corrie is a computer scientist from Simon Fraser University in British Columbia, Canada. Brian is the Technical Director for the iReceptor Plus Project, and architect behind the iReceptor repository (https://www.ireceptor-plus.com).

Dr. Scott Christley‬ is a computational biologist from UT Southwestern, Texas, USA. Scott is the software development manager for VDJServer (https://vdjserver.org).

In this episode we discuss ...

Today we discuss machine learning with Dr. Lindsay Cowell and Dr. Victor Greiff. Machine learning is about pattern recognition and in AIRR-seq the patterns link to diseases and antigen binding. AIRR is nearly a perfect machine learning problem because the underlying patterns are unclear and complex - it is essentially looking for the needle in a needle stack.

Dr. Cowell is from the Biomedical Informatics Division in the Department ...

Dr. Jacob Glanville is founder and CEO of Centivax and  founder of Distributed Bio, acquired by Charles River in 2021. His work focuses on understanding and engineering  the repertoires of T and B cells to improve the response to pathogens. In this episode we discuss how to analyze receptor specificity and use this to create therapeutic antibodies and optimize vaccine response.

AIRR Community Meeting VI: “Exploring New Frontiers”: ...

Anton Langerak is Professor and head of Laboratory Medical Immunology at the Department of Immunology, Erasmus MC in Rotterdam, Netherlands and chair of coordination of the EuroClonality-NGS working group (https://euroclonality.org/ngs/about and https://euroclonality.org). He has been working on chronic lymphocytic leukemia (CLL) for many years and in this episode we discuss the signatures of B cell receptors in CLL.

AIRR Community...

Today's guest is Nina Luning Prak from the University of Pennsylvania. We talk a bit about the AIRR-Community but mostly about diagnosis of B or T cell malignancies and minimal residual disease evaluation and tracking of B cell clones in autoimmunity.

Comments are welcome at the inbox of onairr@airr-community.org or on social media under the hashtag #onAIRR. Further information can be found here: https://www.antibodysociety.org/the...