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You are here: Home / Archives for Pam Borghardt

Announcing the AIRR Community Seminar Series!

April 6, 2023 by Pam Borghardt

Join the AIRR Community for a 90 minute “lab-style” virtual seminar.  Each month an established and an early career scientist will discuss their AIRR-seq related research. Seminar time will be 16:00 – 17:30 Central European Time (CET), typically on the 4th Thursday of the month.  Most talks will be recorded and posted on the AIRR Community YouTube channel.  In the spirit of open science collaboration we want to give credit where credit is due – this seminar series is modelled after and a follow-up to the highly successful iReceptor Plus Seminar Series: Theories and Applications of Immune Repertoires which ran from 2020-2022. Check out their website for many scientifically related talks!

Register today for the April 27th talks presented by Hashem Koohy from Oxford University and Marcos Vieria from University of Chicago.

Check out the seminar series web page for upcoming seminars and registration links.

 

Filed Under: Adaptive immune receptor repertoire, AIRR Community

AIRR Data Commons and iReceptor Science Gateway Start Major Collaboration with Type-1 Diabetes Researchers

January 11, 2023 by Pam Borghardt

The AIRR Community is pleased to announce the addition of a new Type 1 Diabetes (T1D) focused repository in the AIRR Data Commons. This is a collaboration between the iReceptor team (Simon Fraser University), The Sugar Science group, the Aaron Michels Lab (University of Colorado), and the Todd Brusko Lab (University of Florida) among others. This repository contains the first fully HLA/MHC genotyped study that adheres to the the AIRR v1.4 MHC genotype standard, with over 62 million annotated sequences from 359 repertoires from the Mitchell et al. longitudinal study of TCR repertoires (TRB locus) in children who progressed to T1D. This new T1D AIRR-seq data is searchable through the iReceptor Gateway and there is of course more T1D data to come from this collaboration. We encourage the community to share this valuable type of data!

Filed Under: Adaptive immune receptor repertoire, AIRR Community

On AIRR Podcast Episode 10 Now Available!

December 30, 2022 by Pam Borghardt

A new episode of #OnAIRR – the podcast of the AIRR Community is now available. Prof Ralf Küppers, @UniklinikEssen, Germany discusses AIRR-Seq in understanding B cell lymphomas. Building upon Ralf’s background in B cell differentiation in health and pathogenesis of human B cell lymphomas, we discuss how micro-dissection and Sanger sequencing is still the method of choice when analysing Hodgkin lymphoma and the V-gene usage and mutations in CLL as prognostic indicators before talking about tracking pathogenic clones when surveying for relapse during clinical follow up.

Subscribe and listen in your favourite app or check out all of the On AIRR episodes here: http://onairr.airr-community.org

Filed Under: AIRR Community Tagged With: Adaptive Immune Receptor Repertoire Community, podcast

On AIRR Podcast Episode 9 Available Now

November 29, 2022 by Pam Borghardt

Interested in studies of the adaptive immune receptor repertoire (AIRR)? Catch up on the latest in this new episode of On AIRR – An AIRR-C Podcast Series. Dr. Ulrik Stervbo and Dr. Zhaoqing Ding sit down with Vadim Nazarov the Co-Founder & CEO of the startup ImmunoMind to discuss the use of AI for repertoire insights.

Check out On AIRR Podcast #9 The ImmunoMind or wielding an AI for repertoire insights with Vadim Nazarov.

Filed Under: AIRR Community Tagged With: Adaptive Immune Receptor Repertoire Community, podcast

Join us for the next AIRR-C webinar on Nov 15th!

November 13, 2022 by Pam Borghardt

Machine learning for the analysis of adaptive immune receptors and repertoires

Speakers: Maria Chernigovskaya, University of Oslo and Milena Pavlović, University of Oslo

Adaptive immune receptor repertoires (AIRRs) capture past and present immune responses and therefore represent a powerful resource for developing diagnostics and therapeutics. Machine learning (ML) has the ability to discover complex sequence patterns and help further these diagnostic and therapeutic aims. However, to exploit these opportunities, it is necessary to overcome the intrinsic challenges of AIRR data: unknown rules determining antigen binding, high diversity and specificity of receptors with low overlap between AIRRs, and low signal-to-noise ratio. Further, different ML approaches need to be validated and compared before they could be deployed in practice. In this webinar, we will focus on standardized and reproducible ML workflows, benchmarking, and comparison of AIRR ML approaches. We will argue for the use of simulation for validation and benchmarking of ML methods before moving to experimental datasets.

Maria Chernigovskaya is a PhD candidate supervised by Prof. Victor Greiff and Prof. Geir Kjetil Sandve at the University of Oslo, Norway. Maria is working on a methodology for simulating synthetic adaptive immune receptor repertoire (AIRR) datasets to guide the development and benchmarking of AIRR-based machine learning.

Milena Pavlović is a postdoctoral researcher in the Sandve lab at the University of Oslo working on machine learning, causal inference, and their application to biomedical domains. During her PhD, Milena developed the immuneML platform (https://immuneml.uio.no) for the analysis of adaptive immune receptors and repertoires (AIRR), focusing on model robustness and reproducibility, and examined how the knowledge of the data generating process and the causal inference framework could improve AIRR machine learning diagnostics.

Registration is open!


 

Filed Under: AIRR Community Tagged With: Adaptive Immune Receptor Repertoire Community, machine learning

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AIRR Community News

Zooming into the Community III Starts Tomorrow!

May 20, 2025 By Lorissa Corrie

Join us tomorrow for our 10th Anniversary AIRR-C online event! 📢 This virtual two-day meeting marks the 10th anniversary of the founding of the AIRR Community. Join us for a celebration of the AIRR Community and two scientific sessions on “Specificity.” ⚠️ Service announcement: Each registration day is independent, with its own unique Zoom link! […]

New episode of the On AIRR podcast is here!

March 25, 2025 By Lorissa Corrie

In this episode of On AIRR, we welcome Dr. Bjoern Peters, Professor at the La Jolla Institute for Immunology, to discuss the crucial role of high-quality data in AI-driven immunological predictions and diagnostics. Dr. Peters shares his journey from theoretical physics to MHC-binding prediction, leading to his work on the Immune Epitope Database (IEDB) — […]

AIRR Community WG Calls

All times are in ET (Americas/New York)

Click here for full calendar view

Webinar - Zooming into the AIRR Community III
11:00
Wed, May 21, 2025
Webinar - Zooming into the AIRR Community III
11:00
Thu, May 22, 2025
Call - ComRepo WG
11:00
Thu, June 5, 2025
Call - Standards WG
12:00
Thu, June 12, 2025
Call - Standards WG
14:00
Mon, June 16, 2025

Recent AIRR Publications

Lees W.D. et al. AIRR Community curation and standardised representation for immunoglobulin and T cell receptor germline sets (Immunoinformatics, 2023)

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