iiinova — where your digital self keeps evolving

Reposted by Hannah Meyer

Ewan Birney @ewanbirney.bsky.social · 10/10/2025

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

embl.wd103.myworkdayjobs.com

Staff Scientist

About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

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Hannah Meyer @hannahvmeyer.bsky.social · 25/07/2025

I had found reshape somewhat unintuitive, pivot_longer and separate_longer_delim from tidyr have been gamechangers for me

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Reposted by Hannah Meyer

amitava banerjee @amitava-immuno.bsky.social · 25/07/2025

Got new #TCR-pMHC data to send our way into BATCAVE? Wanna try BATMAN to predict targets of your #TCR? We would love to hear from you! 💽Database+codes: github.com/meyer-lab-cs... 💻BATMAN software + tutorials: github.com/meyer-lab-cs... 🦇Lets decode TCR-pMHC logic, one mutation at a time🦇

github.com

GitHub - meyer-lab-cshl/BATMAN-paper: Bayesian inference of Activation of TCR by Mutant Antigens

Bayesian inference of Activation of TCR by Mutant Antigens - meyer-lab-cshl/BATMAN-paper

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Hannah Meyer @hannahvmeyer.bsky.social · 25/07/2025

Understanding cross-reactivity is essential for TCR based therapies and we hope BATMAN as a stand alone tool, plus BATCAVE for future methods development can get us one step closer to this goal

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Hannah Meyer @hannahvmeyer.bsky.social · 25/07/2025

We demonstrate the translational potential of BATMAN by accurately ranking immunogenic peptides of clinically relevant TCRs, essential for understanding neoantigen immunogenicity and off-target effects of TCR-based therapies.

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Hannah Meyer @hannahvmeyer.bsky.social · 25/07/2025

We then went on to develop on active learning framework for BATMAN, to minimize the number of TCR-pMHC experiments that need to be performed to learn the xreactivity of a novel TCR, thus guiding experimental biologists in the optimal strategy for designing experiments to determine TCR specificity.

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Hannah Meyer @hannahvmeyer.bsky.social · 25/07/2025

BATCAVE became our benchmark to compare and develop BATMAN, a new probabilistic framework to predict TCR-pMHC activation and cross-reactivity. BATMAN learns interpretable features such as us AA-distance functions and epitope positional weights to correlate with biophysical TCR-pMHC properties

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Hannah Meyer @hannahvmeyer.bsky.social · 25/07/2025

For BATCAVE, we scoured the TCR-pMHC literature from the past 20 years, collecting any mutational scan data that we could get our hands; we then processed these in a common framework, obtaining a databases of more than 22k+ TCR-pMHC activation datasets across human and mouse, CD4 and CD8 epitopes.

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Hannah Meyer @hannahvmeyer.bsky.social · 25/07/2025

The work was a great collaborative effort between my lab and Saket Navlakha's lab at @cshlaboratory.bsky.social, largely driven by @amitava-immuno.bsky.social, @davipatti.bsky.social. Curious about BATCAVE and BATMAN? Read on ->

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