Happy to have been part of this work with Karen Hastings and team at the Univ of Arizona quantifying the impact of structure on neoAg immunogenicity. Kudos to @chadbrambley.bsky.social and the others for their awesome work. Look for modeling to improve neoAg prediction! jitc.bmj.com/content/13/1...

Structural changes from wild-type define tumor-rejecting neoantigens

Background Challenges in predicting which neoantigens mediate tumor rejection limit the efficacy of neoantigen vaccines to treat cancers, especially for cancers with a high mutational burden like cuta...

jitc.bmj.com

Let's go home

I had a blast presenting our work on T cell mimotope discovery! A huge thank you to @epivax.bsky.social for hosting such a great meeting and inviting us to speak. I don't want to leave Rhode Island!

Baker Lab @ Notre Dame@nd-bakerlab.bsky.social · last yr.

Super postdoc @chadbrambley.bsky.social killing it at the AI/HI Immunoinformatics workshop, telling us about finding molecular mimics of antigenic epitopes. Thanks to @epivax.bsky.social for the invitation and opportunity!

It was a cold and snowy one, but today we stood up for science! The fight is just beginning though, don't let them dismantle OUR research.

Ok, I've GOT to share this one. Genius might be a tad strong, but who am I to refute my boss haha

Baker Lab @ Notre Dame@nd-bakerlab.bsky.social · 2y ago

I am so excited. Small victories - find joy where you can. Preliminary data for the grant. @chadbrambley.bsky.social is a genius. Big errors because these are log scales, but still.

PDB viewer integration into Obsidian - I need this yesterday (source in alt text)

In a world of Kid Rocks and Carrie Underwoods, be a Woody Guthrie.

Can NOT believe we pulled it off in regulation! #GoIrish #NotreDame

The Athletic@theathletic.com · 2y ago

NOTRE DAME IS ONTO THE CFP TITLE GAME AFTER A GAME-WINNING FG 🍀 The Fighting Irish are back in the national championship game for the first time since 2013.

Marcus Freeman might just be the smartest coach in the game. This was a fun one! #goirish 🍀

RedditCFB@redditcfb.com · 2y ago

Notre Dame gets 13 wins for the first time ever!

#immunosky Anyone else wake up to good news from grant Santa? This one's an F32 fellowship, to help take on TCR cross reactivity. Honored and excited to be working on this and grateful for the support!

Student: I want to master #Linux, but I can’t grow a beard.  Master Foo: Once you master linux you become the beard. Upon hearing this, the student was enlightened.

Design of high specificity binders for peptide-MHC-I complexes https://www.biorxiv.org/content/10.1101/2024.11.28.625793v1

Design of high specificity binders for peptide-MHC-I complexes https://www.biorxiv.org/content/10.1101/2024.11.28.625793v1

Class I MHC molecules present peptides derived from intracellular antigens on the cell surface for i

biorxiv.org

Will save more time that asking ChatGPT!

Stephen Turner@stephenturner.us · 2y ago

This is pretty dope. Add pylustrator.start() at the top of a script and your plots are interactively scalable, composable, movable, etc with your mouse www.youtube.com/watch?v=xXPI... pylustrator.readthedocs.io/en/latest/ h/t @tommytang.bsky.social

🚀 Advancing T-cell receptor (TCR) research! We developed tcrBLOSUM, a specialized substitution matrix for sensitive alignment of distant epitope-specific TCRs. Find out how our findings expand TCR analysis: doi.org/10.1093/bib/... #Bioinformatics #Immunology #AIRR with @pmeysman.bsky.social

tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs

Abstract. Deciphering the specificity of T-cell receptor (TCR) repertoires is crucial for monitoring adaptive immune responses and developing targeted immu

doi.org

I called both Wilson and Rutherford counties home during grad school. Not exactly surprised by my former neighbors, but I am both ashamed and embarrassed for them.

The Tennessee Holler @thetnholler.bsky.social · 2y ago

CHALKBEAT — After Wilson County removed 400 books from their school libraries after the new GOP law, other counties are using their list as a cheat sheet, including Montgomery and Rutherford, where Frances Rosales asked for 150 books to be removed. www.timesfreepress.com/news/2024/no...

I think this will do nicely for my inaugural skeet. Thanks boss for the shout out! Eagerly (and cautiously) excited to get this thing funded. We have work to do! #immunosky

Baker Lab @ Notre Dame@nd-bakerlab.bsky.social · 2y ago

My postdoc Chad is happy today - kudos and congratulations!! More when (if?) the news becomes official. TCR cross-reactivity, you are on notice! #immunosky 🧬🧶🤘🤘