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Baker Lab @ Notre Dame

@nd-bakerlab.bsky.social
2.1K followers 1.7K following 184 posts

Structural and molecular immunology and protein biophysics at the University of Notre Dame. T cell receptors, MHC proteins, specificity, and cross-reactivity. Plus drums, odd time signatures, Iron Maiden, and much Rush. Opinions mine alone. bmblab.nd.edu

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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 21/09/2026
PSA - if you write me about being a postdoc or grad student and your message has something like "I believe my background in blah *aligns closely* with your group's ongoing work in blah " it's a dead AI giveaway. Don't do it, you get no response. AI has its good uses - this isn't one of them.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 22/07/2026
It begins.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 03/07/2026
Coming up this month...we've added an alternate/emo set...chose your flyer, we have rocker red or party pink!
Poster for the Standard Deviants gig this month in rocker red.Poster for the Standard Deviants gig this month in party pink.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 28/06/2026
Great review - pretty much sums up the field!! link.springer.com/article/10.1...
link.springer.com
Computational prediction of TCR cross-reactivity: principles, challenges and translational opportunities - Journal of Translational Medicine
T-cell receptor (TCR) cross-reactivity, whereby a single TCR recognizes multiple peptide–MHC (pMHC) ligands, is essential for immune surveillance but also represents a major safety challenge for TCR-b...
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Reposted by Baker Lab @ Notre Dame
Nature Methods @natmethods.nature.com · 11/06/2026
A Perspective discusses challenges in macromolecular ensemble prediction and the methodological advances that are needed. @stephanieaw.bsky.social www.nature.com/articles/s41...
nature.com
From possibility to precision in macromolecular ensemble prediction - Nature Methods
This Perspective discusses current challenges in macromolecular ensemble prediction and the infrastructure and methodological advances needed to overcome these barriers.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 10/06/2026
Short break from grant writing. New rehearsal space coming together.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 01/06/2026
Congratulations to super star Jiaqi Ma and the rest of the lab. An ongoing part of our exciting collaboration with Chris Klebanoff and team @klebanofflab.bsky.social - important clinical implications for targeted T cell therapy, vaccines, and transplantation.
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 01/06/2026
New work from the lab showing how micropolymorphisms in HLA superfamilies can dramatically impact TCR specificity, even in the absence of changes to static structure or peptide binding. The secret's in how the peptides move around - or not, in the case of A0302 vs A0301. www.pnas.org/doi/full/10....
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 07/05/2026
Ah wow, wish I could have gone this time!! Next spring!
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 18/04/2026
Exactly!!! 😮
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 16/04/2026
Dive bar tour begins (and ends?) in a week and half! Maybe we should decide on a tour poster.
Standard Deviants deviated rock band gig advertisement for April 25.Standard Deviants local community tour sign, with Esher level geometrical problems.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 14/04/2026
I know paylines aren't a thing anymore, but I think this is ok...? T cell targets in transplantation, your time is coming! Thank you nice reviewers, even #3 I suppose!!! 😀
Image highlighting showing a 5% score on an NIH grant submission.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 06/04/2026
Gotta have the umlaut. Otherwise it's just an ordinary gate ;)
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 05/04/2026
@gezelter.bsky.social
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 01/04/2026
Huge congratulations to Chukwunalu "Chuks" Chukwuma for successfully defending his PhD thesis on interrogating the specificity of alloreactive T cells and the implications for organ transplant rejection! Another newly minted structural immunologist setting out to make the world a better place.
Soon to be former graduate student Chuks celebrating the wildly successful defense of his PhD thesis studying the specificity of alloreactive T cells with a bottle of champagne.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 30/03/2026
Same :)
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 11/03/2026
A terrible scientist. This is scientific misconduct.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 11/03/2026
What's also infuriating is that publishing companies could address this. Remind me again what those outrageous publication/subscription fees are used for? Oh I know, nothing that relates to actually improving the peer review and overall publication process.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 04/03/2026
Ditto no. But this might be the BEST thing since stepping down as an administrator. Morning email dread GONE. That plus zealous use of labels & inbox skipping to send all the boring/hyped-up university stuff to the megahype folder that mostly gets ignored. Course, I still have morning news dread...
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 03/03/2026
Total prohole.
Electron density of a proline from a high resolution protein crystal structure, showing the hole in the middle of the ring - a prohole.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 03/03/2026
Lab people: "Hey, look at all these cool AI models, AlphaFold, Chai, Boltz, gazillion models per week, blah blah, cool new relationships, experiments schmeriments." Me, looking at one model: "Huh, arginine and tyrosine in the same volume of space, right where the receptor would sit. Nifty." Sigh.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 25/02/2026
Agreed, nobody is off the hook and that's on us as reviewers. But this is an added responsibility for the chair that often doesn't happen. I always took my "facilitate discussion" role seriously, especially when there was divergence and nobody was pipping up.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 25/02/2026
Yes, but that happens less frequently with study sections over zoom, elevating the importance of the chair in facilitating this.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 25/02/2026
You can give feedback to CSR on both, although since your knowledge of what exactly went on is circumspect, it's an uphill battle and I suspect it takes a lot of feedback from multiple applicants to resonate.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 25/02/2026
Pt 1: As noted SROs have outsized influence by choice of ad hocs AND reviewer assignments. While SROs are professionals, they are not all equal. Pt 2: If an app is discussed, the chair should call for discussion on opinionated/divergent reviews if it isn't happening. Not all chairs will do this.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 22/02/2026
Wonderful evening with the Rush Tribute Project in Indianapolis. Absolutely nailed every note. They make it look so easy. Wonderful guys - thank you! #Rush
Rush Tribute Project on stage in IndianapolisMeeting the Rush Tribute Project after the show. Thomas (drummer, right) absolutely nailed it.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 05/02/2026
Always love some tasty double mutant cycles.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 29/01/2026
Agree, that seems very likely. But it's all so dumb. We've been certifying our other support pages for a couple of years now with digital signatures. There's no reason we couldn't all have been told to put the same boiler plate text at the end of our biosketches then sign off. But efficiency!
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 29/01/2026
Yay. But technical issues? I'm guessing complaints. This whole thing is the perfect definition of make-work. Maybe even worse - they made a problem out of a non-problem.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 23/01/2026
Thanks Chris and team!
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 22/01/2026
(R21 so not percentiled)
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 22/01/2026
Super surprised and super grateful, to the reviewers and more importantly the talented team and collaborators that made this possible (particularly @chadbrambley.bsky.social). I suppose we'll see how changes to advisory councils and MYF play out...?
Surprisingly good score of an NIH R21 proposal to study molecular mimics in T cell recognition.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 21/01/2026
It's like the same with predicting T cell epitopes.
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Reposted by Baker Lab @ Notre Dame
Jeremy Berg @jeremymberg.bsky.social · 20/01/2026
The conference (agreement between House and Senate) appropriations bill that includes HHS and NIH was released this morning. www.appropriations.senate.gov/news/majorit... 1/5
appropriations.senate.gov
Committee Releases Conferenced Defense, Homeland Security, Labor, Health and Human Services, Education, and Related Agencies, and Transportation, Housing and Urban Development, and Related Agencies Bi...
United States Senate Committee on Appropriations
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 27/12/2025
Latest preprint from the team: micropolymorphisms in HLAs tune peptide conformational ensembles, altering structural adaptability & contributing to TCR specificity. Even if static structures & pep affinites are the same, closely related HLAs may not be. #immunosky www.biorxiv.org/content/10.6...
biorxiv.org
HLA micropolymorphisms confine neoantigen conformational adaptability and guide T cell receptor selectivity
T cell receptor (TCR) restriction by highly polymorphic major histocompatibility complex (MHC) proteins is a foundation of cellular immunity. Although the effects of MHC polymorphisms on peptide bindi...
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Reposted by Baker Lab @ Notre Dame
Stephanie Wankowicz @stephanieaw.bsky.social · 01/12/2025
New preprint! Entropy drives molecular recognition, yet most structure-based drug design ignores it because it is difficult to measure. X-ray crystallography captures ensembles, not single structures. Can we extract thermodynamically meaningful entropy from them? www.biorxiv.org/content/10.1...
biorxiv.org
Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain
Structure-based drug design has traditionally focused on optimizing static, enthalpic interactions between ligands and proteins or on displacing binding site solvent molecules to entropically favor bi...
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Reposted by Baker Lab @ Notre Dame
George Musser @georgemusser.com · 03/12/2025
"Everything that isn’t a ghost is usually woven." LLMs’ style is hilarious but sobering: They make the curious word choices they do because that’s what most people rate as good writing. (PSA: When you see me using “delve,” “—”, and descriptive triplets, it’s really me!)
nytimes.com
Why Does A.I. Write Like … That?
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 23/11/2025
Definitely another variable to consider.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 22/11/2025
They missed the control experiment of someone dressed up as Cobra Commander. And then the mindless god Azathoth at the center of the universe. Pretty much the whole alignment chart. Batman is just one corner.
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Mindy Weisberger @laminda.bsky.social · 21/11/2025
Science will often take you to unexpected and delightful places. In this study, researchers hypothesized that riders in a crowded subway car would be more likely to offer their seat to a pregnant person if there were someone in the subway car dressed as Batman 🧪🦇 www.nature.com/articles/s44...
A man in a Batman costume and a pregnant woman in a crowded subway car, their faces obscured by pixelation. Text on top of the image reads: "Fig. 1: An example of the experimental setting, with Batman and a woman simulating pregnancy stand in a crowded metro"
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 19/11/2025
Because when I decide to sit around and be lazy, all my socks and other freshly washed laundry start spontaneously organizing into a predictive algorithm that tells me almost ok information half the time, as opposed to slowly adopting an ever more disordered distribution of messy if clean clothes.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 13/11/2025
w/o validation reports, send it back and say it's not reviewable. Reports should be required (and for many journals are, but that's often ignored). After that it's your prerogative to ask for coordinates, maps, etc. Blows my mind we're still talking about this in 2025, but victims of success, etc.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 13/11/2025
Hey #immunosky people - anyone got any experience encoding multiple MHC-I binding peptides in APCs using minigenes and care to give some advice?
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Reposted by Baker Lab @ Notre Dame
Fred Hutch @fredhutch.org · 07/11/2025
Viral immunologist @pgtimmune.bsky.social, who recently joined Fred Hutch's Vaccine and Infectious Diseases Division, aims to harness the "incredible potential" of the immune system to advance diagnostics, vaccines and cancer therapies. bit.ly/3WJVpos
bit.ly
Viral immunologist taps ‘incredible potential’ of immune system
New Fred Hutch Cancer Center viral immunologist Dr. Paul Thomas is working to turn the "incredible potential" of the immune system into real-life diagnostic and therapeutic applications. He studies ho...
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 24/10/2025
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...
jitc.bmj.com
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...
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Reposted by Baker Lab @ Notre Dame
Jason McLellan @mclellanlab.bsky.social · 08/10/2025
I'm honored to receive a MacArthur Fellowship. As always, I extend my sincerest thanks to all my wonderful mentors, colleagues, collaborators, admins, and trainees who make this work possible. #MacFellow
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 08/10/2025
I at least now have another reason. 🙌😁🙌
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 08/10/2025
Players who might have seemed the obvious choice for name recognition and a cash grab. Such amazing grace and humility from Alex and Geddy and the Rush family. This is going to be amazing. There's a reason why so many of us cried like babies when Neil passed.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 08/10/2025
What an amazing way to honor Neil's legacy by selecting someone not in the limelight (at least this scale) - an amazing talent with everything to gain, as opposed to some of the other super talented players who are already widely known and already at the top.
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Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 08/10/2025
Some thoughts on #Rush touring with a surprising choice of the super talented Anika Nilles for a drummer, instead of some of the bigger names that have been thrown around by everybody but Alex and Geddy over the years. Neil Peart of course eschewed the limelight.
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