Sign in

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

PostsRepliesMedia
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.
020
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 22/07/2026
It begins.
020
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.
021
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...
052
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.
0155
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 10/06/2026
Short break from grant writing. New rehearsal space coming together.
000
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...
181
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.
010
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.
060
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 05/04/2026
@gezelter.bsky.social
100
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.
180
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.
060
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.
050
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.
230
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
39575
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...
081
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...
13110
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?
032
Reposted by Baker Lab @ Notre Dame
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"
24748257
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?
021
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...
0238
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...
051
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
3222034
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.
140
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 06/10/2025
It's a good day.
010
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 26/09/2025
Tom Sawyer is now airport music.
030
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 16/09/2025
Lecturing on biomolecular equilibria this semester. This is in the classroom. Turns out it 100% lives up to the hype. Amazing stuff.
Picture of a piece of Hagoromo chalk. The best chalk ever made.
010
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 01/09/2025
A big chunk of the lab works on TCR cross-reactivity - the subgroup is called TCR-X. They made an image for their T shirts... Well played, TCR-X. #immunosky
Image for the TCR cross-reactivity group: The big baddy Titin attacking a magician named A3.
060
Reposted by Baker Lab @ Notre Dame
Michael Stipe @michaelstipe.bsky.social · 30/08/2025
I can
I can
349171514039
Reposted by Baker Lab @ Notre Dame
Martin Pacesa @martinpacesa.bsky.social · 27/08/2025
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...
14305109
Reposted by Baker Lab @ Notre Dame
Sam "The Mug Guy" Horrell @drhorrell.bsky.social · 20/08/2025
I don't want to alarm anyone, but I think my electron density might be haunted. 💎👻💀
2445
Reposted by Baker Lab @ Notre Dame
Leonardo Ferreira @drleoferreira.bsky.social · 16/08/2025
A new engineered regulatory T cell is born. Chimeric anti-HLA receptor regulatory T cells (CHAR Tregs) inhibit antibody production by B cells from HLA sensitized transplant patients, offering a precise approach to tackle antibody-mediated organ rejection. www.frontiersin.org/journals/imm...
093
Reposted by Baker Lab @ Notre Dame
Omer Dushek @tcell.bsky.social · 04/08/2025
If you're a postdoc interested in starting your own group, please consider the Dunn School at Oxford, UK. It's a fantastic department and university for molecular immunology and all aspects of immune research!
0105
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 13/08/2025
Getting so many emails about people wanting to do research in our lab and so many of them are obviously AI enhanced, with oddly specific details and common phrasing. A couple have even had an em dash! Hot tip: if you want to work in somebody's lab, don't send the signal you are intellectually lazy.
050
Reposted by Baker Lab @ Notre Dame
Elle Cordova @ellecordova.bsky.social · 01/08/2025
Federal agencies hiding out in a bunker
7634081187
Reposted by Baker Lab @ Notre Dame
Timothy P. Jenkins @tpjenkins.bsky.social · 24/07/2025
Thrilled to announce our paper, "De novo-designed pMHC binders facilitate T cell-mediated cytotoxicity toward cancer cells," is officially out in @science.org! We used generative AI to build a 'GPS' for immune cells to hunt cancer. Read it here: doi.org/10.1126/scie...
1376
Reposted by Baker Lab @ Notre Dame
Klebanoff Lab @klebanofflab.bsky.social · 23/07/2025
🚨Today, in #NatureCancer, we show that #CAR-T cells and #CAR-NK cells contain the seeds of their own self-destruction. Disruption of a FAS-L/FAS enhances CAR potency against liquid and solid cancers. rdcu.be/exjEy. @mskcancercenter.bsky.social @parkerici.bsky.social
rdcu.be
CAR-engineered lymphocyte persistence is governed by a FAS ligand–FAS autoregulatory circuit
Nature Cancer - Klebanoff and colleagues report that survival and persistence of CAR-T and CAR-NK cells are regulated by a FAS ligand–FAS autoregulatory circuit, showing that disabling FAS...
0129
Reposted by Baker Lab @ Notre Dame
Bryan Bryson @thebrysonlab.bsky.social · 21/07/2025
Newest paper from the lab out today (doi.org/10.1084/jem....)! Here, we describe PathMHC, a novel MS-based approach to identify rare pathogen-derived peptides on MHC-I and MHC-II. We apply this to a range of pathogens Mtb, SARS-CoV-2, and Listeria.
doi.org
Targeting infection-specific peptides in immunopeptidomics studies for vaccine target discovery
MS-based immunopeptidomics can facilitate vaccine antigen discovery, but self-MHC peptides greatly outnumber pathogen-derived MHC peptides, presenting a ch
1308
Reposted by Baker Lab @ Notre Dame
Rob Klose @robklose.bsky.social · 15/07/2025
My wonderful colleage Colin Kleanthous is raising money for the MND association. Please support Colin in this worthy endeavor! www.justgiving.com/page/colin-k... (Please repost!)
justgiving.com
Colin Kleanthous' fundraiser for Motor Neurone Disease Association
Help Colin Kleanthous raise money to support Motor Neurone Disease Association
01211
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 11/07/2025
Congratulations to the newly minted structural immunologist Dr. George Gray! George made killer progress quantifying TCR cross-reactivity and built a foundation we'll build on for years. The last of our COVID babies - we will miss him as he goes off to train the next generation! #immunosky
Dr. George Gray at his thesis defense.Dr. George Gray destroying his celebratory bottle of Champagne.
060
Reposted by Baker Lab @ Notre Dame
chasingmicrobes @chasingmicrobes.bsky.social · 03/07/2025
"CASP, the 3-decade-old competition has run out of funding from the U.S. National Institutes of Health (NIH) and will exhaust emergency support from the University of California (UC) Davis... on 8 August. UC Davis has told the two researchers who run the program that their jobs will end in weeks"
science.org
Exclusive: Famed protein structure competition nears end as NIH grant money runs out
Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold
133
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 26/06/2025
Think I might build a little drum kit for my office. @gezelter.bsky.social are you going to be ok with that?
100
Reposted by Baker Lab @ Notre Dame
Fenit Nirappil @fenitn.bsky.social · 18/06/2025
NIH cuts have life and death consequences. How a cancer patient became collateral damage to Trump’s purge of the federal workforce, @carolynyjohnson.bsky.social reports wapo.st/44ntbo4
wapo.st
His custom cancer therapy is in an NIH freezer. He may not get it in time.
The purge of probationary federal workers included skilled lab personnel who would have finalized a customized cell immunotherapy for cancer patients.
813283
Reposted by Baker Lab @ Notre Dame
Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 10/06/2025
For non-scientists: the funding rate is somewhere between 7% to ~25% (rare) for NIH or NSF grants, depending on where you are applying. Grants are reviewed by a panel of peers who read the grants, score them, then debate the ratings for 1-2 days to rank them. It is INCREDIBLY competitive already.
6239105
Reposted by Baker Lab @ Notre Dame
Allie Sinclair @asinclair.bsky.social · 02/06/2025
Out now in @nathumbehav.nature.com: Cuts to NIH funding will impact the economy and employment nationwide. We visualize these losses and advocate for a theory-driven approach to communicating local, self-relevant impact. w/ @joshuasweitz.bsky.social + SCIMaP team: www.nature.com/articles/s41...
nature.com
NIH indirect cost cuts will affect the economy and employment - Nature Human Behaviour
Nature Human Behaviour - NIH indirect cost cuts will affect the economy and employment
518697
Reposted by Baker Lab @ Notre Dame
Kristian G. Andersen @kgandersen.bsky.social · 06/06/2025
In 2019, NIAID proposed an ambitious scientific network focused on pandemic preparedness, research, and response - the "CREID Network". Ten centers kicked off just as the pandemic was taking off, playing critical roles throughout. We were just notified the whole network is terminated. Reason? 👇
16206125
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 06/06/2025
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!
Postdoc Chad Brambley presenting at the AI/HI workshop. The AI/HI workshop sponsored by Epivax.
070
Reposted by Baker Lab @ Notre Dame
Gabriele Corso @gcorso.bsky.social · 06/06/2025
Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀
1021391
Reposted by Baker Lab @ Notre Dame
Holden Thorp @holdenthorp.bsky.social · 06/06/2025
Marcia McNutt has been saying that the US is doing a huge experiment with China as the control. The global scientific community will still produce knowledge. But not being in the lead has bad implications for US flourishing. My column: www.science.org/doi/10.1126/...
science.org
America is ceding the lead in creating the future
The renowned American management consultant and author Peter Drucker is often credited as saying that “the best way to predict the future is to create it”—a view that applies to science as much as to ...
212947
Baker Lab @ Notre Dame @nd-bakerlab.bsky.social · 04/06/2025
Congratulations to the newly minted PhD, Dr. Sarah Catherine Baker Hawthorne! A cell biologist not a structural biologist, and not one of my students but still one of mine :) Super proud dad today. Next step California Science & Technology Policy. 💪🧪💪
Picture of me with the new Dr. Hawthorne. Dr. Sarah Catherine Baker Hawthorne.
1121