Baker Lab @ Notre Dame
@nd-bakerlab.bsky.social
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
bmblab.nd.edu
Hey #immunosky people - anyone got any experience encoding multiple MHC-I binding peptides in APCs using minigenes and care to give some advice?
November 13, 2025 at 4:05 AM
Hey #immunosky people - anyone got any experience encoding multiple MHC-I binding peptides in APCs using minigenes and care to give some advice?
Reposted by Baker Lab @ Notre Dame
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
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...
bit.ly
November 7, 2025 at 6:08 PM
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
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/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
October 24, 2025 at 8:08 PM
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/content/13/1...
Reposted by Baker Lab @ Notre Dame
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
UT Austin has a new “genius grant” recipient!
Texas Science professor Jason McLellan has been awarded a MacArthur Fellowship — aka the “genius grant” — by The MacArthur Foundation.
#TexasScience @mclellanlab.bsky.social #MacArthurGenius @utaustin.bsky.social
cns.utexas.edu/news/accolad...
Texas Science professor Jason McLellan has been awarded a MacArthur Fellowship — aka the “genius grant” — by The MacArthur Foundation.
#TexasScience @mclellanlab.bsky.social #MacArthurGenius @utaustin.bsky.social
cns.utexas.edu/news/accolad...
Virus Slayer Awarded ‘Genius Grant’ by MacArthur Foundation
The award recognizes Jason McLellan’s work to investigate how viruses infect our cells and to develop new treatments for infectious disease.
cns.utexas.edu
October 8, 2025 at 7:59 PM
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
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.
Neil Peart of course eschewed the limelight.
October 8, 2025 at 6:27 PM
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.
Neil Peart of course eschewed the limelight.
It's a good day.
🚨BREAKING NEWS!!!! 🚨
Geddy Lee and Alex Lifeson have decided to dust off their instruments and bring back the #Rush tour machine with new drummer Anika Nilles for a 7 city, 12 date tour in 2026! www.rushisaband.com/blog/2025/10...
Geddy Lee and Alex Lifeson have decided to dust off their instruments and bring back the #Rush tour machine with new drummer Anika Nilles for a 7 city, 12 date tour in 2026! www.rushisaband.com/blog/2025/10...
October 6, 2025 at 2:24 PM
It's a good day.
Tom Sawyer is now airport music.
September 26, 2025 at 10:32 AM
Tom Sawyer is now airport music.
Lecturing on biomolecular equilibria this semester. This is in the classroom. Turns out it 100% lives up to the hype. Amazing stuff.
September 16, 2025 at 4:08 PM
Lecturing on biomolecular equilibria this semester. This is in the classroom. Turns out it 100% lives up to the hype. Amazing stuff.
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
#immunosky
September 1, 2025 at 7:51 PM
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
#immunosky
Reposted by Baker Lab @ Notre Dame
Reposted by Baker Lab @ Notre Dame
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...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
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...
www.nature.com/articles/s41...
Reposted by Baker Lab @ Notre Dame
I don't want to alarm anyone, but I think my electron density might be haunted.
💎👻💀
💎👻💀
August 20, 2025 at 3:47 PM
I don't want to alarm anyone, but I think my electron density might be haunted.
💎👻💀
💎👻💀
Reposted by Baker Lab @ Notre Dame
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...
www.frontiersin.org/journals/imm...
August 16, 2025 at 1:49 PM
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...
www.frontiersin.org/journals/imm...
Reposted by Baker Lab @ Notre Dame
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!
It's a fantastic department and university for molecular immunology and all aspects of immune research!
📣 Applications now open 📣
We are seeking outstanding ECRs looking for a stimulating and supportive environment in which to establish their research group as externally-funded fellows, in any area or cell or molecular biology underlying disease!
Please share!
www.path.ox.ac.uk/work-with-us...
We are seeking outstanding ECRs looking for a stimulating and supportive environment in which to establish their research group as externally-funded fellows, in any area or cell or molecular biology underlying disease!
Please share!
www.path.ox.ac.uk/work-with-us...
August 4, 2025 at 5:58 PM
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!
It's a fantastic department and university for molecular immunology and all aspects of immune research!
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.
August 13, 2025 at 4:15 PM
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.
Reposted by Baker Lab @ Notre Dame
Federal agencies hiding out in a bunker
July 31, 2025 at 11:46 PM
Federal agencies hiding out in a bunker
Reposted by Baker Lab @ Notre Dame
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...
We used generative AI to build a 'GPS' for immune cells to hunt cancer.
Read it here: doi.org/10.1126/scie...
July 24, 2025 at 6:27 PM
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...
We used generative AI to build a 'GPS' for immune cells to hunt cancer.
Read it here: doi.org/10.1126/scie...
Reposted by Baker Lab @ Notre Dame
🚨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
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...
rdcu.be
July 23, 2025 at 8:39 PM
🚨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
Reposted by Baker Lab @ Notre Dame
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.
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
doi.org
July 21, 2025 at 2:19 PM
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.
Reposted by Baker Lab @ Notre Dame
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!)
(Please repost!)
Colin Kleanthous' fundraiser for Motor Neurone Disease Association
Help Colin Kleanthous raise money to support Motor Neurone Disease Association
www.justgiving.com
July 15, 2025 at 7:21 AM
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!)
(Please repost!)
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
July 11, 2025 at 6:05 PM
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
Reposted by Baker Lab @ Notre Dame
"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"
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
www.science.org
July 3, 2025 at 6:19 PM
"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"
Think I might build a little drum kit for my office. @gezelter.bsky.social are you going to be ok with that?
June 26, 2025 at 8:29 PM
Think I might build a little drum kit for my office. @gezelter.bsky.social are you going to be ok with that?
Reposted by Baker Lab @ Notre Dame
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
How a cancer patient became collateral damage to Trump’s purge of the federal workforce, @carolynyjohnson.bsky.social reports wapo.st/44ntbo4
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.
wapo.st
June 18, 2025 at 12:03 PM
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
How a cancer patient became collateral damage to Trump’s purge of the federal workforce, @carolynyjohnson.bsky.social reports wapo.st/44ntbo4
Reposted by Baker Lab @ Notre Dame
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.
Republican Senator Katie Britt: We need to create a system "where the beat idea wins... This is our opportunity to make a dollar go further and to make it have a greater impact."
(NIH already generates $2.56 for every $1 spent it spends on research.)
(NIH already generates $2.56 for every $1 spent it spends on research.)
June 10, 2025 at 5:07 PM
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.