Irish immigrant in USA. Professional sceptic. He/his. Interested in social justice, mucosal immunology, gut microbes & immune tolerance. CD4+ T cell obsessive.
Cleveland, OH
Joined October 2011
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Not sure if anyone is still on here but, does anyone have any expertise/experience with interrogating SNP/InDel in a mouse genome using a reference genome. We have an alignment and are using Integrated Genomics Viewer, but are having trouble figuring some stuff out.
I'm going to deactivate this account. I'm probably not going to be on Bluesky, but I've enjoyed a lot of scientific interactions on here, so my email (which can be found on my institution's website) is always open to hash out science stuff. Be well.
Does anyone know if there is an algorithm that can predict the likelihood a given epitopes will be generated upon antigen processing based on AA sequence? We're playing around with sites outside a known epitope, and are interested to know if they likely impact antigen processing.
PhilipAhern retweeted
Delighted to share our manuscript @ImmunityCP ! Thanks to the editorial team and reviewers for an outstanding process, to all the coauthors, and to Steve @Jamequistlab, who is an incredible mentor!
Glad to take questions
Quick thread 1/5
free access link
authors.elsevier.com/c/1khA8…
I'm not qualified to assess the science described, but this excellent thread is exactly what science should be but rarely is.
PhilipAhern retweeted
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS, indeterminate dendritic cell histiocytosis or other (non-LCH) histiocytic sarcomas cases.
I'm trying to understand non-surgical chemo and targeted therapy options, new pathology markers to better diagnose subtypes/treatments, and any data on progression in pediatric patients. Please feel free to share – I’m trying to cast a wide net due to the rarity of this condition and how little is known.
People can contact me directly at my first name (as written in my profile) at octant.bio.
PhilipAhern retweeted
Today, Trayvon Martin should be celebrating his 30th birthday.
He should be surrounded by friends and family.
Trayvon deserved to see 30. Happy heavenly birthday 🕊️
PhilipAhern retweeted
Our research is expanding beyond pregnancy. Excited to share our results by @Hilmill1113 (doi.org/10.1093/jimmun/vkae0…) investigating transplantation tolerance; and grateful to @J_Immunol, @ImmunologyAAI for streamlined review and support
Microbiologists are underrepresented in the microbiome field...helps explain why we focus largely on a handful of microbes (this is getting better), and why we can genetically modify very few microbiome members (good luck getting a grant to address that):
nature.com/articles/s41564-0…
PhilipAhern retweeted
Honored to have been named a Distinguished Fellow of the American Association of Immunologists. @ImmunologyAAI Particularly honored to be in a class with my cytokine/STAT heroes John O'Shea and Warren Leonard.
AAI congratulates the 2025 Class of Distinguished Fellows!
These long-term members are honored for their outstanding scientific contributions and service to the #immunology community. See the complete list of 2025 honorees: ow.ly/aiXE50UHGW6.
ALT Image of the 2025 Class of AAI Distinguished Fellows. This award recognizes members for distinguished careers and outstanding scientific contributions in immunology.
PhilipAhern retweeted
Our new work!
The 3D affinities of the OT-I TCR to foreign and self-antigens predict their 2D affinities and reveal imperfect antigen discrimination
biorxiv.org/content/10.1101/…
PhilipAhern retweeted
Starting the year with a brand #NOA from #NIAID #NIH and funding from Cure Alz Fund -if anyone would like to join as a #postdoc in our lab, please let me know -#TCR #structure #function and #crossreactivity
PhilipAhern retweeted
Our new work on optimising CAR-T cell sensitivity is now on bioRxiv!
Optimising CAR-T cell sensitivity by engineering matched extracellular sizes between CAR/antigen and CD2/CD58 adhesion complexes
biorxiv.org/cgi/content/shor…
PhilipAhern retweeted
Everyone says “Today’s PhD students are so accomplished I wouldn’t have gotten in today” as if it’s a good thing. It’s not. There are amazing young scientists out there today. But grad admissions is ignoring wide swaths of them because it’s been infected with the same credentialist bullshit of faculty hiring and grants.
PhilipAhern retweeted
[To the three scientists still left here]:
Interested in T cells and where they come from? Then now is the perfect opportunity to register for ThymUS (thymusmeeting.org). Don't miss out on what is shaping up to be a fantastic meting in gorgeous Kauai.
PhilipAhern retweeted
Ever wondered how gut microbes control immune responses at extra-intestinal locations?
Here, #theonlylabever reports how a gut protozoan commensal microbe remotely shapes pulmonary immunity to exacerbate asthma and limit the dissemination of mycobacteria.
@CellCellPress ⬇️(1/X)
Really interesting finding showing that the inflammatory environment can generate neo epitopes that contribute to T1DM. Xiaoxiao Wan is continuing to provide amazing insights into the pathogenesis of T1DM.
biorxiv.org/content/10.1101/…
PhilipAhern retweeted
I don’t understand why there has to be one dominant explanation for Harris’s loss. Multiple things can be true at once, and the need for ONE reason will keep us from learning what we need to from this moment.
