Matthew McCullen

Happy to share new work from #theonlylabever, lead by the phenomenal @sltai.bsky.social - who developed a tool to study the biology of ILC3s, identifying their role in controlling CSF2-dependent myeloid cells. 🤗
@mucosalimmunol.bsky.social @societymucosalimm.bsky.social
OA: doi.org/10.1016/j.mu...

Tertiary lymphoid structures support the development of allergen-specific progenitor CD4+ T cells Tissue-resident memory CD4+ T cells (TRM) are key sentinels of the adaptive immune response that provide a rapid, robust inflammatory response upon reactivation in non-lymphoid tissues. While CD4+ TRM...

Asthma is a chronic disease characterized by acute, intermittent, recurrent episodes of airway inflammation. A decade of work developing the tools, techniques and collaborations needed to figure out how CD4+ T cells in the lungs propagate disease can be found here:
www.biorxiv.org/content/10.1...

We are currently in the process of recruiting a technician. 🥼🐭🔬

If you know anyone with enthusiasm to learn new skills and stamina to hear me go on and on about IFNs, please have them reach out to me for more details!

STAT3 operates as an inflammation-dependent transcriptional switch https://www.biorxiv.org/content/10.1101/2025.09.26.678857v1

Dear friends,
As have become a habit, I mark each #autumnequinox by sharing a small poem by Xin Qiji. I also start my translation cycle of Chinese and Japanese poems and prose that mark the twenty-four lunisolar micro-seasons. Translation notes blogged here:
#everynightapoem

For our #flowcytometry peeps, would you like to have a single fix/perm protocol that is optimised for everything? One that preserves fluorophores while allowing simultaneous TF and cytokine staining? How about 100-fold cheaper?

You got it:
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...

Dryad partnership brings easier data sharing to bioRxiv bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

bioRxiv partners with Dryad to enable easier, better linking to curated datasets connect.biorxiv.org/news/2025/09...

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

Distinct roles for B cell-derived LTα3 and LTα1β2 in TNF-mediated ileitis - Nature Immunology Erlich et al. show that soluble LTα and membrane-bound LTα1β2 lymphotoxins expressed by B cells play distinct roles to attenuate the pathology observed in ileitis.

Distinct roles for B cell-derived LTα3 and LTα1β2 in TNF-mediated ileitis doi.org/10.1038/s415...

IL-25-induced memory type 2 innate lymphoid cells enforce mucosal immunity IL-25 treatment induces persistent adaptation of the small intestine, which is maintained by ILC2s with functional and epigenetic qualities of immune memory. Effector-memory ILC2s arise in multiple ti...

IL-25-induced memory type 2 innate lymphoid cells enforce mucosal immunity

Cell www.cell.com/cell/fulltex...

🧵How to write and manage your first research budgets

The point of funding is to convert it into quality research. A well-spent research budget should fund the idea it was raised on, plus revision experiments, plus preliminary data for the next grant. So you need to spend, while avoiding waste.

A screenshot of the old style '10 PM, do you know where your children are?' PSA poster, with the 'children are?' scribbled out and 'TCR germline gene reference comes from?' crudely pasted over the top.

I've got a PSA to the T cell receptor researchers of #immunosky to let you know about a new paper we've just got out: doi.org/10.1016/j.im...

This covers how our field is handling the sets of germline #TCR genes used in our research. Maybe not the most glamorous topic, but it’s kind of a big deal…

Targeting LAIR1-mediated immunosuppression adds a new weapon to our immunotherapy arsenal: buff.ly/aJxzdS4

Ezri P. Perrin, Hannah K. Dorando & Jacqueline E. Payton provide a Commentary on Tao et al. (buff.ly/uaGEIUb)

NKG2A-mediated immune modulation of natural killer cells by Staphylococcus aureus Abstract. Natural killer (NK) cells are specialized lymphocytes that help protect against viruses and cancer. However, in the context of bacterial infectio

Meanwhile in scientific news - our latest paper.

In his lecture on “The Generation and Modification of Lymphocyte Antigen Receptor Genes,” Eugene Oltz, @ohiostatemed.bsky.social, described how chromatin accessibility controls where V(D)J recombination occurs during immune cell development. #AAIcourses

Image credit: @gloglita.bsky.social‬ @lifescienceeditors.bsky.social‬ captured DynaTag in action: a pA-Tn5 probe (multicoloured) binds an antibody (white), which binds p53 DNA-binding domain (green) on DNA (blue) within 2 nucleosomes

🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town.
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)

Transcription factors create accessibility through distinct mechanisms involving nucleosome sliding and eviction. A) Estimation of nucleosome-free (NFR) and nucleosomal fragment probabilities using ATAC-seq fragment size distributions. B) Example genomic locus showing ATAC insertion profile, nucleosome occupancy scores, and dyad positions inferred from NucleoATAC.

Liu et al., 2025. An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin www.biorxiv.org/content/10.1...
▶️RoboATAC - automated ATAC-seq
▶️Deep learning models: motif orientation, spacing, flanking bases
▶️Nucleosome positioning analysis

A New Shearwater Album Help beloved indie-rock band Shearwater produce, distribute, and publicize a new LP. | Check out 'A New Shearwater Album' on Indiegogo.

Shearwater is crowdfunding a new album, definitely art worth contributing to. www.indiegogo.com/projects/a-n...

🚨 New #preprint alert!
We're excited to share the latest work from the brilliant Sora Yoon: "Inference of multi-enhancer interactions in T lymphocytes using Hi-Cociety"🔗 www.biorxiv.org/content/10.1...

Aiolos restricts the generation of antigen-inexperienced, virtual memory CD8+ T cells https://www.biorxiv.org/content/10.1101/2025.06.11.659122v1

GitHub - RILAB/statements: Successful Job Applications and Grants Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.

New additions in fellowships, industry, and academic jobs! If you've recently gotten a fellowship or a job (research, industry, PUI) please consider contributing your application materials. It's a helpful resource for those on the job market! github.com/RILAB/statem...

An Il12 mRNA-LNP adjuvant enhances mRNA vaccine–induced CD8 T cell responses IL-12 is dispensable for CD8 T cell responses to mRNA vaccination, but an Il12 mRNA-LNP enhances CD8 T cell memory and protection.

mRNAs encoding adjuvant proteins boost immunity. A fantastic study from Hunter et al shows the value of IL12. Study validates original work on this concept, ref below.
Kudos to the authors on this exciting discovery!
www.science.org/doi/10.1126/...

🚨 New #preprint alert!
We're excited to share our latest work:
"Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells"🔗 tinyurl.com/4ve26tbd

“America First” Will Destroy U.S. Science The U.S. government has sought to restrict immigration under the “America First” doctrine. These policies severely harm American science by stripping it of talent and eliminating a major driver of its...

25 years ago, I came to Stanford on a J1 visa and worked so hard to be worthy of that privilege. Today, I lead Immunology at Mount Sinai and I am the one who feel privileged when brilliant international trainees chose to join us.

Join us for a July Community Call to discuss reimagining scholarly communication! 📝

‪@brembs.mastodon.social.ap.brid.gy‬ will discuss replacing traditional journals with decentralized, community-governed infrastructure.

🔗 Register us02web.zoom.us/meeting/regi...

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations!

These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.

Save and share the post!

A letter from Jeremy Berg to NIH Director Jayanta Bhattacharya about the need to award grants promptly.

As a follow-up to the Kaiser interview, here is my exchange with Dr. Bhattacharya starting Sunday evening...

1/n

Cell type-specific enhancers regulate IL-22 expression in innate and adaptive lymphoid cells
www.biorxiv.org/content/10.1...

if you've had an NIH grant terminated, I want to hear about it. Signal: katherinejwu.12

Estimated Single Year Loss of NIH Funding if 15% Indirect Cost Rate is Imposed Based on analysis of 2024 NIH funding data. Sums are totals of losses in funding to programs if indirect costs had been capped at 15%

Helpful table to determine how much your University or health system is set to lose if the NIH indirect cap is suddenly lowered to 15%. For SJSU it is $374k which is on the smaller end but devastating considering our other budget issues. datawrapper.dwcdn.net/l0ZqA/8/