Matthew McCullen

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/

Thought it might be good to put some human faces on NIH indirects. We had an IT guy at Stanford who supported school of medicine even though he could have made way more at a tech company. Said both his parents died of cancer. Though not a researcher, this is the way he said he could help the mission

Traumatic brain injury invokes infiltration of NK, ILC1, Th1, and CD8 T cells into thalamus, which produce IFNγ to restrict seizure
www.biorxiv.org/content/10.1...
@arimolofskylab.bsky.social

Ep. 95: "Lymphocyte Signaling" Featuring Dr. Gail Bishop - The Immunology Podcast Dr. Gail Bishop is a Professor of Microbiology and Immunology at the University of Iowa, where her lab studies the molecular mechanisms underlying lymphocyte activation and tolerance.  She talks about...

#ICYMI Dr. Gail Bishop from the @uiowa talks about her research on TRAF signaling and her work as Editor-in-Chief of The Journal of Immunology! 📚

Listen now: bit.ly/3ZGdo0a

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...

Single cell profiling of Hematopoietic Stem Cell Transplant recipients reveals TGF-β1 and IL-2 confer immunoregulatory functions to NK cells Natural Killer (NK) cell activity is influenced by cytokines and microenvironment factors, resulting in remarkably diverse functions, by contributing to inflammatory responses or serving as rheostats ...

Will have a more detailed post soon, but sharing advanced online pre-proof version of our new study
- Single cell profiling of Hematopoietic Stem Cell Transplant recipients reveals TGF-β1 and IL-2 confer immunoregulatory functions to NK cells: www.cell.com/iscience/ful...

JCI Insight - Aiolos promotes CXCR3 expression on TH1 cells via positive regulation of IFNγ/STAT1 signaling insight.jci.org/articles/vie...