David E Sanin

Register for IMMUNOLOGY2026™ | April 15-19, 2026 The leading annual all-immunology event worldwide!

I'll be heading to IMMUNOLOGY2026™ from April 15–19, 2026!

Hexokinase detachment from mitochondria drives the Warburg effect to support compartmentalized ATP production Nature Metabolism - Hexokinase detachment from the outer mitochondrial membrane is shown to support aerobic glycolysis in cancer cells. Differential localization of the HK1 isoform to the outer...

Context is everything in metabolism! This super elegant study on how hexokinase isoforms are conditionally essential depending on culture media and mitochondrial association highlights how much we need to work towards methods that let us probe these phenomena in vivo!

rdcu.be/e3xOV

The transition from monocyte to tissue-resident macrophage requires DHPS Nature - In mice, DHPS supports the maturation, maintenance and function of tissue-resident macrophages via the polyamine–hypusine axis, with implications for macrophage-targeting therapies.

Metabolic control of immune cells impacts every aspect of their function. We show that monocytes transitioning to tissue resident macrophages need DHPS, otherwise monocytes are stalled in an immature state.

Super excited to see this story published after a ton of work!
rdcu.be/e3wKe

This is so cool!! Amazing work expanding single cell metabolomics to thousands of metabolites and hundreds of thousands of cells! Shame you need a custom built mass cytometer to do this 🥲 but hopefully someone is on this to make it widely accessible!

Looking forward to reading this!! Always fascinating how cells fine tune responses to common cytokines.

‘A bombshell’: doubt cast on discovery of microplastics throughout human body Exclusive: Some scientists say many detections are most likely error, with one high-profile study called a ‘joke’

I can't say I'm surprised by this

www.theguardian.com/environment/...

Holy smokes

I've seen some cool gesture-based point cloud controllers.

So I noted the JS libraries used and vibe coded a similar web app to explore the relationship between spatial, UMAP, and PCA embeddings for spatial transcriptomics data. Next level interactivity via 🖐️

Try it out: jef.works/GestureGraph/

All models are wrong, and yours is useless

www.nature.com/articles/s41...

Super proud of Andrei Dorobantu who was named a @society4science.bsky.social #RegeneronSTS scholar for work that he performed in my lab. Only 300 young scientists are selected for this honor. bit.ly/4j6k8Oe

Newfound disappointment: receiving shallow peer reviews that are entirely AI-generated.

The whole point is critical feedback from YOU as a real expert. If reviewers are outsourcing to AI, I think we've lost the plot 🤷‍♀️

As an editor, I'm definitely keeping better track of reviewers I can trust...

Join us in advancing data science and AI research! The Johns Hopkins Data Science and AI Institute Postdoctoral Fellowship Program is now accepting applications for the 2026–2027 academic year. Apply now! Deadline: Jan 23, 2026. Details and apply: apply.interfolio.com/179059

🚀 New preprint!
The Human Cytokine Dictionary - 9.7M cells, 12 donors, 90 cytokines - our largest human single-cell perturbation atlas yet. Users can map cytokine activity in their own data. Huge thanks to Lukas, Sören, Larsen, Parse Bio & Seelig lab!
🔗 www.biorxiv.org/content/10.6...

Hot from the presses!

Laura Sena's @laurasenamd.bsky.social team at at Johns Hopkins working hard to expand the toolkit to treat patients with prostate cancer! Super excited to see out:
doi.org/10.1158/0008...

This study was made possible by the support of the PCF @pcf-science.bsky.social

This study was only made possible with the incredible support of the Prostate Cancer Foundation @pcf-science.bsky.social

Excited to dig into this!!!

The Social Security Administration wants to share your data with the Department of Homeland Security. You might have something to say about that, and if you do, comment here:

https://www.federalregister.gov/documents/2025/11/12/2025-19849/privacy-act-of-1974-system-of-records

q.e.d Science Critical Thinking AI for constructive criticism and science evaluation

Just tried q.e.d. by @odedrechavi.bsky.social et al. with a few papers including by myself & others where I knew a claim within was flawed based on a misunderstanding of the signal.

1) it was impressive. I see what the hype is about.
2) it hallucinated.

www.qedscience.com

Overly long #SciPub🧵 1/n

I love this tool and recommend it to anyone working with single cell data!

This work is the first publication from my lab and I could not be more proud!!!!
/end

Transcriptional shifts in scRNAseq revealed through Missingness OAR (observed at random) score is a measure of transcriptional shifts among cells, allowing cell prioritization for downstream applications. For best results, test a group of similar cells where you e...

We provide lots more details about this in our pre-print and helpful examples on how to run this for yourself in your own data using our package (sanin-lab.github.io/OARscRNA/).
7/n

We also use this method to predict how Dictyostelium discoideum changes their mitochondrial biology to go from an amoeba to multi-cellular aggregates! (Mitochondrial function sensing dye on the right lights up when cells aggregate and mitochondria lower membrane potential).
6/n

UMAP of plasmacytoid DCs showing OAR scores at the top and expression of 3 type I IFN genes and one solute carrier gene at the bottom. High OAR scores are associated with high expression of selected genes.

For example, in these plasmacytoid DCs, the transcriptional shift we detect is because of type I IFN production!
5/n

Diagnostic Test for Realized Missingness in Mixed-type Data - Sankhya B A frequent concern in analyzing incomplete multivariate measurements in mixed categorical and quantitative scales is whether missing completely at random (MCAR) is an appropriate model. Realized MCAR ...

Cells where missing data patterns are not good predictors, score HIGHER because they have transcriptional programs that are different and therefore you should go and study why!
We are borrowing from statistical methods that examine missingness: doi.org/10.1007/s135...
4/n

Missing data patterns are used to group genes within each cell and the distribution of those groupings is examined for homogeneity. A score is calculated based on a statistical test that determines how well the patterns explain gene expression.

2️⃣ We examine how well missing data patterns explain gene expression and derive a score from this result.
3/n

A matrix of raw counts from single cell RNA sequencing data is converted into a binary matrix with 0s and 1s, where patterns of co-expression (also referred to as missing data patterns) are extracted.

An OAR (Observed At Random) score links co-expression patterns and gene expression. A high OAR score indicates a poor prediction (an interesting cell!).
Our method has 2 main steps:
1️⃣ We define a set of co-expression patterns based on zero-counts, which we call missing data patterns.
2/n

Missing data in single-cell transcriptomes reveals transcriptional shifts Profiling thousands of single cell transcriptomes is routine, yet cell prioritization based on response to biological perturbations is challenging and confounded by clustering, normalization and dimen...

🚨 Want to find interesting cells in single-cell RNAseq data independently of clusters? Try our method to identify transcriptional shifts using OAR scores!
Pre-print: doi.org/10.1101/2025...
R tool and tutorials: sanin-lab.github.io/OARscRNA/
@biorxiv-bioinfo.bsky.social
1/n

Regulation of inflammatory responses by pH-dependent transcriptional condensates BRD4 functions as an intracellular pH sensor through a conserved histidine-rich intrinsically disordered region. Inflammation-associated acidification triggers a pH-dependent switch in transcriptional...

Interesting study showing macrophage gene regulation in response to cellular pH changes!

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

Stimulating immune cells in vitro is a common experimental lab model. We profiled 150K blood immune cells treated with 11 different stimuli to compare the effects. The data are freely available for researchers. See the preprint for our findings and to access the data 🧪 doi.org/10.1101/2025...