🚨 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

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...

Meant to mention this last week, but if you have a young person in your life who’s into history or graphic novels or just good books, buy them George Takei’s “They Called Us Enemy.” My oldest couldn’t put it down.

Research Saves Lives At Hopkins, we just went live with an expansive website showing the extraordinary value of research, the impact of cuts to research, what's at stake, resources for our research community, etc. Check it out: researchsaveslives.jhu.edu

This is cool! Electron transport chain imbalance leading to RET and health complications, with evidence in human settings. www.nature.com/articles/s41...

Dream Police alert: InterpolAI for enhanced 3D imaging (CODA, MRI, EM, confocal). Read about and InterpolAI here: www.nature.com/articles/s41...

This is WILD! 85% reduction in NAD+ and the tissue just functions as if nothing had happened!?! NAD depletion in skeletal muscle does not compromise muscle function or accelerate aging: Cell Metabolism www.cell.com/cell-metabol...

Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs github.com/arcInstitute...

The power of data!!! Dispassionately analyzed and meaningfully visualized!!! Just wow!! www.nytimes.com/interactive/...

This integrated method shows how misleading traditional 2D assessments of immune cells localization in tissues is misleading. 3D assessments are a must.

Over the past few decades the world has collectively reduced poverty and disease at an outstanding rate! Collectively, we should continue doing that! There is no other moral position. www.nytimes.com/interactive/...

Thanks to everyone for a fantastic meeting #SACB2025 @cancersysbio.bsky.social (I sure needed an injection of great science in *these times*) @mathcancer.bsky.social closing out the show...

I'm co-organizing a Cell Symposia on Metabolites in Organellar Communication with @robzonculab.bsky.social, Kivanc Birsoy, and Allyson Evans (@cp-cellmetabolism.bsky.social). It will be in Sitges May 11-13. Submit an abstract by Feb 14. Hope to see you in Spain! cell-symposia.com/metabolites-...

The #SACB2025 immunology session closes out with @davidesanin.bsky.social discussing myeloid cell regulation in prostrate cancer

Enjoying day one of #SACB2025! Amazing line up of speakers today!! Good reminder of the amazing communities of scientists using all kinds of tools and working towards helping patients with cancer!

How to get 146% return on investment? The NIH. That's just the economic benefit. Biomedical research promotes human health.

Interesting (and thorough) demonstration that tissue resident macrophages (at least Alveolar ones) can be far from their niche for a VERY long time and still retain their identity when they get back! Also remarkable epigenetic and transcriptional plasticity! Cool paper!!! rdcu.be/d8BBH

Asteroid fragments upend theory of how life on Earth bloomed Samples from Bennu contain the chemical building blocks of life — but with a twist. www.nature.com/articles/d41...

My lab studies how immune cells use the nutrients to effectively combat diseases. We proudly collaborate with a large group of clinicians and other researchers to advance therapies to treat *metastatic prostate cancer*. A terrible disease that kill thousands of men every year. Help us help them!

More than ever, researchers need to explain how they use taxpayer money to provide tangible benefits. I'll start: My lab has developed a completely novel way to make cellular therapies a lot more effective. Our approach shows promising results in pancreatic, ovarian and lung cancer.

Really interesting paper 🧪 🤩 Immune evasion through mitochondrial transfer 😮 Ikeda et al find that #mitochondria from cancer cells can #transfer over to T cells - altering their #metabolism & reducing antitumour immunity www.nature.com/articles/s41... www.nature.com/articles/d41... @nature.com

Exploring Augur!! Such a cool tool to run an unbiased exploration of the effect of a treatment at the single cell level! Also very important discussion around the effect of cell number on the apparent number of DEGs detected! rdcu.be/d64P8

A favorite commission this year, a dividing cell with an extra detail. Colleagues of a retiring researcher commissioned me to add the specific structure she worked on—the spindle pole body—to the sculpture. Here it is close up, in sterling silver embedded in the bronze nuclear membrane. 🔬#SciArt

Stoked to share TWO preprints on mitochondrial pearling! 🎉 We uncover how spontaneous #mitochondria pearling drives #mtDNA nucleoid distribution (doi.org/10.1101/2024...), and @gavsturm.bsky.social et al. dissect the biophysics behind it (doi.org/10.1101/2024...). Details below! 🔬🧵🧪

We were seeing a 98% drop in exposure over on Twitter. The censorship was so extreme we thought it best to start over somewhere else. We chose Bluesky. Help us gain our following back Follow Retweet Repeat Join the park side @altyellonatpark.org

Such a cool paper showing how NAD+ pools interact with one another and how the mitochondrial NAD+ pool is a rheostat for the cell! Incredible tools here! rdcu.be/d3O14

Woo hoo! Our latest neoadjuvant clinical trial results are out! www.cell.com/iscience/ful...

Celebrating Christmas with my lab!

Happy to share an educational case that demonstrates that selection can drive acquired therapy resistance in metastatic prostate cancer rdcu.be/d15Ph Wonderful collab with @rachelkarchin.bsky.social @davidesanin.bsky.social

Really cool paper delving into the way macrophages limit the effectiveness of ICB therapy in prostate cancer!! rdcu.be/d2MPC

A common question nowadays: Which is better, diffusion or flow matching? 🤔 Our answer: They’re two sides of the same coin. We wrote a blog post to show how diffusion models and Gaussian flow matching are equivalent. That’s great: It means you can use them interchangeably.

Hopkins faculty: Need editorial assistance for a proposal or an article? Make use of our services at no charge. Contact my office here: research.jhu.edu/rdt/easi/ Happy writing!

Methods for exploring the geography of molecular-scale processes within tissue samples are transforming cancer research, but the toolbox can be daunting. Read the Nature technology feature. 🧪

Interleukin-1α release during necrotic-like cell death generates myeloid-driven immunosuppression that restricts anti-tumor immunity 🧪 www.cell.com/cancer-cell/...

Will be interesting to find out how IMI (intrinsic molecular identifiers) will perform vs UMI in scRNAseq data! Specially with the issues like dropout and zero-inflation that UMIs correct for! www.biorxiv.org/content/10.1...

Out today in Nature: "The Human Cell Atlas"! In my News and Views, I compare the cell atlas to early naturalists creating an atlas of South America. Researchers mining this cell atlas can now make big discoveries, just as the next naturalists then discovered evolution. www.nature.com/articles/d41...

Would love to build this out!! Let me know if you want to join!

Interested in #singlecell and #spatial #metabolomics? Then book your calendar for December 10th! – Our online, free event will summarize major achievements of the field in 2024. #metabolism #omics #MALDI #EPFL With Giovanni D'Angelo and our #PhD students we prepared for you a fantastic lineup. 🧵 1/5

Elucidating the spatiotemporal dynamics of glucose metabolism with genetically encoded fluorescent biosensors doi.org/10.1016/j.cr...

Post a picture you took (no description) to bring some zen to the timeline

Download our database of 313 different postdoctoral fellowships. For each entry, we provide link to funder, description, amount, deadline, and eligibility criteria (e.g. citizenship). Download our database here: research.jhu.edu/rdt/funding-...

The slide that you insist on keeping even though it'll make your presentation go over time

Excited to announce my move to a new role as Director of @genomescience.bsky.social at University of Maryland starting in Dec! www.medschool.umaryland.edu/news/2024/le...

So cool! Understanding how mtDNA regulates their movement inside cells will be possible with tools like these!