David E Sanin
@davidesanin.bsky.social
Assistant Professor at Johns Hopkins University and macrophage enthusiast! | he/him 🏳️🌈
Opinions are my own!
https://linktr.ee/davidesanin
Opinions are my own!
https://linktr.ee/davidesanin
Pinned
David E Sanin
@davidesanin.bsky.social
· Aug 22
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...
doi.org
🚨 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
Pre-print: doi.org/10.1101/2025...
R tool and tutorials: sanin-lab.github.io/OARscRNA/
@biorxiv-bioinfo.bsky.social
1/n
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
rdcu.be/e3xOV
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...
rdcu.be
February 11, 2026 at 8:48 PM
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
rdcu.be/e3xOV
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
Super excited to see this story published after a ton of work!
rdcu.be/e3wKe
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.
rdcu.be
February 11, 2026 at 5:58 PM
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
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!
An ion mobility-resolved mass cytometry method enables multidimensional metabolomic profiling of single cells.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometry - Nature Methods
An ion mobility-resolved mass cytometry method for single-cell metabolomics enables multidimensional metabolomic profiling. The approach was used to curate a metabolic single-cell atlas containing 45,...
www.nature.com
February 11, 2026 at 5:52 PM
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.
☕ @karsten-rippe.bsky.social & co analyse #chromatin accessibility to identify sites that open simultaneously in response to TNF. They discover 2 distinct types of co-accessible regulatory module for controlling the induction of #proinflammatory gene expression.
👉https://rdcu.be/e2WwS
bit.ly/3MiB4oH
👉https://rdcu.be/e2WwS
bit.ly/3MiB4oH
Two distinct chromatin modules regulate proinflammatory gene expression - Nature Cell Biology
Seufert et al. analyse chromatin accessibility to identify sites that open simultaneously in response to TNF. They discover two distinct types of co-accessible regulatory module for controlling the in...
bit.ly
February 8, 2026 at 3:42 PM
Looking forward to reading this!! Always fascinating how cells fine tune responses to common cytokines.
Reposted by David E Sanin
Reposted by David E Sanin
Holy smokes
We've got ISSUES. Literally.
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
January 13, 2026 at 9:59 AM
Holy smokes
Reposted by David E Sanin
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/
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/
January 13, 2026 at 3:10 PM
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/
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/
Reposted by David E Sanin
January 13, 2026 at 4:56 PM
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
bit.ly
January 12, 2026 at 5:48 PM
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
Reposted by David E Sanin
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...
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...
January 11, 2026 at 9:07 PM
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...
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...
Reposted by David E Sanin
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
December 19, 2025 at 1:29 PM
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
Reposted by David E Sanin
🚀 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...
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...
December 15, 2025 at 10:42 PM
🚀 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...
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
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
Androgen receptor drives polyamine synthesis creating a vulnerability for prostate cancer
Abstract. Supraphysiological androgen (SPA) treatment can paradoxically restrict growth of castration-resistant prostate cancer with high androgen receptor (AR) activity, which is the basis for use of...
doi.org
November 25, 2025 at 3:26 PM
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
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
Excited to dig into this!!!
☕Liu et al. present TemporalVAE, a method for integrating single-cell time course data. The model proposes a workflow to determine the biological timing of samples and its temporally sensitive genes, enabling single-cell developmental stage inference.
👉https://rdcu.be/eP9HH
bit.ly/49VARB8
👉https://rdcu.be/eP9HH
bit.ly/49VARB8
TemporalVAE: atlas-assisted temporal mapping of time-series single-cell transcriptomes during embryogenesis - Nature Cell Biology
Liu et al. present TemporalVAE, a method for integrating single-cell time course data. The model proposes a workflow to determine the biological timing of samples and its temporally sensitive genes, e...
bit.ly
November 17, 2025 at 5:13 AM
Excited to dig into this!!!
Reposted by David E Sanin
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
https://www.federalregister.gov/documents/2025/11/12/2025-19849/privacy-act-of-1974-system-of-records
November 13, 2025 at 8:50 PM
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
https://www.federalregister.gov/documents/2025/11/12/2025-19849/privacy-act-of-1974-system-of-records
Reposted by David E Sanin
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
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
www.qedscience.com
November 1, 2025 at 12:15 PM
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
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n
🚨 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
Pre-print: doi.org/10.1101/2025...
R tool and tutorials: sanin-lab.github.io/OARscRNA/
@biorxiv-bioinfo.bsky.social
1/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...
doi.org
August 22, 2025 at 2:11 AM
🚨 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
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...
www.cell.com/cell/fulltex...
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...
www.cell.com
July 20, 2025 at 2:59 PM
Interesting study showing macrophage gene regulation in response to cellular pH changes!
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by David E Sanin
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...
July 3, 2025 at 3:39 PM
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...
Reposted by David E Sanin
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.
June 21, 2025 at 7:45 PM
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.
Reposted by David E Sanin
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
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
June 2, 2025 at 9:24 PM
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
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...
www.nature.com/articles/s41...
CoQ imbalance drives reverse electron transport to disrupt liver metabolism - Nature
Reverse electron transport is the mechanism behind excess mitochondrial reactive oxygen species in the livers of obese mice, which has implications for developing therapeutics for fatty liver dis...
www.nature.com
May 29, 2025 at 5:47 PM
This is cool! Electron transport chain imbalance leading to RET and health complications, with evidence in human settings.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by David E Sanin
Dream Police alert: InterpolAI for enhanced 3D imaging (CODA, MRI, EM, confocal).
Read about and InterpolAI here: www.nature.com/articles/s41...
Read about and InterpolAI here: www.nature.com/articles/s41...
InterpolAI: deep learning-based optical flow interpolation and restoration of biomedical images for improved 3D tissue mapping
Nature Methods - InterpolAI leverages optimal flow-based artificial intelligence to produce synthetic images between pairs of images for diverse three-dimensional image types. InterpolAI is more...
www.nature.com
May 28, 2025 at 11:42 AM
Dream Police alert: InterpolAI for enhanced 3D imaging (CODA, MRI, EM, confocal).
Read about and InterpolAI here: www.nature.com/articles/s41...
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...
NAD depletion in skeletal muscle does not compromise muscle function or accelerate aging: Cell Metabolism www.cell.com/cell-metabol...
NAD depletion in skeletal muscle does not compromise muscle function or accelerate aging
NAD depletion in skeletal muscle does not impair tissue integrity and function or
accelerate aging, as shown in a mouse model with an 85% decrease in muscle NAD+ levels.
Muscle structure, metabolism, ...
www.cell.com
May 2, 2025 at 9:39 PM
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...
NAD depletion in skeletal muscle does not compromise muscle function or accelerate aging: Cell Metabolism www.cell.com/cell-metabol...