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
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...
Reposted by David E Sanin
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...
github.com/arcInstitute...
GitHub - ArcInstitute/xsra: An efficient CLI to extract sequences from the SRA
An efficient CLI to extract sequences from the SRA - ArcInstitute/xsra
github.com
April 29, 2025 at 9:03 PM
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...
github.com/arcInstitute...
The power of data!!! Dispassionately analyzed and meaningfully visualized!!!
Just wow!!
www.nytimes.com/interactive/...
Just wow!!
www.nytimes.com/interactive/...
Opinion | To Understand Global Migration, You Have to See It First (Gift Article)
These estimates, drawn from the location data of three billion Facebook users, provide a view of human migration in extraordinary detail.
www.nytimes.com
April 17, 2025 at 4:34 PM
The power of data!!! Dispassionately analyzed and meaningfully visualized!!!
Just wow!!
www.nytimes.com/interactive/...
Just wow!!
www.nytimes.com/interactive/...
Reposted by David E Sanin
Reposted by David E Sanin
This integrated method shows how misleading traditional 2D assessments of immune cells localization in tissues is misleading.
3D assessments are a must.
3D assessments are a must.
New paper from the lab: Integration of nuclear morphology and 3D imaging to profile cellular neighborhoods
Read it here: www.biorxiv.org/content/10.1...
Read it here: www.biorxiv.org/content/10.1...
April 4, 2025 at 1:38 PM
This integrated method shows how misleading traditional 2D assessments of immune cells localization in tissues is misleading.
3D assessments are a must.
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/...
www.nytimes.com/interactive/...
Opinion | Musk Said No One Has Died Since Aid Was Cut. That Isn’t True. (Gift Article)
A journey through the front lines of global poverty shows that when the world’s richest men slash aid for the world’s poorest children, the result is sickness, starvation and death.
www.nytimes.com
March 16, 2025 at 2:06 AM
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/...
www.nytimes.com/interactive/...
Reposted by David E Sanin
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 sure needed an injection of great science in *these times*)
@mathcancer.bsky.social closing out the show...
February 12, 2025 at 7:11 PM
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 sure needed an injection of great science in *these times*)
@mathcancer.bsky.social closing out the show...
Reposted by David E Sanin
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-...
Home – Cell Symposia: Metabolites: organellar communication in health and disease
Cell Symposia: Metabolites: organellar communication in health and disease
cell-symposia.com
February 12, 2025 at 9:04 PM
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-...
Reposted by David E Sanin
The #SACB2025 immunology session closes out with @davidesanin.bsky.social discussing myeloid cell regulation in prostrate cancer
February 11, 2025 at 5:31 PM
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!
February 11, 2025 at 2:39 AM
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!
Reposted by David E Sanin
How to get 146% return on investment?
The NIH. That's just the economic benefit.
Biomedical research promotes human health.
The NIH. That's just the economic benefit.
Biomedical research promotes human health.
February 10, 2025 at 5:27 PM
How to get 146% return on investment?
The NIH. That's just the economic benefit.
Biomedical research promotes human health.
The NIH. That's just the economic benefit.
Biomedical research promotes human health.
Reposted by David E Sanin
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
rdcu.be/d8BBH
Long-term culture-expanded alveolar macrophages restore their full epigenetic identity after transfer in vivo
Nature Immunology - Sieweke and colleagues show that alveolar macrophages maintain a core gene expression program even after several months in culture and reacquire full transcriptional and...
rdcu.be
February 4, 2025 at 7:27 PM
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
rdcu.be/d8BBH
Reposted by David E Sanin
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...
Samples from Bennu contain the chemical building blocks of life — but with a twist.
www.nature.com/articles/d41...
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
February 2, 2025 at 1:24 AM
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...
Samples from Bennu contain the chemical building blocks of life — but with a twist.
www.nature.com/articles/d41...