Ethan Armand
@ethan-armand.bsky.social
Bioinformatics PhD Student in the Ren lab at UCSD. Modeling gene regulation across species.
Reposted by Ethan Armand
Last week I released bpnet-lite v0.5.0.
BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch
Try it out with `pip install bpnet-lite`
BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch
Try it out with `pip install bpnet-lite`
June 18, 2025 at 9:48 AM
Last week I released bpnet-lite v0.5.0.
BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch
Try it out with `pip install bpnet-lite`
BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch
Try it out with `pip install bpnet-lite`
Reposted by Ethan Armand
EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!
June 13, 2025 at 4:30 AM
EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!
Reposted by Ethan Armand
Reposted by Ethan Armand
As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...
False positives in study of memory-related gene expression - Nature
Nature - False positives in study of memory-related gene expression
www.nature.com
June 4, 2025 at 5:59 PM
As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...
Reposted by Ethan Armand
Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv
May 27, 2025 at 5:37 PM
Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv
Reposted by Ethan Armand
Yes, it is hard being a data scientist sometimes....
May 25, 2025 at 10:15 PM
Yes, it is hard being a data scientist sometimes....
Reposted by Ethan Armand
One thousand candidate enhancers tested in vivo in the mouse brain! A massive resource and oh so useful as validation set for genome-wide enhancer prediction methods. Super fun to be involved in one of the papers: ‘the prediction challenge paper’ by Nelson&Niklas et al www.cell.com/cell-genomic...
May 21, 2025 at 4:50 PM
One thousand candidate enhancers tested in vivo in the mouse brain! A massive resource and oh so useful as validation set for genome-wide enhancer prediction methods. Super fun to be involved in one of the papers: ‘the prediction challenge paper’ by Nelson&Niklas et al www.cell.com/cell-genomic...
Reposted by Ethan Armand
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature
The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...
www.nature.com
May 7, 2025 at 3:23 PM
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
Reposted by Ethan Armand
Thrilled to share our latest study out in @natureportfolio.nature.com led by the fantastically talented Jing Liu. Our study provides insight into a long standing question in biology: What molecular features make us uniquely human and how do these function? www.nature.com/articles/s41...
A human-specific enhancer fine-tunes radial glia potency and corticogenesis - Nature
HARE5, a human accelerated region enhancer, modulates cortical development by influencing neural progenitor cell behaviour, leading to an enlarged neocortex with increased functional independence betw...
www.nature.com
May 14, 2025 at 4:09 PM
Thrilled to share our latest study out in @natureportfolio.nature.com led by the fantastically talented Jing Liu. Our study provides insight into a long standing question in biology: What molecular features make us uniquely human and how do these function? www.nature.com/articles/s41...
Reposted by Ethan Armand
May 18, 2025 at 2:37 PM
Reposted by Ethan Armand
openRxiv has arrived!
We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...
#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv
We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...
#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv
March 11, 2025 at 1:18 PM
openRxiv has arrived!
We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...
#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv
We’re thrilled to announce the launch of openRxiv as an independent, researcher-led nonprofit to oversee bioRxiv and medRxiv, the world’s leading preprint servers for life and health sciences.
openrxiv.org/introducing-...
#openRxiv #OpenScience #Preprints #bioRxiv #medRxiv
Reposted by Ethan Armand
personally would like to see every store show what part of the price increase is due to tariffs bc if these tariffs ever come down, i need to see that price go right back down
April 29, 2025 at 6:48 PM
personally would like to see every store show what part of the price increase is due to tariffs bc if these tariffs ever come down, i need to see that price go right back down
Reposted by Ethan Armand
🚨 Practical URGENT tip for NSF grantees:
Out of an abundance of caution, I would right now go into Research.gov and…
1. Download your NSF award letters.
2. Print PDF your annual reports.
3. Screenshot the status table for annual reports.
NSF is planning maintenance tomorrow to Research.gov
Out of an abundance of caution, I would right now go into Research.gov and…
1. Download your NSF award letters.
2. Print PDF your annual reports.
3. Screenshot the status table for annual reports.
NSF is planning maintenance tomorrow to Research.gov
April 24, 2025 at 9:32 PM
🚨 Practical URGENT tip for NSF grantees:
Out of an abundance of caution, I would right now go into Research.gov and…
1. Download your NSF award letters.
2. Print PDF your annual reports.
3. Screenshot the status table for annual reports.
NSF is planning maintenance tomorrow to Research.gov
Out of an abundance of caution, I would right now go into Research.gov and…
1. Download your NSF award letters.
2. Print PDF your annual reports.
3. Screenshot the status table for annual reports.
NSF is planning maintenance tomorrow to Research.gov
Reposted by Ethan Armand
genomebiology.biomedcentral.com/articles/10....
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Zero-shot evaluation reveals limitations of single-cell foundation models - Genome Biology
Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode...
genomebiology.biomedcentral.com
April 20, 2025 at 4:14 PM
genomebiology.biomedcentral.com/articles/10....
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Reposted by Ethan Armand
Colours correspond to infinite-dimensional vectors, since there are infinitely many wavelengths of light.
But humans can only perceive a three-dimensional projection of colour (red, green, & blue).
What's interesting is that it's *not* an orthogonal projection. Here's a plot of the basis vectors.
But humans can only perceive a three-dimensional projection of colour (red, green, & blue).
What's interesting is that it's *not* an orthogonal projection. Here's a plot of the basis vectors.
April 19, 2025 at 10:12 PM
Colours correspond to infinite-dimensional vectors, since there are infinitely many wavelengths of light.
But humans can only perceive a three-dimensional projection of colour (red, green, & blue).
What's interesting is that it's *not* an orthogonal projection. Here's a plot of the basis vectors.
But humans can only perceive a three-dimensional projection of colour (red, green, & blue).
What's interesting is that it's *not* an orthogonal projection. Here's a plot of the basis vectors.
Reposted by Ethan Armand
I am elated to share that our manuscript describing Variant-EFFECTS, a high-throughput technology we developed to precisely and quantitatively measure the effects of CRISPR-mediated edits on gene expression, is now published at @cellpress.bsky.social: authors.elsevier.com/c/1kxgiL7PXu...
authors.elsevier.com
April 17, 2025 at 6:20 PM
I am elated to share that our manuscript describing Variant-EFFECTS, a high-throughput technology we developed to precisely and quantitatively measure the effects of CRISPR-mediated edits on gene expression, is now published at @cellpress.bsky.social: authors.elsevier.com/c/1kxgiL7PXu...
Reposted by Ethan Armand
Just a gentle reminder that deceptive hyping in scientific publications (which includes preprints) is actually antithetical to the core mission of the scientific process. We can stay grounded, truthful, humble while being ambitious. Revealing caveats, pitfalls & limitations speeds up progress.
April 8, 2025 at 9:03 AM
Just a gentle reminder that deceptive hyping in scientific publications (which includes preprints) is actually antithetical to the core mission of the scientific process. We can stay grounded, truthful, humble while being ambitious. Revealing caveats, pitfalls & limitations speeds up progress.
Reposted by Ethan Armand
NEW: The Trump administration swiftly cancelled dozens of international student visas Friday at Stanford and University of California campuses, including UCLA, UC Berkeley and UC San Diego. One UC San Diego student was taken into custody at the border for deportation: www.latimes.com/california/s...
Trump administration cancels more than a dozen international student visas at University of California, Stanford
Amid a national sweep over student visas that has hit colleges across the U.S., the Trump administration on Friday canceled more than a dozen international student visas at the University of Californi...
www.latimes.com
April 5, 2025 at 9:02 PM
NEW: The Trump administration swiftly cancelled dozens of international student visas Friday at Stanford and University of California campuses, including UCLA, UC Berkeley and UC San Diego. One UC San Diego student was taken into custody at the border for deportation: www.latimes.com/california/s...
Reposted by Ethan Armand
We identify evidence of off-target probe binding in the 10x Genomics #Xenium v1 Human Breast Gene Expression Panel, compromising the accuracy of resulting #singlecell #spatialtranscriptomics profiles
See our preprint for more details: www.biorxiv.org/content/10.1...
#AcademicSky
🧵👇 1/n
See our preprint for more details: www.biorxiv.org/content/10.1...
#AcademicSky
🧵👇 1/n
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling
The accuracy of spatial gene expression profiles generated by probe-based in situ spatially-resolved transcriptomic technologies depends on the specificity with which probes bind to their intended tar...
www.biorxiv.org
April 3, 2025 at 3:35 PM
We identify evidence of off-target probe binding in the 10x Genomics #Xenium v1 Human Breast Gene Expression Panel, compromising the accuracy of resulting #singlecell #spatialtranscriptomics profiles
See our preprint for more details: www.biorxiv.org/content/10.1...
#AcademicSky
🧵👇 1/n
See our preprint for more details: www.biorxiv.org/content/10.1...
#AcademicSky
🧵👇 1/n
Reposted by Ethan Armand
Thank you for sharing news of our initiative... we are an interdisciplinary team of researchers from U of Maryland, UPenn, and Georgia Tech + more whose aim is to communicate the impacts of federal cuts on science and health research nationwide. Full explainer thread here:
bsky.app/profile/josh...
bsky.app/profile/josh...
March 29, 2025 at 10:10 PM
Thank you for sharing news of our initiative... we are an interdisciplinary team of researchers from U of Maryland, UPenn, and Georgia Tech + more whose aim is to communicate the impacts of federal cuts on science and health research nationwide. Full explainer thread here:
bsky.app/profile/josh...
bsky.app/profile/josh...
Reposted by Ethan Armand
Celebrating 10 years of our lab with a new preprint:
www.biorxiv.org/content/10.1...
How does enhancer location within a TAD control transcriptional bursts from a cognate promoter?
Experiments by Jana Tünnermann and modelling by Gregory Roth
www.biorxiv.org/content/10.1...
How does enhancer location within a TAD control transcriptional bursts from a cognate promoter?
Experiments by Jana Tünnermann and modelling by Gregory Roth
March 29, 2025 at 12:46 PM
Celebrating 10 years of our lab with a new preprint:
www.biorxiv.org/content/10.1...
How does enhancer location within a TAD control transcriptional bursts from a cognate promoter?
Experiments by Jana Tünnermann and modelling by Gregory Roth
www.biorxiv.org/content/10.1...
How does enhancer location within a TAD control transcriptional bursts from a cognate promoter?
Experiments by Jana Tünnermann and modelling by Gregory Roth
Reposted by Ethan Armand
ATTENTION:
Do you or someone you know get fired or have a job offer rescinded because of uncertainty due to the NIH funding freeze?
Please DM me!
THANK YOU!
Do you or someone you know get fired or have a job offer rescinded because of uncertainty due to the NIH funding freeze?
Please DM me!
THANK YOU!
a yellow piece of paper is laying on a brown background
ALT: a yellow piece of paper is laying on a brown background
media.tenor.com
March 19, 2025 at 7:06 PM
ATTENTION:
Do you or someone you know get fired or have a job offer rescinded because of uncertainty due to the NIH funding freeze?
Please DM me!
THANK YOU!
Do you or someone you know get fired or have a job offer rescinded because of uncertainty due to the NIH funding freeze?
Please DM me!
THANK YOU!
Reposted by Ethan Armand
Fantastic study and collaboration led by stellar postdoc @ioansarr.bsky.social, it was a pleasure to host you in the lab (& thanks to @embo.org for the visiting fellowship)
How does gene regulation shape brain evolution? Our new preprint dives into this question in the context of mammalian cerebellum development! rb.gy/dbcxjz
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
March 16, 2025 at 12:55 PM
Fantastic study and collaboration led by stellar postdoc @ioansarr.bsky.social, it was a pleasure to host you in the lab (& thanks to @embo.org for the visiting fellowship)
Reposted by Ethan Armand
How does gene regulation shape brain evolution? Our new preprint dives into this question in the context of mammalian cerebellum development! rb.gy/dbcxjz
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
March 16, 2025 at 10:31 AM
How does gene regulation shape brain evolution? Our new preprint dives into this question in the context of mammalian cerebellum development! rb.gy/dbcxjz
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
Led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social
Reposted by Ethan Armand
Bluetorial: Metal regulation, an unexpected connection, and a deep evolutionary insight
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
December 31, 2024 at 1:09 PM
Bluetorial: Metal regulation, an unexpected connection, and a deep evolutionary insight