Sean Simmons
@seankenneths.bsky.social
Computational biologist at the Broad Institute
Reposted by Sean Simmons
I really hate it when scientists keep saying that “we need to rebuild trust in science,” because it implies that scientists are to blame for the mistrust rather than the millions of dollars of dark money that have funded political attacks on science in order to advance a far right agenda.
November 19, 2025 at 9:48 PM
I really hate it when scientists keep saying that “we need to rebuild trust in science,” because it implies that scientists are to blame for the mistrust rather than the millions of dollars of dark money that have funded political attacks on science in order to advance a far right agenda.
Reposted by Sean Simmons
This is functionally a robbery of New York City and New York State taxpayers, who contribute billions more to the federal government annually than we get back.
Stealing our money, blocking our bus lanes.
Stealing our money, blocking our bus lanes.
NEW: White House announces it's going to pause, and potentially cancel, $11 billion in infrastructure funding (via the Army Corps of Engineers), specifically citing cities, like New York, represented or led by Democrats. More to come.
October 17, 2025 at 6:44 PM
This is functionally a robbery of New York City and New York State taxpayers, who contribute billions more to the federal government annually than we get back.
Stealing our money, blocking our bus lanes.
Stealing our money, blocking our bus lanes.
Reposted by Sean Simmons
"In this review, we provide a comprehensive overview of the clinical features, disease course and management of AYA patients with MPN and, in doing so, highlight key characteristics that distinguish them from their older counterparts."
onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com/doi/10.1111/...
Myeloproliferative neoplasms in the adolescent and young adult population: A comprehensive review of the literature
Adolescents and young adults (AYA) with myeloproliferative neoplasms (MPN) demonstrate notable differences compared to older patients with MPN. With the most common MPN in this group being essential ....
onlinelibrary.wiley.com
September 10, 2025 at 6:30 PM
"In this review, we provide a comprehensive overview of the clinical features, disease course and management of AYA patients with MPN and, in doing so, highlight key characteristics that distinguish them from their older counterparts."
onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Sean Simmons
"Sweeteners can harm cognitive health equivalent to 1.6 years of ageing, study finds"
Or does it? Let's take a look at this "study"...
www.theguardian.com/food/2025/se...
Or does it? Let's take a look at this "study"...
www.theguardian.com/food/2025/se...
Sweeteners can harm cognitive health equivalent to 1.6 years of ageing, study finds
Researchers say low- and no-calorie sweeteners appear to affect thinking and memory in middle age
www.theguardian.com
September 5, 2025 at 4:46 PM
"Sweeteners can harm cognitive health equivalent to 1.6 years of ageing, study finds"
Or does it? Let's take a look at this "study"...
www.theguardian.com/food/2025/se...
Or does it? Let's take a look at this "study"...
www.theguardian.com/food/2025/se...
Reposted by Sean Simmons
Last week, I talked to a DC-based PhD student who told me she's now afraid to leave her house after dark. Not because of any crime threat, but because of all the federal agents swarming her neighborhood.
More proof Trump is bad for business: restaurant reservations fell by 30 percent during Trump's occupation of Washington DC
August 17, 2025 at 10:20 PM
Last week, I talked to a DC-based PhD student who told me she's now afraid to leave her house after dark. Not because of any crime threat, but because of all the federal agents swarming her neighborhood.
Reposted by Sean Simmons
Shortcomings of silhouette in single-cell integration benchmarking - @uweohler.bsky.social @prauten.bsky.social @mdc-bimsb.bsky.social @mdc-berlin.bsky.social @humboldtuni.bsky.social go.nature.com/4fcQzZr
Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology
Silhouette score is unsuitable as a metric for single-cell data integration.
go.nature.com
July 30, 2025 at 3:26 PM
Shortcomings of silhouette in single-cell integration benchmarking - @uweohler.bsky.social @prauten.bsky.social @mdc-bimsb.bsky.social @mdc-berlin.bsky.social @humboldtuni.bsky.social go.nature.com/4fcQzZr
Reposted by Sean Simmons
Well this is bad. Google is indexing ChatGPT conversations exposing sensitive user data
I tried a few quick searches. I found someone's chat where I can see their api key
I found some building their resume. Their name, email and phone numbers are exposed.
www.fastcompany.com/91376687/goo...
I tried a few quick searches. I found someone's chat where I can see their api key
I found some building their resume. Their name, email and phone numbers are exposed.
www.fastcompany.com/91376687/goo...
Exclusive: Google is indexing ChatGPT conversations, potentially exposing sensitive user data
Thousands of shared ChatGPT chats are now appearing in Google search results.
www.fastcompany.com
July 31, 2025 at 8:59 PM
Well this is bad. Google is indexing ChatGPT conversations exposing sensitive user data
I tried a few quick searches. I found someone's chat where I can see their api key
I found some building their resume. Their name, email and phone numbers are exposed.
www.fastcompany.com/91376687/goo...
I tried a few quick searches. I found someone's chat where I can see their api key
I found some building their resume. Their name, email and phone numbers are exposed.
www.fastcompany.com/91376687/goo...
Reposted by Sean Simmons
AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done.
clauswilke.substack.com/p/no-alphafo...
clauswilke.substack.com/p/no-alphafo...
No, AlphaFold has not completely solved protein folding
Biology is hard. Yes, even for AI.
clauswilke.substack.com
July 12, 2025 at 6:19 PM
AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done.
clauswilke.substack.com/p/no-alphafo...
clauswilke.substack.com/p/no-alphafo...
Reposted by Sean Simmons
Glad I'm not the only one observing the irony of tech billionaires handing out science prizes while backing an admin that has dismantled American science. New level of #respect for Seth Rogan
Seth Rogen goes rogue at science awards show to slam tech billionaires for backing Trump: 'It's amazing how much good science you can destroy with $320 million and RFK Jr'
You invite Seth Rogen on stage, you take your chances, as the scientific community recently discovered.
www.pcgamer.com
April 17, 2025 at 1:29 AM
Glad I'm not the only one observing the irony of tech billionaires handing out science prizes while backing an admin that has dismantled American science. New level of #respect for Seth Rogan
Has anyone else been having issues accessing papers on biorxiv?
April 14, 2025 at 5:29 PM
Has anyone else been having issues accessing papers on biorxiv?
Reposted by Sean Simmons
More in No, Other People:
New poll:
“America would be better off if more people worked in manufacturing.”
• 80% of Americans agree
• 20% disagree
“I would be better off if I worked in a factory.”
• 25% of Americans agree
• 73% disagree
• 2% currently work in a factory
New poll:
“America would be better off if more people worked in manufacturing.”
• 80% of Americans agree
• 20% disagree
“I would be better off if I worked in a factory.”
• 25% of Americans agree
• 73% disagree
• 2% currently work in a factory
April 13, 2025 at 5:06 PM
More in No, Other People:
New poll:
“America would be better off if more people worked in manufacturing.”
• 80% of Americans agree
• 20% disagree
“I would be better off if I worked in a factory.”
• 25% of Americans agree
• 73% disagree
• 2% currently work in a factory
New poll:
“America would be better off if more people worked in manufacturing.”
• 80% of Americans agree
• 20% disagree
“I would be better off if I worked in a factory.”
• 25% of Americans agree
• 73% disagree
• 2% currently work in a factory
Reposted by Sean Simmons
Marco Rubio just announced 10 more people were sent to be imprisoned in CECOT. They were flown there from Gitmo to be imprisoned potentially for life based not on any crime for which they were convicted, but on unproven allegations of gang membership with no due process.
This is not lawful.
This is not lawful.
April 13, 2025 at 4:16 PM
Marco Rubio just announced 10 more people were sent to be imprisoned in CECOT. They were flown there from Gitmo to be imprisoned potentially for life based not on any crime for which they were convicted, but on unproven allegations of gang membership with no due process.
This is not lawful.
This is not lawful.
Reposted by Sean Simmons
Booker: "This isn't just about Mr. Garcia. This is about every American understanding that this president is making an assault on the due process rights that are afforded to people in our country ... you cannot disappear people off American streets."
April 13, 2025 at 2:40 PM
Booker: "This isn't just about Mr. Garcia. This is about every American understanding that this president is making an assault on the due process rights that are afforded to people in our country ... you cannot disappear people off American streets."
Reposted by Sean Simmons
Making my inaugural Bluesky post to share my latest preprint! Here, we meta-analyzed #brain #transcriptomic data from seven #schizophrenia associated mouse mutant models in order to find convergence at the molecular level. Check out our findings here!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
April 2, 2025 at 3:13 PM
Making my inaugural Bluesky post to share my latest preprint! Here, we meta-analyzed #brain #transcriptomic data from seven #schizophrenia associated mouse mutant models in order to find convergence at the molecular level. Check out our findings here!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sean Simmons
🚀 New Preprint Alert! 🚀 With the Standards and Technology Working Group of the @humancellatlas.org, we present a new preprint guiding multimodal #singlecell data integration and human organ atlas generation! 📄
Read the preprint: www.biorxiv.org/content/10.1...
Read the preprint: www.biorxiv.org/content/10.1...
Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas.
The integration of multimodal single-cell data enables comprehensive organ reference atlases, yet its impact remains largely unexplored, particularly in complex tissues. We generated a benchmarking da...
www.biorxiv.org
March 7, 2025 at 9:54 AM
🚀 New Preprint Alert! 🚀 With the Standards and Technology Working Group of the @humancellatlas.org, we present a new preprint guiding multimodal #singlecell data integration and human organ atlas generation! 📄
Read the preprint: www.biorxiv.org/content/10.1...
Read the preprint: www.biorxiv.org/content/10.1...
Reposted by Sean Simmons
In our updated TraitGym preprint (w/ @gonzalobenegas.bsky.social & Gökcen Eraslan), we evaluate Evo 2 on regulatory variants associated with human traits. We see marked performance gains with scale on Mendelian traits, although still a bit behind alignment-based methods.
doi.org/10.1101/2025...
1/n
doi.org/10.1101/2025...
1/n
March 4, 2025 at 7:54 PM
In our updated TraitGym preprint (w/ @gonzalobenegas.bsky.social & Gökcen Eraslan), we evaluate Evo 2 on regulatory variants associated with human traits. We see marked performance gains with scale on Mendelian traits, although still a bit behind alignment-based methods.
doi.org/10.1101/2025...
1/n
doi.org/10.1101/2025...
1/n
Reposted by Sean Simmons
I really enjoyed my visit with @noorpratap.bsky.social to the Schmidt Center at the Broad Institute yesterday. Thanks especially to our host Tavor Baharav. The MIA seminar is a great resource, and you can find Noor's and my talks here:
youtu.be/cAJNqu50YkM?...
youtu.be/cAJNqu50YkM?...
MIA: Noor Pratap Singh, RNA-Seq data using a tree-based framework; Primer: Rob Patro
YouTube video by Broad Institute
youtu.be
February 27, 2025 at 6:30 PM
I really enjoyed my visit with @noorpratap.bsky.social to the Schmidt Center at the Broad Institute yesterday. Thanks especially to our host Tavor Baharav. The MIA seminar is a great resource, and you can find Noor's and my talks here:
youtu.be/cAJNqu50YkM?...
youtu.be/cAJNqu50YkM?...
Reposted by Sean Simmons
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
February 12, 2025 at 11:41 AM
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Sean Simmons
One of the reasons Horror is such an important genre right now — besides the fact that reality is a horror show — is that it’s a genre where people still regularly manage to make original and interesting films and increasingly that’s just not true about filmmaking in general
January 27, 2025 at 2:23 AM
One of the reasons Horror is such an important genre right now — besides the fact that reality is a horror show — is that it’s a genre where people still regularly manage to make original and interesting films and increasingly that’s just not true about filmmaking in general
Reposted by Sean Simmons
A month ago we @vevotherapeutics.bsky.social announced that we have generated the largest single-cell perturbation atlas in history, Tahoe-100M. Today, we announce that we will fully open-source Tahoe-100M in Feb, as part of a collaboration with NVidia health to train cell state models.
January 13, 2025 at 4:23 PM
A month ago we @vevotherapeutics.bsky.social announced that we have generated the largest single-cell perturbation atlas in history, Tahoe-100M. Today, we announce that we will fully open-source Tahoe-100M in Feb, as part of a collaboration with NVidia health to train cell state models.
Reposted by Sean Simmons
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics
Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...
www.nature.com
January 8, 2025 at 1:30 PM
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Sean Simmons
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Single cell – ENCODEHomo sapiens clickable body map
www.encodeproject.org
January 7, 2025 at 9:29 PM
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Reposted by Sean Simmons
Just in time for Christmas, a new release of simpleaf! This is a big one (0.18.0). Now simpleaf has an atac sub-command to handle scATAC-seq preprocessing with alevin-fry-atac! 1/5
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment
Ultrafast mapping of short reads to transcriptomic and metagenomic references via lightweight mapping techniques such as pseudoalignment has demonstrated success in substantially accelerating several ...
www.biorxiv.org
December 24, 2024 at 2:58 PM
Just in time for Christmas, a new release of simpleaf! This is a big one (0.18.0). Now simpleaf has an atac sub-command to handle scATAC-seq preprocessing with alevin-fry-atac! 1/5
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sean Simmons
A scientist's perspective on why this is a terrible article. A summary - a woman with a rare mutation that puts her at risk of a severe, untreatable, degenerative disease. She has dedicated her live to supporting the science to find a solution. Left there, it is a beautiful piece. 1/
(gift link)
(gift link)
A Woman With a Rare Gene Mutation Fights to Avoid Her Mother’s Fate (Gift Article)
A mutant gene is coming to steal Linde Jacobs’s mind. Can she find a way to stop it?
www.nytimes.com
December 22, 2024 at 3:10 PM
A scientist's perspective on why this is a terrible article. A summary - a woman with a rare mutation that puts her at risk of a severe, untreatable, degenerative disease. She has dedicated her live to supporting the science to find a solution. Left there, it is a beautiful piece. 1/
(gift link)
(gift link)
Reposted by Sean Simmons
Preprint + Xmas present from Maria Herrero, a gifted postdoc in my research group, working with colleagues in Søren Brunak's group - "Clinical + Biological Stratification in 121,560 Antidepressant Prescription Trajectories using Unsupervised Modelling and Clustering" www.medrxiv.org/content/10.1...
Clinical and Biological Stratification in 121,560 Antidepressant Prescription Trajectories using Unsupervised Modelling and Clustering
Major depressive disorder is a complex condition with diverse presentations and polygenic underpinnings. Leveraging large biobanks linked to primary care prescription data, we developed a data-driven ...
www.medrxiv.org
December 21, 2024 at 3:35 PM
Preprint + Xmas present from Maria Herrero, a gifted postdoc in my research group, working with colleagues in Søren Brunak's group - "Clinical + Biological Stratification in 121,560 Antidepressant Prescription Trajectories using Unsupervised Modelling and Clustering" www.medrxiv.org/content/10.1...