Sean Simmons

Exclusive: Google is indexing ChatGPT conversations, potentially exposing sensitive user data Thousands of shared ChatGPT chats are now appearing in Google search results.

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...

No, AlphaFold has not completely solved protein folding Biology is hard. Yes, even for AI.

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...

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?

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

Rubio on X: Last night, another 10 criminals from the MS-13 and Tren de Aragua Foreign Terrorist Organizations arrived in El Salvador.  The alliance between @POTUS and President @nayibbukele has become an example for security and prosperity in our hemisphere.

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.

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."

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...

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...

🚀 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...

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

YouTube video by Broad Institute MIA: Noor Pratap Singh, RNA-Seq data using a tree-based framework; Primer: Rob Patro

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?...

Just rewatched Arcane on Netflix, highly recommend if you haven't seen it, way better than one would think based on the 'source' material...

Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.

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...

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

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.

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...

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...

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/...

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 ...

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...

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?

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)

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 ...

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...

Excited to share our lab's first preprint: we used spatial transcriptomics to dissect how aging disrupts the cycling ovary! 🧵

This was an incredible team effort w/ @jennifergarrison.bsky.social #TammyLan @davidsebfischer.bsky.social #AlisonKochersberger #RuthRaichur #SophiaSzady

Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/

scRNA-seq data sets exploding in number and size - check out scanpy & anndata for >1b cells: new experimental update includes APIs for scaling with dask from anndata, integrated with lots of scanpy and rapids-singlecell functions.
gist.github.com/ilan-gold/98...

Caritas in a pot with utensils

That was us last week, highly recommend!

Selective targeting of mutated calreticulin by the monoclonal antibody INCA033989 inhibits oncogenic function of MPN Key PointsWe describe the characterization of INCA033989, a monoclonal antibody that potently and selectively targets mutCALR-positive MPN cells.Data show

Congrats to all involved in this study of a monoclonal antibody targeting mutant CALR in #MPN, first presented at #ASH23, this mAb is now in a phase 1 multicenter clinical trial, open at Stanford #Hematology @stanforddeptmed.bsky.social @bloodjournal.bsky.social
ashpublications.org/blood/articl...

*than, gotta love typos

Promising. Going from Seurat to Scanpy and back has always been a pain, we have some work arounds but hope this is more reliable (so many of the current packages that claim to do it just crash more often then not)....

Part of the reason this is promising--our data is ATAC and RNA so using the same ecosystem for both would be great. Also, an excuse to finally try alevin-fry (has been on my list for years....)

Yeah! Have used sinto before and chromap is on my list, just excited to have another option as well!

Exciting, congrats! Perfect timing for us, I was just looking for non-CellRanger scATAC pipeline options earlier this week! Will have to give it a try....