The MOSAIC paper is out in Nature Methods. For the record I went after this paper for *years* and was so happy when they sent it to me/us. www.nature.com/articles/s41...

Reptiles with longer Wikipedia pages tend to be bigger. The relationship is a power law with exponent = 0.85. I guess humans really like writing about big lizards? The longest article is the Komodo Dragon.

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

The old internet still exists y'all neocities.org

before the internet was a corporate hellscape it was built by ordinary people! the slop was wacky and homemade just like mom (and David) used to make. alas the good old days are over but I can't believe how lucky we are to have @archive.org to remember them :') web.archive.org/web/20080803...

Hello all, our lab is recruiting a PhD candidate to study how 3D genome folding impacts gene regulation in development. We're located at the Center for Integrative Genomics department of the University of Lausanne, Switzerland. Please email me if interested. #PhDPosition, #PhDOpportunity

This is great. I've given an example in class showing how priors can make some unidentified problems identifiable: a+b=6, solve for b. Prior: a=0~4

Had a few days home in México, had a beautiful view as I left #Teotihuacan

There's been endless talk about an AI bubble, but less about exactly how, why, and how much it's a bubble. So I turned to the framework put forward by scholars Brent Goldfarb and David A. Kirsch, authors of "Bubbles and Crashes," for assessing tech bubbles. Spoiler: On a scale of 1 to 8, AI is an 8

Why aren’t language models acting/interacting like a graph? (Or are they? Idk). It seems so obvious that while human conversations are iterative, they’re nonlinear and that’s how you get to the point/good stuff

The strongest argument I keep hearing for AI is that it makes many admin tasks and paperwork easy. This basically rephrases what many have been saying for decades - there is a vast and unnecessary administrative bloat mandated by “business best practice” that needs to vanish.

Yesterday I attended Harin’s excellent defense where he talked about this study, which is a great reason to give it another shoutout. Does population size affect the diversity of the music that people listen to? Really nice example how to make use of a DAG in practice!

Are housekeeping genes now the ones we see expressed in every single single-cell cell?

We just launched Foursquare Spatial Desktop – a geospatial analysis tool powered by embedded DuckDB and built on sqlrooms.org. Everything runs locally: your data stays on your machine, no cloud needed. A modern reimagining of Kepler.gl. Mac only for now. More coming. foursquare.com/products/spa...

A single-cell transposable element atlas of human cell identity

Thrilled to share this work! I am honored to learn from @mlbendall.bsky.social and so grateful for his guidance and mentorship. Stellarscope is just the beginning! There is so much to learn about TEs and now we can all explore the uncharted territory of single cell retro-genomics 🧬🔭

do you ever stare at the ceiling and think about how the worldwide scientific establishment did the impossible and created a COVID vaccine in under a year and the response of the general public has been to go on an unstoppable rampage to destroy science and scientists

I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms www.nature.com/articles/s41...

Sad news: The dataset behind this famous chart on the decline in costs of genome sequencing has had its NIH funding cut. I loved this chart because it was the first that made me appreciate the impact of dataviz. But it also tracked progress towards an ambitious goal ($1000 genome) that succeeded.

Thanks @lecteroide.bsky.social for the opportunity to share the efforts developed in MexOmics www.the-scientist.com/mexomics-map...

One old fish needed to sense its environment and now I have to floss every night (Isn’t evolution the coolest thing ever?! 👹🌀🧬🤗)

I wonder if easy-to-remember memories that are accompanied by ‘negative’ strong emotion (i.e. the opposite of insight?) follow the same or a different pathway in the brain activity

Been horrifying teammates by referring to undocumented information that's held only in people's heads as "locked in meat storage". Please use this with your teams/projects and report back on how they like it?

@dartar.bsky.social: Why Latin America? @chanzuckerberg.bsky.social #CZIAcceleratingScienceLA

My train does epigenetics and I love it #LIRR

🚨 Excited to share our latest work: 🚨 @bhavyasighs.bsky.social et al. show that locus-specific #HERV expression can reveal the origins and heterogeneity of B-cell lymphomas! Locus-specific human endogenous retroviruses reveal lymphoma subtypes www.cell.com/iscience/ful... #TEsky #TEworldwide 1/

My first #bluesky "flutter" I guess 🦋🌪️ o o o o o o o o o o o \ o o o o / o o o o / o o o o \ o o o o o o o o o o o