It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging www.owlposting.com/p/why-recurs... After over a decade,Recursion Pharmaceuticals changed its primary assay. Why is that? I answer that question over 5.6k words (26 minutes to read) first journalism-y piece!

Why Recursion Pharmaceuticals abandoned cell painting for brightfield imaging

5.7k words, 26 minutes reading time

owlposting.com

*Thread* The life science community frequently publishes new, often fundamental, insights in molecular and cellular biology. However, there does not exist a way to access this information in a summarized manner. We only access the information we need for our specific questions/use case. 1/yy

Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale! www.biorxiv.org/content/10.1... A 🧵about what it can do: #SynBio #DeepLearning #GeneRegulation

EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication

Precise control of gene expression is essential for cellular function, but the mechanisms by which enhancers communicate with promoters to coordinate this process are not fully understood. While seque...

biorxiv.org

Spatial imaging of transcripts without tissue dissociation www.biorxiv.org/content/10.1...

Super cool - esp the breadth of markers being covered. I especially love fig 6 showing gene density enrichment in different groups of histone mods co-occurring with k4me3. I think this is going to be adopted real fast by discovery teams!

Mitch Guttman@mitchguttman.bsky.social · 2y ago

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...

Well articulated post on what if Bluesky goes awry one day. I like the idea of building real relationships that may originate here, outside of it. But, connections existing only here are no less real or meaningful.The rate at which the scientific community reconnected here is good evidence of that.

Chris Holdgraf@choldgraf.com · 2y ago

I'm going to try using BlueSky more reliably for a while. Here are a few thoughts that are guiding my engagement here, and hopefully learning from our collective experience over at Twitter. chrisholdgraf.com/blog/2024/bl...

Join in to meet people who like to focus on science and answer interesting questions in biology with computational tools

🧬Jacob L Steenwyk@jlsteenwyk.bsky.social · 2y ago

TechBio Transformers (founded by @dr-alphalyrae.bsky.social) is a growing global community of folks who want to (+)ly impact the field of technology & biology, while also intentionally building healthy dialogue and community Follow along, & even consider joining the group! bsky.app/starter-pack...

changes in chromatin accessibility and loss of cell identity with age

Christian Nefzger@nefzgerlab.bsky.social · 2y ago

Our recent study in Cell Metabolism provides compelling evidence that chromatin accessibility and transcription factor network remodeling in aging reflect the predictable degrading effects of a mechanism initially driving organismal maturation. Link: doi.org/10.1016/j.cmet.2024.06.006 Thread 🧵👇1/9

One of my dream for this year is to host a Jeffersonian dinner. I hope to reconnect with old connections and meet cool new ones to make this dream a reality.

Like ‘old Twitter’: The scientific community finds a new home on Bluesky https://www.science.org/content/article/old-twitter-scientific-community-finds-new-home-bluesky 🧬🖥️🧪

Bluesky (so far) is a blast from the past when Twitter buzzed with good scientific conversations and scientists !

Genomics, Evolution, and More @jlsteenwyk.bsky.social bsky.app/starter-pack...

Prepping for class this spring, this playlist of videos on diffusion models for proteins are great! Series is led by @maom.bsky.social and Nick Randolph of UNC. www.youtube.com/playlist?lis...

Molecular ML Reading Group

The Molecular ML Reading Group aims to explore foundational and recent applications of machine learning models to modeling molecular system.

youtube.com

New on BioRxiv: We report a new, endogenous molecular clock in unmodified human cells and tissues. It is ticking away right now in almost every cell in your body. Paper here: www.biorxiv.org/content/10.1... 1/