Aditi Qamra

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 5.7k words, 26 minutes reading time

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!

ps I forgot, bluesky posts are also not editable. yy=4

I don't have a solution ready, but in the age of LLMs, this is a problem waiting to be solved.

Currently, I envision this as an interactive model of cells that supplements textbooks and is available to everyone in the scientific community.

Ideas and critique welcome!

4/4

In some cases, multiple groups have built the same section because we have multiple copies of the pieces.

But no one paused to step back and look at the emerging picture. It may not be complete, but it might be enough for us to guess the reference image and or make new breakthroughs.

3/4

While that is pragmatic and works for short term, I think we are completely missing the big picture.
Imagine a federated team building a jigsaw puzzle without a reference image (which is hard enough). Someone completed the edges, and another group unknown to the other has filled in the middle.
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*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

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...

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

Method of the Year 2024: spatial proteomics - Nature Methods Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.

Method of the Year 2024: spatial proteomics | Nature Methods www.nature.com/articles/s41...

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!

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.

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

changes in chromatin accessibility and loss of cell identity with age

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.

This is so cool - like git for transcription!

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...

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

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...

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...

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