Anil Raj

Disease-associated loci share properties with response eQTLs under common environmental exposures Many of the genetic loci associated with disease are expected to have context-dependent regulatory effects that are underrepresented in the transcriptomes of healthy, steady-state adult tissues. To un...

www.biorxiv.org/content/10.1...

Congratulations @jkpritch.bsky.social !!

being an indie bookseller in the helltimes has felt both very stable and very stabilizing, and part of me wishes everyone could be on my side of the counter for a little while, because I think it would help some of you be a little less cynical and doomy right now. so here is my VERY anecdotal data:

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Bluetorial: Women, courage, and leadership

What follows will include some generalizations based on population averages of what I have experienced over the course of my career. There are, of course, exceptions in every group who are substantially more to one extreme or the other.

I have a brilliant scientist in my group. She proposed we approach our science as a once in a lifetime opportunity. So, let's do the risky experiments, think deeply, write beautifully, and show reverence to the most awe-some career

@inikon.bsky.social

Thanks to all of the NIHers and their friends who reached out to me. I am still here (DM me or Signal jeremymberg.78)

I still have a very incomplete picture but based on what I have been told, the damage to NIH and to many wonderful people who work(ed) there is/was impossible for me to imagine

1/n

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.

1. Today the NIH director issued a new directive slashing overhead rates to 15%.

I want to provide some context on what that means and why it matters.

grants.nih.gov/grants/guide...

INTRODUCTION

Modern-Day Oracles or Bullshit Machines?

Jevin West (@jevinwest.bsky.social) and I have spent the last eight months developing the course on large language models (LLMs) that we think every college freshman needs to take.

thebullshitmachines.com

scATAC-seq generates more accurate and complete regulatory maps than bulk ATAC-seq - Scientific Reports Scientific Reports - scATAC-seq generates more accurate and complete regulatory maps than bulk ATAC-seq

scATAC-seq generates more accurate and complete regulatory maps than bulk ATAC-seq

www.nature.com/articles/s41...

The thing about science is that if a phenomenon such as climate science weren’t real, they wouldn’t need an executive order forbidding its study.

The better we explain the social processes of science, the clearer it will be to everyone that this EO is an admission that climate change is real.

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease?

I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.

It’s available on Amazon: tinyurl.com/mx2hewen

Graphical abstract of the Organelle Profiling paper, showing the workflow: Endogenously tagged organelle library; Native IP proteomics; Data-driven graph clustering; resulting in a subcellular proteome map with more than 7,600 proteins localized across 19 subcellular compartments.

Time to share our organelle proteome paper
out in @cellcellpress.bsky.social: doi.org/nzwz
We created a spatial map of human cells using organelle immunoprecipitation at scale.
Locate your fav protein among the 7,600 we mapped across 19 subcellular compartments: organelles.sf.czbiohub.org/

1/3 🧪

Friends and colleagues, I’ve written a book on effective functional genomics study design, which will be available on Amazon in a couple of weeks. Sharing the TOC to spark interest. I hope students and those planning genomics experiments will find it useful! I’ll share updates soon

Pea aphids extracting sap from the stem and leaves of garden peas. One large and two small green-colored insects feed on a green stalk. The background is a flat black. Shipher Wu (photograph) and Gee-way Lin (aphid provision), National Taiwan University - PLoS Biology,

I'm gathering that Bluesky is less interested in long science threads 🧪, but I need you all to know the majesty that is the pea aphid, Acyrthosiphon pisum:

It can 'feed' on sunlight;

gives birth to live, pregnant clone-babies;

needs to be bacterially infected to survive.

Photo by Shipher Wu.

So, you may ask, why do I get so angry about the new liberal spin on RFK Jr, as in, "he gets some things right, so let's collaborate on those" or "we have to work with him because he has a huge following we need to reach"? Because I've seen this movie before. 1/

Why probability probably doesn’t exist (but it is useful to act like it does) All of statistics and much of science depends on probability — an astonishing achievement, considering no one’s really sure what it is.

Why probability probably doesn’t exist (but it is useful to act like it does) www.nature.com/articles/d41...

David Spiegelhalter doesn't appear to be on bsky but he wrote this wonderful piece that came out in Nature just before the holidays

my #1 duty to students is to teach them how to think. AI makes this job harder not easier. A closely related duty I owe is to not let students become accomplices in their own future irrelevance just because it’s easier short term to cheat thinking w AI

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Bluetorial: Adventures with tenure-Part 1

Spatial transcriptomic clocks reveal cell proximity effects in brain ageing Nature - A spatially resolved single-cell transcriptomics map of the mouse brain at different ages reveals signatures of ageing, rejuvenation and disease, including ageing effects associated with T...

Thrilled to see this paper out!! 🧪

Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors!

Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social!

rdcu.be/d33uQ 🧵

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies https://www.biorxiv.org/content/10.1101/2024.12.12.628073v1

Thank you!

Could you please add me?

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Today's Bluetorial: Dealing with Deans (Part 1)

Genetic basis of early onset and progression of type 2 diabetes in South Asians - Nature Medicine In a cohort of 50,556 South Asian individuals, partitioned polygenic scores helped identify genetic susceptibility to insulin deficiency and unfavorable fat distribution as key drivers of young-onset ...

Great stuff from the Genes & Health team!

www.nature.com/articles/s41...

@moneeza-ks.bsky.social @sarahfiner.bsky.social
@drmariespreckley.bsky.social
And many more

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A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.

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Following a suggestion from @benecal.bsky.social I will refer to these threads as "skeetorials" and will use this gif logo.

Today's skeetorial is about the NIH Director's New Innovator Award with three different heroes (all in government).

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In a new preprint led by @TheNikhilMilind, we explored a fascinating paradox:
For many traits the number of duplications or loss-of-function (LoF) mutations is correlated with phenotype. Curiously, for most traits, the AVERAGE direction of LoFs and Dups is the SAME. Why?

Atlas of the plasma proteome in health and disease in 53,026 adults A large-scale proteomics study involving 53,026 individuals maps 2,920 plasma proteins to 406 prevalent diseases, 660 incident diseases, and 986 health-related traits, identifying promising biomarkers...

Atlas of the plasma proteome in health and disease in 53,026 adults 👩‍🔬🥼👨‍🔬🧪. #proteomics #proteome #plasma #MedSky 👇👇

www.cell.com/cell/fulltex...