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Anil Raj

@anilraj.bsky.social
418 followers 1.7K following 25 posts

principal data scientist @ calico life sciences | applied mathematics | statistical and population genetics | genetics and biology of complex traits in mice and humans | humans as model organisms

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Reposted by Anil Raj
Nikhil Milind @nikhilmilind.dev · 27/05/2026
I'm excited to share that our work studying gene dosage response curves (GDRCs) is now out in Cell Genomics (@cellpress.bsky.social). www.cell.com/cell-genomic... [1/n]
cell.com
Buffering of gene dosage response curves for human complex traits
Milind et al. explore why loss-of-function variants and duplications tend to have average effects in the same direction on 94 complex traits. Using gene dosage response curves (GDRCs), they gather evi...
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
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Sohini Ramachandran @sramach.bsky.social · 05/03/2026
If you research or are simply interested in human genetic variation, ancient and modern, read my and Noah Rosenberg's latest in GENETICS academic.oup.com/genetics/art... 1/2
academic.oup.com
Reflections on the Human Genome Diversity Project: a conversation with Marcus W. Feldman, Henry T. Greely, and Mary-Claire King
Abstract. The Human Genome Diversity Project (HGDP) began in 1991 as an initiative to study genetic variation from human populations worldwide. In 2002, th
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Irene Gallego Romero @ee-reh-neh.bsky.social · 28/02/2026
First, a couple of weeks ago: www.biorxiv.org/content/10.6... Single cell RNAseq on blood from 200 donors across 4 sites in Indonesia spanning regional axes of genetic and environmental diversity. This is one of very few scRNA data sets from the Global South, including urban and rural settings.
biorxiv.org
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Irene Gallego Romero @ee-reh-neh.bsky.social · 28/02/2026
Finally, today's offering! www.biorxiv.org/content/10.6... This began life as a very different project which failed because we couldn't agree on defining eqtl sharing across cohorts. So two young members of the lab dug deeply into this - first @ijbeasley.bsky.social, then @patrickgibbs.bsky.social
biorxiv.org
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Anil Raj @anilraj.bsky.social · 16/02/2026
Over a year ago, along with Gary Churchill at Jackson Labs, we explored the impact of dietary restriction on lifespan in one of the largest studies using 960 female Diversity Outbred mice. Caloric restriction and intermittent fasting both extended lifespan proportionally to the level of restriction.
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daphnarothschild.bsky.social @daphnarothschild.bsky.social · 19/11/2025
Ribosomal RNA (rRNA) genes are found in hundreds of copies in the human genome. Do sequence variations in these paralogs change the ribosome function? Yes! I am excited to share our new preprint @mbarnalab @jkpritch in collaboration with Calico: www.medrxiv.org/content/10.1... 1/8
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Anil Raj @anilraj.bsky.social · 22/01/2026
Three years ago, we showed ~70% of lifespan variation in yeast traces to rDNA copy number. Ribosomal DNA, encoded as 5S and 45S subunits in hundreds of copies, vary substantially across humans. Does this copy number variation, and sequence variation within these paralogs, matter for humans?
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Yoav Gilad @ygilad.bsky.social · 05/05/2025
www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Charlotte Moore-Lambert @charlottereads.com · 22/03/2025
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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Jeremy Berg @jeremymberg.bsky.social · 09/03/2025
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.
media.tenor.com
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Maureen Barr @barrlab.bsky.social · 01/03/2025
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
opportunity.do
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Jeremy Berg @jeremymberg.bsky.social · 16/02/2025
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
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Sri Kosuri @srikosuri.bsky.social · 08/02/2025
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.
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Carl T. Bergstrom @carlbergstrom.com · 08/02/2025
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...
grants.nih.gov
NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
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Carl T. Bergstrom @carlbergstrom.com · 04/02/2025
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
thebullshitmachines.com
INTRODUCTION
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Jacob Schreiber @jmschreiber91.bsky.social · 01/02/2025
scATAC-seq generates more accurate and complete regulatory maps than bulk ATAC-seq www.nature.com/articles/s41...
nature.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
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Carl T. Bergstrom @carlbergstrom.com · 29/01/2025
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.
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Jonathan Pritchard @jkpritch.bsky.social · 26/01/2025
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 🧵
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Yoav Gilad @ygilad.bsky.social · 17/01/2025
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
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Marco Hein @marco.heinlab.org · 14/01/2025
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 🧪
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.
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Yoav Gilad @ygilad.bsky.social · 10/01/2025
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
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c0nc0rdance @c0nc0rdance.bsky.social · 15/08/2023
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.
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,
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Gregg Gonsalves @gregggonsalves.bsky.social · 02/01/2025
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/
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Mike Inouye @mikeinouye.bsky.social · 30/12/2024
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
nature.com
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.
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Salomé Viljoen @salome.bsky.social · 26/12/2024
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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Jeremy Berg @jeremymberg.bsky.social · 18/12/2024
Bluetorial: Adventures with tenure-Part 1
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BrunetLab @brunetlab.bsky.social · 18/12/2024
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 🧵
rdcu.be
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...
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 16/12/2024
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies www.biorxiv.org/content/10.1101/202…
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Jeremy Berg @jeremymberg.bsky.social · 29/11/2024
Today's Bluetorial: Dealing with Deans (Part 1)
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Eric Fauman (he/him) @ericfauman.bsky.social · 26/11/2024
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
nature.com
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 ...
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Jeremy Berg @jeremymberg.bsky.social · 24/11/2024
A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.
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Jeremy Berg @jeremymberg.bsky.social · 23/11/2024
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). 1/n
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Jonathan Pritchard @jkpritch.bsky.social · 22/11/2024
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?
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Prof Claire Hills @chillslincoln79.bsky.social · 23/11/2024
Atlas of the plasma proteome in health and disease in 53,026 adults 👩‍🔬🥼👨‍🔬🧪. #proteomics #proteome #plasma #MedSky 👇👇 www.cell.com/cell/fulltex...
cell.com
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...
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