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Robin Friedman @robinfriedman.bsky.social · 3d

Might explain some features of Lupus etiology?

Ryan Flynn @raflynn5.bsky.social · 6d

We’re excited to report work led by postdoc Jennifer Porat in the lab, finding that DNA accumulates on the surface of living cells and that the secreted extracellular protein DNASE1L3 can modulate its levels on B and T cells. With a new twist for ATAC-seq as well www.biorxiv.org/content/10.1...

DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells

The extracellular space is a critical environment for discriminating self versus non-self nucleic acids and initiating the appropriate immune responses through signaling cascades to relay information ...

www.biorxiv.org

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Reposted by Robin Friedman

Simon Rosenberg @simonwdc.bsky.social · Aug 19

2 bits of data from new Economist/YouGov poll.....

13% support for cutting research funding to universities. 24% among Republicans. Polling on this continues to be catastrophic for the Rs, suggests Dems should be learning far harder into standing up for science and our universities. 1/

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Reposted by Robin Friedman

Ryan Flynn @raflynn5.bsky.social · Aug 6

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis by chemically caging acp3U. Excited to report this work lead by Vinnie @vinnieviruses.bsky.social and in collaboration with @vijayrathinam.bsky.social in @nature.com www.nature.com/articles/s41...

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Reposted by Robin Friedman

Robin Hofmeister @rjhfmstr.bsky.social · Aug 6

🚨 Our parent-of-origin study is out in Nature! 🧬
Maternal and paternal alleles can have distinct — even opposite — effects on human traits, revealing a hidden layer of genetic architecture that standard GWAS miss.
🔗 www.nature.com/articles/s41...

Highlights below!

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Reposted by Robin Friedman

Julio Saez-Rodriguez @juliosaezrod.bsky.social · Jun 23

I wrote a short piece on how becoming an IgA Nephropathy patient has changed my perspective on biomedical research, developing an appreciation for the challenges in data interpretability & availability and the importance of patient engagement www.nature.com/articles/s41...

Leveraging data as a patient–scientist: frustrations and opportunities - Nature Reviews Nephrology

The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability h...

www.nature.com

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Reposted by Robin Friedman

Andrea Love, PhD | Biomedical Scientist @drandrealove.bsky.social · May 5

Which FDA-approved vaccines had randomized, placebo-controlled trials?

ALL OF THEM.

Polio?
Measles, mumps, rubella?
Haemophilus influenzae B?
Diphtheria, tetanus, pertussis?
Meningococcus?
Varicella?
Pneumococcus?
Rotavirus?
RSV?
Hepatitis B?
Influenza?
HPV?
COVID-19?
Shingles?

YEP.

A thread🧵
1/

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Robin Friedman @robinfriedman.bsky.social · May 3

If true, that has implications for how western biotech can compete. I'm not holding my breath for a change in the regulatory regime to rescue us.

Robin Friedman @robinfriedman.bsky.social · May 3

1. Scale. I'm sure China's huge population helps with trial enrollment across many indications
2. Cost. If research costs are 4x lower, you can place 4x the number of bets and/or throw more people and experiments at problems to accelerate timelines.

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Robin Friedman @robinfriedman.bsky.social · May 3

Haven't seen anything saying it's a lower bar than Australia, for example. Instead, low visibility into the Chinese biotech ecosystem probably contributed to the perception of fast clinical data. Other factors seem more important:

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Robin Friedman @robinfriedman.bsky.social · May 3

After reading several pieces about the rise of China biotech, I think one of the narratives seems to be incorrect. The assumption that a faster regulatory path to first-in-human clinical trials compared to the west doesn't seem borne out by the data.

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Robin Friedman @robinfriedman.bsky.social · Apr 25

Nice list of thoughtful starting places for thinking about the implications of China's rising drug discovery capabilities.

Brian Naughton @btnaughton.bsky.social · Apr 24

There are now a trio of great pieces covering the rapid rise of Chinese biotech:
- atelfo.github.io/2024/12/20/w...
- centuryofbio.com/p/commoditiz...
- www.asimov.press/p/china-trials

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Robin Friedman @robinfriedman.bsky.social · Apr 25

Strange, works now for me. Thanks for posting!

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Robin Friedman @robinfriedman.bsky.social · Apr 25

Looks like the Asimov Press link is broken?

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Reposted by Robin Friedman

immunoboys @immunoboys.bsky.social · Apr 24

Tissue-resident memory T cells have high levels of mRNA of proinflammatory cytokines but produce the proteins only upon stimulation. 🧪⑂
The integrated stress response inhibits mRNA translation in these cells, having these cells poised for rapid responses in 🐭 and 🧓. 1/2

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Reposted by Robin Friedman

Anshul Kundaje @anshulkundaje.bsky.social · Apr 20

genomebiology.biomedcentral.com/articles/10....

Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.

Zero-shot evaluation reveals limitations of single-cell foundation models - Genome Biology

Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode...

genomebiology.biomedcentral.com

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Reposted by Robin Friedman

Saloni @scientificdiscovery.dev · Apr 5

This was such an interesting post! It's awesome how much bio and biotech blogging are happening now and this is one of my newest favourites.

What happened to pathology AI companies?

4k words, 19 minutes reading time

www.owlposting.com

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Reposted by Robin Friedman

lastpositivist.bsky.social @lastpositivist.bsky.social · Apr 2

Finally read this by @sashagusevposts.bsky.social - very interesting piece. There's some fascinating bit of sociology of science to be done on when things get counted as replication crises versus when they're seen as healthy methodological progress.

theinfinitesimal.substack.com/p/how-popula...

How population stratification led to a decade of sensationally false genetic findings

Stratification makes environments look like genes

theinfinitesimal.substack.com

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Reposted by Robin Friedman

Carolyn Bertozzi @carolynbertozzi.bskyverified.social · Feb 27

Mindblowing new study by @raflynn5.bsky.social @bostonchildrens.bsky.social, cell surface RNA-binding proteins form nanoclusters with #glycoRNA and mediate cell-penetrating peptide entry into cells 👏

www.cell.com/cell/abstrac...

RNA-binding proteins and glycoRNAs form domains on the cell surface for cell-penetrating peptide entry

Mammalian cells present RNA-binding proteins on the cell surface that form clustered domains containing glycoRNAs.

www.cell.com

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Reposted by Robin Friedman

Pearl Freier @pearlf.bsky.social · Feb 16

More below regarding layoffs at FDA h/t @alecgaffney.bsky.social. The layoffs are being run in a disorganized way by the new Secretary of Health & Human Services—Kennedy #medsky #biosky

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Reposted by Robin Friedman

Sri Kosuri @srikosuri.bsky.social · Feb 8

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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Reposted by Robin Friedman

David Robinson @drob.bsky.social · Feb 4

Blown away

Using OpenAI’s Deep Research is like collaborating with a PhD student

(It told me it would get right on it then ghosted me)

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Reposted by Robin Friedman

Fyodor Urnov @urnov.bsky.social · Jan 16

I started working on genetic therapies for Mendelian disease in 2000 - and in the subsequent 25 years have never seen a disease where the molecular aetiology has undergone as giant an "OH WOW" moment as this.
www.cell.com/cell/fulltex...

Long somatic DNA-repeat expansion drives neurodegeneration in Huntington’s disease

Single-cell measurement of the Huntington’s disease-causing CAG repeat reveals that somatic expansion of this repeat drives pathological changes in neurons, providing insights into disease progression...

www.cell.com

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Reposted by Robin Friedman

Vikram Agarwal @vagar.bsky.social · Jan 9

Super excited to announce our latest flagship model Borzoi: major props to Johannes & David Kelley et al for advancing it. It's been a long journey from our prior Enformer model into this one. A few innovations: i) longer DNA context, ii) adaptation to predict RNA-seq abundance and splice isoforms,

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation - Nature Genetics

Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.

www.nature.com

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Reposted by Robin Friedman

Xuebing Wu @xuebingwu.bsky.social · Jan 2

Excited to share our review article "Finding functional microproteins", published in @TrendsGenetics. It was fun writing it together with Alex and @FeiyueYang1 in the lab. #microprotein authors.elsevier.com/a/1kNCscQbJB...

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Reposted by Robin Friedman

Tami Lieberman @contaminatedsci.bsky.social · Dec 26

This pair of papers demonstrating strong and systemic immune responses to skin commensals applied topically to unbroken skin, including induction of B cells for vaccination.
www.nature.com/articles/s41...
www.nature.com/articles/s41...

Skin autonomous antibody production regulates host-microbiota interactions - Nature

Nature - Skin autonomous antibody production regulates host-microbiota interactions

www.nature.com

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