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Indigo V. L. Rose

@ivlrose.bsky.social
1K followers 754 following 56 posts

Neuroscience + functional genomics + CRISPR researcher. Postdoc in @Doudna-lab.bsky.social

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Reposted by Indigo V. L. Rose
Kenneth Loi @kenjmloi.bsky.social · 18/09/2026
VIPR is now out in Science! What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins. So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓
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Indigo V. L. Rose @ivlrose.bsky.social · 02/07/2026
Not Claude advertising their new model to me using a left-handed helix
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Syd Sattler @sydsat.bsky.social · 29/06/2026
What if an embryo made immune cells before it finished building the tissue they usually come from? In our new preprint, we show that annual killifish embryos specify neutrophils before germ layers are fully resolved. www.biorxiv.org/content/10.6... Huge thanks to my PI, @ohnolog.bsky.social ! 🧵
biorxiv.org
Early immune cell development precedes gastrulation in annual killifish
During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...
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Kunal Shroff @kunalshroff.bsky.social · 30/06/2026
I am so excited to share our new preprint! www.biorxiv.org/cgi/content/... This work uncovers a key molecular mechanism that control synapse-specific exposure of the canonical “eat-me” signal phosphatidylserine!
biorxiv.org
Synaptic activity controls local exposure of an 'eat-me' signal via ANO3-ITPR1 signaling
Neuronal synapses are eliminated during brain development and disease through pruning by glial cells. Individual synapses are marked for engulfment by 'eat-me' signals, which include externalized phos...
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Michael Ward @michael-e-ward.bsky.social · 13/05/2026
On July 1st, I'll be joining the faculty at UC Berkeley, with a joint appointment in the Division of Molecular Therapeutics within MCB and the Helen Wills Neuroscience Institute.
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Melissa Cooper, PhD @melcooperphd.bsky.social · 22/04/2026
Astrocytes do so much more than any of us thought - they even communicate among specific brain regions across hemispheres! The journey to this paper spanned nearly a decade, but I'm most excited to see what everyone else does with the tools we've built. There's so much for all of us to explore!
nature.com
Astrocytes connect specific brain regions through plastic networks - Nature
Communication between distant brain regions is mediated by plastic networks of gap junction-coupled astrocytes.
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Daniel Kerschensteiner @kerschensteiner.bsky.social · 09/04/2026
New study led by Ning Shen w/ @phruzycki.bsky.social: a genome-wide in vivo CRISPR screen in a retinitis pigmentosa mouse model identifies genes whose loss accelerates photoreceptor death. Overexpressing two, UFD1 and UXT, preserves photoreceptors, retinal function, and vision. 🧵
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Indigo V. L. Rose @ivlrose.bsky.social · 24/03/2026
Happy to say that I defended my PhD! Very excited to reach a goal I’ve been working towards for so many years. Looking forward to my next chapter in science! #PhDone #neuroskyence 🧠🧪
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Thomas Norman @normanlab.bsky.social · 04/02/2026
My lab at MSKCC in New York is hiring for two positions. Join us at the frontier of functional genomics, studying fibroblast state transitions, combinatorial genetics, and ECM in disease. Please share with anyone who might be a good fit! (Mustache not required.)
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Martin Kampmann @kampmann.bsky.social · 28/01/2026
Our paper is (finally) out in Cell today! CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis www.cell.com/cell/fulltex... Great collaborative effort - read more from first author @asamelson.bsky.social below:
cell.com
CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis
CRISPR screens in iPSC-derived neurons reveal that the E3 ubiquitin ligase CRL5SOCS4 ubiquitinates tau, that CUL5 expression is correlated with resilience in human Alzheimer’s disease, and that electr...
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Alex Pollen @brainevodevo.bsky.social · 23/01/2026
1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification www.nature.com/articles/s41...
nature.com
Dissecting gene regulatory networks governing human cortical cell fate - Nature
Systematic screening of transcription factors reveals conserved mechanisms governing cortical radial glia lineage progression across primates and provides a framework for functional dissecti...
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Arc Institute @arcinstitute.org · 22/01/2026
Arc bioinformatics scientists @noamteyssier.bsky.social and Alex Dobin have just released cyto, an ultra-high throughput processor specifically optimized for @10xgenomics.bsky.social Flex single-cell data. We are excited to make this resource open source: www.biorxiv.org/content/10.6...
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Indigo V. L. Rose @ivlrose.bsky.social · 14/01/2026
Anyone know why astrocytes would be doing this weird stringy thing in the cerebellar peduncles (and a bit in the arbor vitae)? This reporter behaves well astrocyte-wise through the rest of the brain, but herein seems to fill long (astrocyte?) processes. Super strange. #neuroskyence 🧪
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Indigo V. L. Rose @ivlrose.bsky.social · 06/12/2025
Career update: I'm happy to say that I've accepted a postdoc position at UC Berkeley at @innovativegenomics.bsky.social in Jennifer Doudna's lab! I'm looking forward to this exciting new chapter of my scientific career!
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Indigo V. L. Rose @ivlrose.bsky.social · 03/12/2025
NREL’s public outreach programs were formative for developing my interest in science as a kid. I hope they’re able to continue their work leading the way in renewable energy technology development, despite an unfortunate name change…
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Noam Teyssier @noamteyssier.bsky.social · 18/11/2025
I work with large collections of AnnDatas for single-cell work and got tired of opening notebooks for simple operations. Built a CLI tool to handle some common stuff directly from the terminal. Quick ops: downsample, concat, pseudobulk, QC, metadata export, etc. github.com/noamteyssier...
github.com
GitHub - noamteyssier/anntools: a cli-driven anndata toolkit
a cli-driven anndata toolkit. Contribute to noamteyssier/anntools development by creating an account on GitHub.
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Addgene @addgene.bsky.social · 19/11/2025
Who doesn't love a library? A pooled library, that is! Grab a hot drink and your reading glasses and enjoy browsing the libraries Addgene has to offer: twp.ai/4it3AO
A venn diagram comparing Libraries and Pooled Libraries. The Libraries circle reads "made of paper" and shows an illustration of books. The Pooled Libraries circle reads "made of DNA (and sometimes lentivirus)" and shows an illustration of plasmids. In the overlap of the two circles, three entries read: "incredible community driven resource; source of new discoveries; barcodes."
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Indigo V. L. Rose @ivlrose.bsky.social · 18/11/2025
The small conference room on my floor with a wonky door has claimed another victim
Sign reads: This room mat trap you! # people trapped: 3. # escaped: 3.
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Shane Liddelow @liddelowsa.bsky.social · 10/11/2025
@sfn.org #SfN25 #SanDiego starts this Saturday. The lab is going to be there in full force - see our presentations below. Represented this year by @borderbiologist.bsky.social, Nick Kathman, @mrodea.bsky.social, @melcooperphd.bsky.social, @pryprk.bsky.social, @kerrylimberg.bsky.social. (1/2)
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Alex Pollen @brainevodevo.bsky.social · 07/11/2025
Our new manuscript, led by Emily Corrigan, examines inhibitory neuron diversity across approximately 160 million years of evolutionary divergence, as part of BRAIN Initiative Cell Atlas Network (BICAN) developing brain atlas package: www.nature.com/articles/s41...
nature.com
Conservation and alteration of mammalian striatal interneurons - Nature
An analysis of cell-type diversity in brain samples from a variety of mammalian species, both during development and in adult animals, reveals that the TAC3 initial class of striatal interneurons is c...
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allen institute @alleninstitute.org · 03/11/2025
Glia gang, this is for you! In this video by our #ElectronMicroscopy team, shows a pyramidal neuron (PyC) surrounded by 8 glia brain cells – 5 microglia (MG) and 3 oligodendrocyte progenitor cells (OPC). 🧠📈 microns-explorer.org
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Indigo V. L. Rose @ivlrose.bsky.social · 02/11/2025
RIP Kit-Kat 💔
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James Olzmann @olzmannlab.bsky.social · 29/10/2025
Excited to share our study out in @natcellbio.nature.com! Led by @mikelangelipid.bsky.social, we identify the first #LipidDroplet lipid quality control pathway: LD-localized FSP1 protects stored lipids from oxidative damage and prevents LD-initiated #ferroptosis. www.nature.com/articles/s41...
nature.com
FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis - Nature Cell Biology
Lange et al. identify a lipid droplet quality control pathway in which FSP1 safeguards stored neutral lipids from lipid peroxidation, thereby preventing the induction of ferroptosis.
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Shane Liddelow @liddelowsa.bsky.social · 24/10/2025
We've been doing some amazing stuff outside the astrocyte realm. Check out our latest Oligo investigation led by @pryprk.bsky.social !
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Emily Hunt @emily.space · 24/10/2025
uv makes installing and using Python *so* easy! It works on pretty much any computer and it's lightning fast. 🔭☄️ #astrocode If you're still using conda, pyenv, or... basically any other tool, then I can *highly* recommend switching:
emily.space
uv is the best thing to happen to the Python ecosystem in a decade - Blog - Dr. Emily L. Hunt
Released in 2024, uv is hands-down the best tool for managing Python installations and dependencies. Here's why.
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Martin Kampmann @kampmann.bsky.social · 22/10/2025
Thank you Alzforum for featuring our new preprint identifying regulators of disease states of #microglia. Project led by Amanda McQuade, computation by Reet Mishra, collaboration with the Nunez and De Jager labs. Alzforum www.alzforum.org/news/researc... Preprint www.biorxiv.org/content/10.1...
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Celeste Karch @karchlab.bsky.social · 21/10/2025
Excited to share new work from the lab showing that FTD causing mutations in tau cause widespread defects in microglia function www.nature.com/articles/s41...
nature.com
Cell autonomous microglia defects in a stem cell model of frontotemporal dementia tau - Molecular Psychiatry
Molecular Psychiatry - Cell autonomous microglia defects in a stem cell model of frontotemporal dementia tau
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Jun Nagai @junnagai.bsky.social · 15/10/2025
Just out in Nature! “The astrocytic ensemble acts as a multiday trace to stabilize memory.” We identified astrocytic ensembles that link experiences across days to stabilize memory nature.com/articles/s41.... New astrocyte tools are openly available at Addgene: addgene.org/Jun_Nagai/. 1/8
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Keri Martinowich @martinowk.bsky.social · 24/09/2025
In the early years of my PhD I remember being asked if we'd ever treat or cure diseases like HIV or Huntington's. I remember saying maybe, but not knowing if I believed. Seeing research pay off as real impact on human lives is - incredible. www.bbc.com/news/article... www.bbc.com/news/article...
bbc.com
Huntington's disease successfully treated for first time
One of the most devastating diseases finally has a treatment that can slow its progression and transform lives, tearful doctors tell BBC.
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Indigo V. L. Rose @ivlrose.bsky.social · 22/09/2025
Wow now that was an earthquake! Never been shaken awake before
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Rob Patro @robp.bsky.social · 18/09/2025
Rust 1.90.0 is out! blog.rust-lang.org/2025/09/18/R... Major features: * lld as the default linker on x86_64-unknown-linux-gnu * cargo workspace publishing support built into cargo * more const context APIs, and stabilization of new useful APIs
blog.rust-lang.org
Announcing Rust 1.90.0 | Rust Blog
Empowering everyone to build reliable and efficient software.
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Sarah Cohen @cohenlaboratory.bsky.social · 17/09/2025
Wonderful to see our paper on the #organelle signatures of #neurons and #astrocytes out in final form - congratulations, Shannon Rhoads and team!🎉 t.co/BPxKlbU6Ou
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Nadav Ahituv @nadavahituv.bsky.social · 17/09/2025
Most neurodevelopmental disorders are caused by having 1 functional gene copy. Using SCN2A, we show that upregulating the functional copy rescues neuronal phenotypes. Amazing work with @neurobender.bsky.social led by Serena Tamura, Andrew Nelson, Perry Spratt & others. www.nature.com/articles/s41...
nature.com
CRISPR activation for SCN2A-related neurodevelopmental disorders | Nature
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Waggoner Lab @labwaggoner.bsky.social · 11/09/2025
Microglia-astrocyte crosstalk regulates synapse remodeling via Wnt signaling @cellcellpress.bsky.social @travisfaust.bsky.social www.cell.com/cell/fulltex...
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Randall Munroe @xkcd.com · 11/09/2025
Biology Department xkcd.com/3140/
Comic. [Building with large sign in front of it[ SIGN: Welcome to the *Biology Department* It has been [changeable sign: 3] days since we discovered something existentially horrifying about bugs that makes you question your whole reality
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Ishmail Abdus-Saboor @ishmailsaboor.bsky.social · 07/09/2025
David Baltimore, Nobel-Winning Molecular Biologist, Dies at 87 www.nytimes.com/2025/09/07/s...
nytimes.com
David Baltimore, Nobel-Winning Molecular Biologist, Dies at 87
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Indigo V. L. Rose @ivlrose.bsky.social · 07/09/2025
Getting a breathtaking view of the Golden Gate Bridge! Perfect conditions this weekend.
View of the Golden Gate Bridge out the front window of a small airplane on a sunny day
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Indigo V. L. Rose @ivlrose.bsky.social · 05/09/2025
Thanks Nat Neuro for posting about our recent paper! This project goes to show that you can have a really wacky idea and occasionally biology will throw you a bone and it will actually work!
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Indigo V. L. Rose @ivlrose.bsky.social · 04/09/2025
I love this cover art so much!
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The Transmitter @thetransmitter.bsky.social · 03/09/2025
Astrocytes are connected by gap junctions in large, plastic networks that link brain regions not connected by neurons, a new preprint shows. By @callimcflurry.bsky.social #neuroskyence www.thetransmitter.org/astrocytes/a...
thetransmitter.org
Astrocyte networks span large swaths of brain
The networks are plastic, connect brain regions that aren’t connected by neurons and may enable long-distance communication between astrocytes, a new preprint shows.
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Indigo V. L. Rose @ivlrose.bsky.social · 23/08/2025
Ever wanted to do a CRISPR screen directly in the mammalian brain? While perturbing thousands of genes in parallel? All while targeting specific cell types? Check out our latest paper describing CrAAVe-seq, a powerful new functional genomics tool for massively parallel neuroscience research
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Andy Moore @aaandmoore.bsky.social · 18/08/2025
This is an airyscan confocal movie of mitochondria (white) moving around in a mouse astrocyte. Actin filaments are in orange and microtubules are in blue.
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Krissy Lyon @krissylyon.bsky.social · 29/07/2025
Cool astrocyte paper!
nature.com
Astrocyte specification in the mouse septum is shaped by both developmental origin and local signals - Nature Neuroscience
The relative contribution of intrinsic and extrinsic factors to astrocyte heterogeneity is unknown. Using heterotropic transplantation of septal astrocytes with distinct lineage origins, we show that ...
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Jim Woodgett @jwoodgett.bsky.social · 24/07/2025
Good grief, the US National Cancer Institute projects it will fund only one in 25 RO1 grant applications in 2026. This is massively defunding cancer research. Despicable vandalism. www.cancer.gov/grants-train...
National Cancer Institute projection of a 4% pay line in FY2026.
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Martin Kampmann @kampmann.bsky.social · 23/07/2025
Tenure-track faculty search of the UCSF Biochemistry & Biophysics Department is open for applications! We are looking for creative, innovative scientists asking fundamental questions in any area of biology. Join our vibrant, collaborative, and supportive community! aprecruit.ucsf.edu/JPF05702
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 22/07/2025
Astrocytes connect specific brain regions through plastic gap junctional networks www.biorxiv.org/content/10.1101/202…
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Fillip Port @crisprflydesign.bsky.social · 17/07/2025
Pooled #CRISPR screens are a staple of functional genomics in mammalian cells. Yet somehow in the best genetic model™ no equivalent system was available. Until now! The @perrimonlab.bsky.social lab now presents efficient pooled CRISPR screening in #Drosophila cells. www.nature.com/articles/s41...
nature.com
Higher resolution pooled genome-wide CRISPR knockout screening in Drosophila cells using integration and anti-CRISPR (IntAC) - Nature Communications
Genome-wide CRISPR screens map how genes support survival and contribute to diverse biological functions. Here, the authors use antiCRISPR to enhance genome-wide CRISPR screening in Drosophila and gen...
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Malcolm 朝精 Barrett @malcolmbarrett.malco.io · 11/06/2025
Still the ggoat
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Indigo V. L. Rose @ivlrose.bsky.social · 06/06/2025
Today I learned that ultracentrifuge rotors expire?? And need to be repurchased periodically? These things still feel brand new and should last decades...
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parafilm is cool dot com @parafilmm.bsky.social · 26/05/2025
At times like these it's important to remember the 3 branches of science
The side of a box of Parafilm that features the flask, dish, and beaker. Text has been added under them. The flask is labelled chemistry, the dish biology, and the beaker jam making. Jam making is written in a different handwritten font
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