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Reposted by Vinay Kartha

Til Steinicke @til-steinicke.bsky.social · 16d

Epigenetic diagnosis of acute leukemia within two hours from sample receipt 🚀

Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n

Rapid epigenomic classification of acute leukemia - Nature Genetics

The authors present a molecular classification of acute leukemia using 5-methylcytosine signatures, together with a neural network-based classifier for clinical use.

www.nature.com

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siddhartha jena @epijenatics.bsky.social · 27d

Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9

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Michelle Franc Ragsac, PhD 🇵🇭🇺🇸 @mragsac.com · Jul 15

With funding cuts and whatnot going on… I want to say that my experience on the @ucsandiego.bsky.social T32 for Genetics with @bahome.bsky.social was VERY influential in my growth as a scientist 🧪🧬💻 and keeping me in bioinformatics during the early pandemic 🦠 (versus pivoting to Big Tech ✨👩🏽‍💻)

EJVallender @ejvallender.bsky.social · Jul 15

Here are the T32 curves.

T32 curves for 2025 compared to previous years. 2025 is at roughly one third previous years.

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Vinay Kartha @vkartha.bsky.social · Jul 10

Had a super week filled with great science, curiosity and discussions at this year's Gordon Research Conference on Human genetics and genomics. Also fun when you get to give a talk the same day as your postdoc advisor @jbuenrostro.bsky.social

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Vinay Kartha @vkartha.bsky.social · Jul 9

So great meeting and talking to you @mragsac.com ! And I know, small world, we should all hang if you're ever in the Bay area anytime!

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Vinay Kartha @vkartha.bsky.social · Jul 6

Also looking forward to catching up with some old friends, and connecting with many new ones while I'm there!

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Vinay Kartha @vkartha.bsky.social · Jul 6

Excited to be attending this year's Human genetics and genomics Gordon Research Conference in Portland, ME, where I'll be presenting work from @gordianbio.bsky.social related to our in vivo mosaic screening platform applied to accelerate patient-relevant target discovery in complex diseases!

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Evgeny Kvon @evgenykvon.bsky.social · Jun 23

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

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Stephen Turner @stephenturner.us · May 27

Terminal Genome Viewer (tgv), written in Rust github.com/zeqianli/tgv

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Stephen Turner @stephenturner.us · Apr 21

Zero-shot evaluation reveals limitations of single-cell foundation models genomebiology.biomedcentral.com/articles/10.... 🧬🖥️🧪 github.com/microsoft/ze...

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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · Apr 18

Thank you #MIT

Eoin Higgins @eoinhiggins.bsky.social · Apr 15

MIT following Harvard's lead here

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Vinay Kartha @vkartha.bsky.social · Apr 15

💯💯💯

Itai Yanai @itaiyanai.bsky.social · Apr 14

My guidelines for exploratory data analysis

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Hani Goodarzi @genophoria.bsky.social · Feb 25

@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling

Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas ...

www.biorxiv.org

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Surya Nagaraja @snaga13.bsky.social · Feb 18

New to bluesky, but I’m excited to share my work over the last few years with @jbuenrostro.bsky.social! Chronic inflammation creates an epigenetic memory in colonic stem cells, priming them for tumor growth: tinyurl.com/ColitisNagar.... Here’s a walkthrough of what we found (🧵)

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Chenxin Li, PhD @chenxinli2.bsky.social · Feb 15

It's great to see the heatmap icon I contributed to bioicons.com has been used in papers. Bioicons is a open-source repository for vector graphs. There are many very nice icons on there. Please do check it out.

A screenshot at bioicons webpage with a heatmap that goes from light orange color to dark purple. The icon was contributed by ChenxinLi.

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Xin Jin @xinjin.bsky.social · Feb 12

Despite the trying times, thrilled to share our @natprot.bsky.social Nature Protocols on massively parallel in vivo Perturb-seq: www.nature.com/articles/s41...

Grateful for the excellent primer by Christopher Bock and Eugenia Pankevich: www.nature.com/articles/s41...

Massively parallel in vivo Perturb-seq screening - Nature Protocols

This protocol leverages tailored adeno-associated virus vectors for effective delivery of pooled CRISPR-based genetic perturbations in live animals combined with single-cell gene expression readout of...

www.nature.com

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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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Gordian Biotechnology @gordianbio.bsky.social · Feb 3

ICYMI, co-founders Francisco LePort and @martinbjensen.bsky.social were guests of Dr. Moira Gunn on the BioTech Nation podcast.

It ran on our hometown NPR station KQED and about 200 other @npr.org affiliates.

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Rita Strack @ritastrack.bsky.social · Dec 6

I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...

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.

www.nature.com

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Anne Carpenter @drannecarpenter.bsky.social · Dec 4

Now on biorxiv! The JUMP-Cell Painting Consortium’s paper:

“Morphological map of under- and over-expression of genes in human cells”

This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months
www.biorxiv.org/content/10.1...

Morphological map of under- and over-expression of genes in human cells

Cell Painting images offer valuable insights into the state of a cell and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUM...

www.biorxiv.org

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Surag Nair @suragnair.bsky.social · Dec 5

We are hiring an intern to work with our team at Genentech next summer, on exciting projects related to deep learning for DNA/RNA sequences. Please share and apply! roche.wd3.myworkdayjobs.com/ROG-A2O-GENE...

2025 Summer Intern - Biology Research | AI Development

2025 Summer Intern - Biology Research | AI Development Department Summary At Genentech Research & Early Development (gRED) we have initiated an exciting journey to bring together and further stren...

roche.wd3.myworkdayjobs.com

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Junyue Cao @junyuecao.bsky.social · Nov 29

Excited to share our work @science.org. led by our incredible @tommyz626.bsky.social at @rockefelleruniv.bsky.social! By profiling 21 million single cells across life stages, we reveal aging as distinct, development-like transitions, with dramatic cell population changes in specific time windows!

A panoramic view of cell population dynamics in mammalian aging

To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, se...

tinyurl.com

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Vinay Kartha @vkartha.bsky.social · Nov 28

This seems amazing, nice stuff @mitchguttman.bsky.social and co, looking forward to reading

Mitch Guttman @mitchguttman.bsky.social · Nov 27

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics

ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

www.nature.com

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bioRxiv Genomics @biorxiv-genomic.bsky.social · Nov 28

Paired CRISPR screens to map gene regulation in cis and trans https://www.biorxiv.org/content/10.1101/2024.11.27.625752v1

Recent massively-parallel approaches to decipher gene regulatory circuits have focused on the discov

www.biorxiv.org

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John Doench @johndoench.bsky.social · Nov 26

A pair of graphs I think about a lot. On the topic of pooled CRISPR screens, the left is "replicate correlation" when simply examining the abundance of guide RNAs, i.e. log-normalized read counts. On the right is taking those same data and subtracting from a common starting point, i.e. pDNA.

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