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

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

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 ✨👩🏽‍💻)

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

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!

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/

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

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

Thank you #MIT

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@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...

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 (🧵)

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.

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...

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.

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.

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...

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...

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...

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!

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

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

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.

Systematic benchmarking of several enhancer-to-gene association methods that utilize single cell data (including one developed by us earlier), highlighting advantages of the proposed scE2G model over alternatives and SOA metrics

#snPATHO… www.nature.com/articles/s42...

Cool work by Saunders, Allen et al. Some neat enhancements and a nice application of imaging coupled with transcriptomics for pooled screening in vivo A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function www.biorxiv.org/content/10.1...

Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...

The success of AI applied to drug discovery is being decided by a number of clinical trials. So far, the results are lackluster. Why? For AI to have a transformational effect in drug discovery, training data must come from living mammals. (🧵1/9)

in case this is useful to someone in this massive platform migration: a starting pack for single-cell omics computational methods go.bsky.app/GmS1cH

Excited to see our T-cell exhaustion preprint published! This work is led by Tristan Tay and collaborators at AstraZeneca. See the sub-thread (reformatted for bluesky) originally composed and posted by the newly minted Dr. Tay www.cell.com/cell-reports...