Tony Li

PhD student @uwgenome

[Sudarshan Pinglay @sudpinglay]

Now out in @ScienceMagazine we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment.

https://t.co/dKnuHkQ0W9

[Nature Methods @naturemethods]

Out yesterday from the Akilesh and Beliveau labs! pSABER decorates in situ nucleic acid targets with binding sites for an HRP-conjugated oligo, enabling the localized deposition of fluorescent or colorimetric substrates for highly amplified signal.
https://t.co/TbA5LHCaeR

[Michael Kosicki @michaelkosicki]

Updated VISTA Enhancer Browser, 7 years in the making, out in @NAR_Open! >4,500 transgenic in vivo enhancer experiments for all your developmental biology, human variation and #evodevo needs. https://t.co/fE861VE3r7 #enhancers #embryos https://t.co/QxQDzGzBlf

[Yi Fu @Yi__Fu]

Excited to share my PhD work in @Agnelsfeir’s lab describing a method to engineer mitochondrial DNA deletions in human cells and our exploration of how cellular metabolism and transcription respond to deletion heteroplasmy. https://t.co/yK2ns3YpiJ 1/19

[Silvia Domcke @sdomcke]

New synthetic biology / gene regulation lab opening in Zurich! We’re studying how to control cell state transitions – for example, making diseased cells healthy or creating new cellular functions – using systematic perturbations, single-cell genomics and machine learning. 🧵1/4

[Troy McDiarmid @TroyMcDiarmid]

Beyond stoked to share our latest, entitled “Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording” !

https://t.co/8BtGh7th6P

[Troy McDiarmid @TroyMcDiarmid]

Our paper describing a scalable framework for Multiplex, single cell CRISPRa screening for cell-type specific regulatory elements is published! https://t.co/XSq2c5rPY8

See the linked tweet from my awesome co-lead @FloChardon for updates since the preprint!

[Flo Chardon @FloChardon]

Genomic tech dev is my favorite area of science, and today our paper describing our multiplex CRISPRa screening method to identify cell type specific regulatory elements is published! https://t.co/KWmdWZlDpn

[Riddhiman Garge @riddhimankg]

Very happy to share our latest w/ @dschweppe1 and @Nobu_Hamazaki labs, where we map the temporal dynamics and proteomic landscape of mammalian gastruloids. Sneek Peak 🧵below #stembryo #gastruloid #proteomics

https://t.co/ffzQuOXD7W

[Martin Kircher @KircherLab]

We are recruiting two computational biologists/bioinformaticians with ML expertise and a focus on genomics, variant effects and gene regulatory sequences in staff scientist and postdoc roles in Lübeck, Germany. Please find details here: https://t.co/GbfuDN3gha

[wei yang @VinetteY]

I am so thrilled to share our work of human RA gastruloid finally out on @NatureCellBio. It has been a wonderful journey to work with a fantastic stem cell scientist @Nobu_Hamazaki and many talented collaborators in @JShendure lab. Excited to contribute to the field of stembryo!

[Nobu Hamazaki @Nobu_Hamazaki]

Excited to share our human RA-gastruloid model in @NatureCellBio! Early retinoic acid supplementation, followed by later Matrigel addition, robustly induces human embryonic morphologies and diverse cell lineages, including somitic, renal, cardiac, and neural cell types in #gastruloid. https://t.co/buaAcqxGlZ

[Sanjay Srivatsan @SRsrivatsan]

Today out in @biorxivpreprint we present SCOPE. An optics-free, self-registering array of DNA encoded beads for spatial genomics. This was work led by the intrepid duo of Hanna Liao and Sanjay Kottapalli, with @JShendure's lab. https://t.co/ovGaBmQB1V

[Jay Shendure @JShendure]

Our latest, from the brilliant @wchenomics and @_Choi_Junhong, out in @Nature , is ENGRAM, a multiplex method for symbolic recording of signaling and cis regulatory activity to DNA. Final version (not in preprint) includes integration w/ DNA Typewriter. https://t.co/XmiIZSNWpv

[Junhong Choi @_Choi_Junhong]

Our DNA Typewriter protocol (written by @LiaoHanna, @JShendure, and myself) is out! Thank you @NatureProtocols for writing/editing this with us and having it as this week’s #FeaturedProtocol :-)

[Junhong Choi @_Choi_Junhong]

New synthetic biology / molecular recording lab opening in the New York city, and we are hiring at all levels (research tech / grad student / postdoc), so please reach out to me via choij10 _at_ https://t.co/anoNaP7TYN!

[Jay Shendure @JShendure]

Finally out in @naturemethods from the brilliant @jb_lalanne & @SRegalad0, our highly quantitive single cell MPRA (scQer), applied to mammalian embryoids to find autonomous enhancers. Bonus = Tornado circular barcodes that are all kinds of useful. OA link: https://t.co/KtYXuwNOKQ

[Jean-Benoît (JB) Lalanne @jb_lalanne]

After a constructive set of reviews, our single-cell reporter work is OUT https://t.co/ldMqpIJlPs
Check out the briefing if you want the tldr https://t.co/m2Wz5rk28t
I am particularly fond of some of the new applications.
Mini-update.

[Nature Methods @naturemethods]

scQers are quantitative single cell expression reporters reported by @JShendure and colleagues. They enable high-sensitivity quantitative characterization of developmental cis-regulatory elements at the single-cell level.

https://t.co/vGB7oHTBhi

[UW Genome Sciences @uwgenome]

Chromatin context-dependent regulation and epigenetic manipulation of prime editing
https://t.co/LjyHxvoDBh