Chromatin context-dependent regulation and epigenetic manipulation of prime editing pubmed.ncbi.nlm.nih.gov/37090511/

scQers are quantitative single cell expression reporters reported by Jay Shendure and colleagues. They enable high-sensitivity quantitative characterization of developmental cis-regulatory elements at the single-cell level. nature.com/articles/s4159…

After a constructive set of reviews, our single-cell reporter work is OUT nature.com/articles/s4159… Check out the briefing if you want the tldr nature.com/articles/s4159… I am particularly fond of some of the new applications. Mini-update.

Finally out in Nature Methods from the brilliant Jean-Benoît (JB) Lalanne & Samuel Gabriel Regalado, 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: rdcu.be/dHqo1

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_ mskcc.org!

Our DNA Typewriter protocol (written by Hanna Liao, Jay Shendure, and myself) is out! Thank you Nature Protocols for writing/editing this with us and having it as this week’s #FeaturedProtocol :-)

Our latest, from the brilliant Will Chen and Junhong Choi, 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. rdcu.be/dN62L

Today out in bioRxiv 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 Jay Shendure's lab. biorxiv.org/content/10.110…

Excited to share our human RA-gastruloid model in Nature Cell Biology! 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

I am so thrilled to share our work of human RA gastruloid finally out on Nature Cell Biology. It has been a wonderful journey to work with a fantastic stem cell scientist Nobu Hamazaki and many talented collaborators in Jay Shendure lab. Excited to contribute to the field of stembryo!

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: kircherlab.github.io/contact.html

Very happy to share our latest w/ Devin Schweppe and Nobu Hamazaki labs, where we map the temporal dynamics and proteomic landscape of mammalian gastruloids. Sneek Peak 🧵below #stembryo #gastruloid #proteomics biorxiv.org/content/10.110…

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! rdcu.be/dUnoq

Our paper describing a scalable framework for Multiplex, single cell CRISPRa screening for cell-type specific regulatory elements is published! rdcu.be/dUnoq See the linked tweet from my awesome co-lead Flo Chardon for updates since the preprint!

Beyond stoked to share our latest, entitled “Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording” ! biorxiv.org/content/10.110…

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

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. biorxiv.org/content/10.110… 1/19

Updated VISTA Enhancer Browser, 7 years in the making, out in Nucleic Acids Res! >4,500 transgenic in vivo enhancer experiments for all your developmental biology, human variation and #evodevo needs. enhancer.lbl.gov #enhancers #embryos doi.org/10.1093/nar/gk…

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. nature.com/articles/s4159…

Now out in Science Magazine 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. science.org/doi/10.1126/sc…