1/1 "SpRYgest, takes the die out of digest" - Rachel Silverstein We recently repurposed our PAMless Cas9 enzyme SpRY for in vitro DNA digests (so-called “SpRYgests”), as a substitute to overcome the limitations of restriction enzymes . A 🧵: biorxiv.org/content/10.110…

They must be having a bad dream of drowning….

OK, I'm now ~3 years into being a #newPI, and I finally feel like I basically know what the job is and how to do it. One important part was finding an organizational method. Here's what works for me! 🧵 1/

We are ecstatic to have support from @NIGMS through R35 ESI-MIRA award! Our major goal is to understand and control the formation of signaling protein complexes.

Know anyone curious about 21st century bioengineering? Prof. Jenn Brophy (Jennbrophy.bsky.social) & I are sharing ~40 videos comprising most of Stanford's introductory bioengineering course:   introbioe.stanford.edu We'll push updates; feedback welcome #bioe4all #2xplaybackftw

How big are the cells? Microorganisms in perspective

Congratulations to this constantly amazing group of students, postdocs, staff & collaborators including the indomitable @yoon_Seok_Kim, with @emekato, SeeYa & our whole structure team! A new mechanism for K+ selectivity->new tools for biology. shorturl.at/pqDM1

When you're diving into a new field, it can be difficult to know where to start. But if the new field is synthetic biology, Niko McCarty.'s got you covered! Learn more in our latest blog post: hubs.la/Q022c1pz0

And Spatial VDJ is out! More to follow, but for now, joy and gratitude for the privilege to work with the wonderful Kim Thrane Qirong Lin @Jeff_Mold Jonas Frisén Joakim Lundeberg and many more collaborators. Karolinska Institutet SciLifeLab KTH Royal Institute of Technology science.org/doi/10.1126/sc…

Exciting news! Our latest research on "Cell type directed design of synthetic enhancers" has been published in nature. We've harnessed deep learning to design enhancers with cell-type specificity. Find our paper here: nature.com/articles/s4158…. Highlights below: [1/n]

Our first paper is out in Cell! Led by Rohith Rajasekaran, we present a programmable reaction-diffusion system that generates synthetic protein waves, oscillations, and patterns for spatiotemporal circuit design and FM data-encoding in human cells. authors.elsevier.com/a/1iN8ZL7PXmeeN

Short summary thread of our recent review on de novo protein design: (Poster-sized figure (36 x 48 inches) for printing: drive.google.com/file/d/1sG3OlE…)

Do you need a billion parameters and millions of sequences for #proteindesign? Maybe not! See our paper: shorturl.at/novMO We show that interpretable, non-autoregressive structure-based protein design can work! Original thread: shorturl.at/cdgCP

Today we report in Nature Communications the development of laboratory-evolved CBE6 cytosine base editors that offer high on-target C•G-to-T•A editing, virtually no A•T-to-G•C editing, low off-target editing, broad sequence context compatibility, and compatibility with multiple Cas

We’re very excited to share the first preprint from my lab along with Harry McNamara, @BillZJia, Adam Cohen, and Alex Schier. We describe a set of methods for exerting spatial control over Nodal signaling in zebrafish development. biorxiv.org/content/10.110…

After nearly 7 years, my PhD work is out in nature! Big big thank you to everyone involve within the The Rihel lab and the 🐟 floor UCL Research Dept of Cell & Developmental Biology nature.com/articles/s4158…

Figeno, my visualization tool for genomics🎨🧬, is now published in Bioinformatics! doi.org/10.1093/bioinf… It can generate publication-quality figures for sequencing data along genomic coordinates: bigwig, HiC, Oxford Nanopore data with base modifications, and WGS with CNAs and SVs.

Our latest: a new optogenetic system for precise spatiotemporal control of gene expression We use it to dissect the dynamics of Shh gradient formation & patterning A thread 🧵 biorxiv.org/content/10.110…

#SynBYSS 10AM USA CT 128th on Jun 13 with Prof Michael Elowitz ElowitzLab & Brendan Camellato New York University 129th on Jun 20 with Prof Chris Myers at CU Boulder CU Boulder 🦬 & Dr Jingchuan Luo at Whitehead Inst. Whitehead Institute Zoom for general audience👇 us02web.zoom.us/j/88380504839

I am beyond excited to present our work on Vg1 and SynPro system at the 18th International Zebrafish Conference in beautiful Kyoto! #izfc2024