Bashorlab

Really nice work Alex and Garrett!!!!

Now published! Big congrats to first author @gginell.bsky.social

We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions.
www.science.org/doi/10.1126/...

Large-scale control over collective cell migration using light-activated epidermal growth factor receptors Programmable control over tissue movement is a fundamental challenge for tissue engineering and wound healing. Suh, Thornton, et al. discovered that a light-controlled EGF receptor controls long-range...

I'm so happy to report that our preprint on light-induced collective cell migration has now been published in Cell Systems! This project was a lot of fun and will be the basis for a lot of our ongoing & future work.

Big congrats to you and Sofia!

Excited to share our paper in @cp-cellrepphyssci.bsky.social! Building on a fundamental study of bond strength and bursting in textile-based devices, we programmed local failure in a fuse that enables selection and sequencing of tasks with one pressure input. news.rice.edu/news/2025/ha...

Protein codes promote selective subcellular compartmentalization Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. Here, we demonstrate that prote...

🧬🧪Protein codes promote selective subcellular compartmentalization | Science www.science.org/doi/10.1126/...
Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social

SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci - Nature Biotechnology Primary T cells with multiple genetic modifications are rapidly isolated by negative selection.

SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci - @j-eyquem.bsky.social go.nature.com/4gBnaqY

Multiplex generation and single-cell analysis of structural variants in mammalian genomes Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) ...

Now out in @science.org w/ @jshendure.bsky.social 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.

www.science.org/doi/10.1126/...

OxLDL-targeted Chimeric Antigen Receptor T Regulatory Cells Reduce Atherosclerotic Plaque Development https://www.biorxiv.org/content/10.1101/2025.01.24.634830v1

A map of the rubisco biochemical landscape - Nature A massively parallel assay developed to map the essential photosynthetic enzyme rubisco showed that non-trivial biochemical changes and improvements in CO2 affinity are possible, signposting further e...

Fun to see it out in print! I was really lucky to have an amazing team to work with on this. If this sort of work seems interesting to you or someone you know, please feel free to reach out (planning to staff a lab later this year).
www.nature.com/articles/s41...

Multiscale footprints reveal the organization of cis-regulatory elements - Nature We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.

Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning.
Paper: www.nature.com/articles/s41...

This is a scientific figure from the paper mentioned in the post. It shows fluorescence and electron microscopy images and associated schematics for using the ferritag to image clathrin coated pit proteins.

I'd like to draw your attention to this truly excellent paper from the Taraska lab on cryoET of plasma membrane associated proteins. Everyone who is thinking about probes in the cryoET space should also see what they could do with ferritag (fig 6) www.nature.com/articles/s41...

Gene syntax defines supercoiling-mediated transcriptional feedback https://www.biorxiv.org/content/10.1101/2025.01.19.633652v1

Hashing the message with cells - Nature Chemical Biology The programming of multicellular processes for biological computation requires increasingly complex genetic circuit design. Through automated circuit design, it is now possible to systematically break...

Hashing the message with cells by @francolab.bsky.social lab
www.nature.com/articles/s41...

Our global study on the state of trust in scientists is now out in Nature Human Behaviour! 🥳

With a team of 241 researchers, we surveyed 71,922 people in 68 countries, providing the largest dataset on trust in scientists post-pandemic 👇🧵https://www.nature.com/articles/s41562-024-02090-5

Molecular determinants of condensate composition Biomolecular condensates are non-stochiometric assemblies that organize cellular matter in space and time. Despite much work, many questions remain regarding what determines the recruitment and exclus...

New review / perspective with @albertilab-tud.bsky.social on our thoughts on condensate speciality and recruitment, focusing on interplay between site specific and chemically specific interactions

www.cell.com/molecular-ce...

Orthogonalized human protease control of secreted signals Nature Chemical Biology - Engineering of a human-derived protease controlled exogenously by its FDA-approved inhibitor enables control over cytokine activity in cell-based therapies with reduced...

Proteases might serve as versatile control knobs for gene and cell therapies, but there looms the risk of immunogenicity as we and others have been using viral proteases. We now report a control system based on a an engineered human protease and its clinically approved inhibitor. rdcu.be/d6kVt

A foundation model of transcription across human cell types - Nature A foundation model learns transcriptional regulatory syntax from chromatin accessibility and sequence data across a range of cell types to predict gene expression and transcription factor interactions...

A new large language of life model (LLLM) for the transcriptome that predicts gene expression within and across human cell types www.nature.com/articles/s41... @nature.com
For more on the remarkable surge of LLLMs see erictopol.substack.com/p/learning-t...

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation - Nature Genetics Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.

Congrats to Johannes Linder, David Kelley et al. on the journal publication of Borzoi - a long context sequence models of RNA-seq coverage profiles with many nice applications for transcriptional & post-transcriptional regulation & variant effect prediction.

www.nature.com/articles/s41... 1/

Thank you so much!!

Engineering synthetic phosphorylation signaling networks in human cells Protein phosphorylation signaling networks have a central role in how cells sense and respond to their environment. We engineered artificial phosphorylation networks in which reversible enzymatic phos...

🚨NEW PUBLICATION ALERT🚨: In a paper out now in
@science.org we describe a way to build synthetic phosphorylation circuits with customizable sense-and-response functions in human cells. Check it out at science.org/doi/10.1126/....