Bashor Lab in Houston, Texas | Mammalian Synthetic Biology et al.
Houston, TX
Joined December 2022
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Bashor Lab retweeted
Efficiently finding a desired set of mutations to push protein toward a desired property in the sea of 20^L possible mutations is one of the holy grails of molecular engineering. Introducing ProTEUS: a mutation-resolved World Model for closed-loop protein evolution with SOTA performance on various protein engineering tasks and a new axis of scaling.
Bashor Lab retweeted
What can we learn from all cytokines in the human genome? For most, we have limited info on what they do and when to target them
Meet TAPAS & EPICURE: tools to synthesize all human cytokines➡️scRNA data of primary human immune responses➡️🖥️methods to use them in your work (1/n)
Bashor Lab retweeted
Generative protein design is transforming macromolecular drugs, but de novo designed therapeutics could still be hindered by immunogenicity in the clinics. Excited to introduce MESSI, a discrete diffusion model for generative protein deimmunization.
Bashor Lab retweeted
1/ Even bacterial communities can get caught in a bad romance they just can't get over.
A brief encounter with antibiotics can leave a lasting ecological memory of resistance plasmids persisting for weeks after the drug is gone. @DukeBiodesign @DukeUBME
nature.com/articles/s41467-0…
Bashor Lab retweeted
Happy to share our latest preprint in collaboration with @BashorLab. Great work by first author Alena Streletskaia. biorxiv.org/content/10.64898…
ALT Circular stem cell colonies with BMP activated on one side. Brachury and N-CAD positive cells are seen migrating from the light-induced source.
Bashor Lab retweeted
Highly multiplexed mammalian metabolic engineering with a shotgun approach - @sudpinglay @JefBoeke nature.com/articles/s41587-0…
Bashor Lab retweeted
AI in biology may have a data problem before it has a model problem.
It’s easy to use AI to make drug discovery faster & more efficient. The much harder challenge is discovering impactful medicines humans would never have found.
AI models are only as useful as the data they learn from, and it’s especially hard in biotech. The biggest and most valuable goals in AI in biotech are to cure diseases we haven’t been able to cure and design therapeutics capable of doing things that haven’t been possible before. By definition, these goals aren’t represented in our training data.
For our second essay at Waypoint Bio, we wrote about the data we think we’ll need to build out-of-distribution medicines: waypointbio.com/writings
Bashor Lab retweeted
Cell–cell interactions are key to all biological processes, but there hasn't been a good way to perform inter-cellular screens for genetic regulators of these interactions in vivo.
We developed match-seq (multiplexed associative tagging of cell interaction histories) - using engineered virus-like particles to transfer barcoded mRNAs from 'sender' to neighboring 'receiver' cells, so you can reconstruct cellular interactions with sequencing alone, no imaging required.
We coupled match-seq with CRISPR + scRNA-seq in cancer, revealing cancer-immune interaction neighborhoods at scale, and new cancer genes that can be targeted for tumor rejection via immune cell interactions.
Led by the brilliant @peterdu_ with Bassik lab!
biorxiv.org/content/10.64898…
Bashor Lab retweeted
Excited to share our latest work, led by Surbhi Sharma! We study the kinetics of RNA localization to the outer mitochondrial membrane (OMM), building on our 2019 APEX-seq work showing that hundreds of RNAs go to the OMM for local translation. biorxiv.org/content/10.64898…
Bashor Lab retweeted
Excited our ratiometric transcriptional activation (RTA) work led by @Melissa_Gray234 is out online today @CellCellPress! Measurements determine what we can discover in biology; we use RTA to turn protein abundance changes into amplified signals.
cell.com/cell/fulltext/S0092…
Bashor Lab retweeted
Excited to share our new preprint!
We asked how inducible SynNotch-CAR circuits can better discriminate on-target from off-target cells when they share similar antigens.
biorxiv.org/content/10.64898…
Congratulations to Daniel Hoces, Jaclyn Ng and Julian Perez!
Bashor Lab retweeted
1/ Let’s face it: we synthetic biologists are control freaks. We want every component to do exactly what we intend and nothing else.
Our new paper asks what happens if we stop fighting biological “messiness”.
@DukeBiodesign @DukeUBME
nature.com/articles/s41467-0…
Bashor Lab retweeted
Controlling the transcription with the DNA… that stays outside of the cell? Introducing LUNAR, a chemogenetic receptor gated by DNA for sensing applications. This complex project was led by @BoaoXia with collaborators @aliceyting and @nkalogriopoulos.
biorxiv.org/content/10.64898…
Bashor Lab retweeted
Excited to share our new preprint: RegFM, an interpretable context-aware foundation model for human transcriptional regulation. 🧬
There are already a lot scFMs and DNA FMs in the field. We ask: Can a genomic FM understand both DNA sequence and the underlying cellular context?
Bashor Lab retweeted
We've long wondered what gives NETs their branched architecture. Working with @SCWestLab, @DArmstrongJames we found that RAD51—a protein involved in DNA repair—promotes NET branching & stability, spatially restricting NETs to control type-2 inflammation.
science.org/doi/10.1126/scie…
Bashor Lab retweeted
Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote
1/n
Bashor Lab retweeted
Nature research paper: Sequential reading of a stepwise-shortened peptide immobilized on nanopore
go.nature.com/4h4kaHk
Bashor Lab retweeted
Our review is now published in @NatureGenet! We cover all aspects of modeling regulatory genomics, from loss landscapes to OOD generalization to model interp to fixing generalization issues using perturbation data via active and continual learning!
nature.com/articles/s41588-0…
Excited to share a new Review: "Toward Interpretable and Generalizable AI in Regulatory Genomics" with @msyk_nagai @Al_Murphy_ @kae_rizzo
We lay out the landscape of AI x Genomics and offer an opinionated perspective on where the field should go!
arxiv.org/abs/2602.01230
Bashor Lab retweeted
New Toettchlab paper alert! Harrison Oatman just published his beautiful work combining software design for "smart" microscopy+optogenetics and some really beautiful work understanding EGFR-driven collective cell migration.
cell.com/cell-systems/fullte…