Our new paper on “synpoptosis” circuits, led by the amazing Shiyu Xia (夏时雨), is now out: sciencedirect.com/science/articl… (1/3)

As a side product, while developing SMORE, Zain Samadi also reimplemented the original STREME algorithm in MATLAB. This is especially convenient for Windows users: github.com/zsamadi/MATLAB…

I have been thinking about the best approaches for building predictive models in liquid biopsies for many years now! Orion, which was built by the exai bio team with input from our advisors Olivier Elemento and James Zou is the culmination of that effort. medrxiv.org/content/10.110…

Excited to have lineage motifs out in the world. Hoping the concept and methods can be useful in various developmental systems as more lineage data become available. Congratulations to Martin Tran and Amjad Askary on the work, and thanks to Adara Koivula and Inna-Marie for…

Delivering and expressing a gene in cells is usually a messy (heterogeneous) process. The messiness interferes with research and applications such as gene therapy.
In two new papers, we introduce a toolbox of synthetic miRNA-based control circuits that enable more precise, gene…

If you liked this preprint, you are going to love the peer-reviewed version now out in Dev. Cell:
sciencedirect.com/science/articl…

It's great to see the evolution of imaging based molecular recording technology

This is so cool. Imaging-based pooled genetic screens going in vivo!

Our paper with Eric Deeds is now up on PLoS Comp Bio. Some new goodies since the preprint including an implementation of a generalized form of the branch distance!
journals.plos.org/ploscompbiol/a…

Last week, I shared GEDI, our model for interpretable integration of cohort-level single-cell data (biorxiv.org/content/10.110…).
One of GEDI's abilities is cluster-free differential expression analysis. What does it mean, and how do we do it? 1/15

This is now out in Cell Reports!
cell.com/cell-reports/f…
It's accompanied by this very kind preview:
cell.com/cell-reports/f…
by Kronforst and Sheikh, which also looks at really cool work by Nishida et al on a convergently-evolved green liquid wing pigment (!?!?)