Studying genomics, machine learning, and fruit. My code is like our genomes -- most of it is junk.
Assistant Professor UMass Chan
Previously IMP Vienna, Stanford Genetics, UW CSE.
Jacob Schreiber
Loading...
After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out!
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
The @impvienna.bsky.social is a unique place where talented researchers are doing amazing science. I'm glad I had an opportunity to spend some time there, and am looking forward to the next excuse to visit Vienna!
There's a ton of really cool stuff in the paper. Take a skim if you have time!
The Programmable Genomics Lab at @umasschan.bsky.social
just officially launched our site!
We have a "simple" goal: to develop synthetic regulatory elements that target every cell type in every tissue, and control payload dosage/duration
Check it out!
programmable-genomics.github.io
Ledidi is a DNA design method that designs *edits* to a template while explicitly minimizing the number of needed edits. This allows you to build upon informative starting material, which our genomes are full of, and simply edit in the final touches, similar to an Instagram filter or video touch-up.
We designed regulatory DNA in dozens of settings and found that we could achieve our target objective with surprisingly few edits (biology alert). Because we focus on edits, our designs are less likely to overfit to the model or inadvertently alter properties that are not well captured by the model.
In collaboration with @alex-stark.bsky.social , we designed cell type-specific enhancers and experimentally verified them using STARR-seq. Strikingly, we found that Ledidi can even design enhancers with stronger regulatory activity than the strongest endogenous enhancers.
My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up!
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)
Jacob Schreiber
Jacob Schreiber
Jacob Schreiber
Jacob Schreiber
Tune in for a great MIA talk on ML for regulatory genomics by @jmschreiber91.bsky.social and Gregory Andrews now! 🧪
broad.io/mia
(Will also be available online on our YouTube playlist later: www.youtube.com/watch?v=sMTO...)
Jacob Schreiber
Jacob Schreiber
Jacob Schreiber
Jacob Schreiber
Alex Stark
The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...
