Jacob Schreiber
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.
- Reposted by Jacob SchreiberOur 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)
- 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...
- 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.
- 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!
- 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...
- Reposted by Jacob Schreiber[Not loaded yet]
- Reposted by Jacob Schreiber[Not loaded yet]
- had to land in a nor'eastern storm in boston and i'm ready to move back to the west coast forever
- Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians! The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
- We have an array of ML-based projects for going after this, focusing on the following topics: - DNA Design ( 🧬 ) We have shown that Ledidi (www.biorxiv.org/content/10.1...) can precisely design DNA, and now it's time to push the boundaries in several directions w/ some very cool collaborations.
- is it a good idea to wear a "join, or die!" hat to a big talk in europe? please say yes
- the greatest productivity hack is having a grant deadline. there's so much other stuff you can do when you're supposed to be working on a grant.
- I was delighted to have the unexpected opportunity to give a keynote at MLCB 2025 in NYC last week. I used it to explain how I view deep learning models in genomics not as "uninterpretable black boxes" but as indispensable tools for understanding genomics + designing the next gen of synthetic DNA.
- for some reason i thought being a professor would involve more mentoring and research and less filling out disclosures concerning whether plants and seeds were used in my computational study
- stocking up the new apartment with essentials
- For some reason, hitting "comment" on GitHub is significantly more responsive than a month ago and it freaks me out. Surely there are some important calculations that need to be done before letting my thoughts into the wild?
- In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance. While undoubtedly important, how we *use* these models after training is potentially even more important. tangermeme v1.0.0 is out now. Hope you find it useful!
- Preprint: biorxiv.org/content/10.1... Installation: `pip install tangermeme`
- An excellent post about the receptive range of convolution models. "You might reasonably ask: "If I have 100 layers with W=1000W=1000, that's a theoretical receptive field of 100,000 tokens. Doesn't that matter?" The answer is no, and here's why:" guangxuanx.com/blog/stackin...
- First week as a faculty was successful: one grant submitted, one paper submitted, and revision requests back on one paper. If we extrapolate, by the time I'm up for tenure I'll have 260 grants submitted (none awarded) and 260 papers submitted/reviewed (none accepted). ` lgtm
- Almost a year ago I submitted a NIH grant and federal funding collapsed. Continuing on that success, I'm proud to announce that I've just submitted a local grant...
- now i get to be happy, right?
- I'm glad that I had a chance to contribute to this wide-ranging article discussing the myriad ways ML is being used in genomics: www.nature.com/articles/d41...
- First day 🥰🥰
- sitting across the train from a very polite customer
- Reposted by Jacob Schreiber[Not loaded yet]
- medium demand expected
