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

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)

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo

Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...

biorxiv.org

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...

Programmatic design and editing of cis-regulatory elements

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...

biorxiv.org

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!

IMP@impvienna.bsky.social · 8mo ago

“…[at the IMP] collaborations can develop naturally across many projects…” We sat down with Jacob Schreiber after he wrapped up his one-year stay at the IMP, and he told us all about it: www.imp.ac.at/news/article... @jmschreiber91.bsky.social, @viennabiocenter.bsky.social

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...

Tomtom-lite: accelerating Tomtom enables large-scale and real-time motif similarity scoring

AbstractSummary. Pairwise sequence similarity is a core operation in genomic analysis, yet most attention has been given to sequences made up of discrete c

academic.oup.com

Jacob Schreiber@jmschreiber91.bsky.social · last yr.

Last week I shared a preprint on tomtom-lite, a super fast re-implementation of Tomtom for annotating short genomic spans with the motifs they most resemble. Now, there's a convenient command line tool `ttl` that comes with the installation. You can get it with `pip instal memelite`

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...)

I'm happy to share that our gReLU package is now published in Nature Methods! www.nature.com/articles/s41...

gReLU: a comprehensive framework for DNA sequence modeling and design - Nature Methods

gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.

nature.com

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.

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.

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

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!

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!

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...

Beyond AlphaFold: how AI is decoding the grammar of the genome

Scientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools.

nature.com

First day 🥰🥰

sitting across the train from a very polite customer

I’m also excited to be presenting Oxbow as part of my talk on composability at the #SciPy2025 Conference on Wednesday! Hope to see some of you there. cfp.scipy.org/scipy2025/ta...

Breaking the silo: composable bioinformatics through cross-disciplinary open standards SciPy 2025

The practice of data science in genomics and computational biology is fraught with friction. This is in large part because bioinformatic tools tend to be tightly coupled to file input/output. As a res...

cfp.scipy.org

medium demand expected

Today marks the end of en-JUNE-eering, the month where I focused mostly on the nitty gritty of improving genomics ML infrastructure. Here are some of the highlights:

Today marks the end of en-JUNE-eering, the month where I focused mostly on the nitty gritty of improving genomics ML infrastructure. Here are some of the highlights:

Thank you, Google Flights, for recommending this 10 hour layover in Athens first by "convenience" when trying to find a Frankfurt -> Vienna flight.