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)

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!

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...

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...

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...

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...

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.

This evaluation of DNA design methods is very well written. If you're interested in the field, you should def take a look. Also, glad to see Ledidi performing so well! www.biorxiv.org/content/10.1...

very sad to report that I have begun adopting the verbal ticks of my first advisor

8 months after submitting my first grant, and a month after my advisory council met, I'm thrilled to report that the council's recommendation is in. 🥳 Hopefully, soon I'll find out what that was.

In vivo mapping of mutagenesis sensitivity of human enhancers www.nature.com/articles/s41...

Last week I released bpnet-lite v0.5.0. BPNet/ChromBPNet are powerful models for understanding regulatory genomics from @anshulkundaje.bsky.social's group, and now it's way easier to go from raw data to trained models and analysis + results in PyTorch Try it out with `pip install bpnet-lite`

It was great to have a chance to share some of my work and to meet everyone there. Thanks for having me!

Honestly, one of the nicest stations I've ever been in. I'll even forgive them for having a J in the word.

Just released tangermeme v0.5.0! tangermeme implements "everything-but-the-model" for genomic ML Essentially, train your model your way using your code-base (or load someone else's model), and tangermeme handles the discovery + design with it. Try it out with `pip install tangermeme`.

Had a lot of fun writing this “tools of the trade” highlight for our Variant-EFFECTS technology. Check it out! 🛠️

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`

Released a new version of my little data processing tool, `bam2bw`. As you might expect, it goes directly from BAM to un/stranded bigwig(s), but now also supports fragment.tsv files. No more intermediary sorting and bedGraph steps! Way faster + less disk than before. github.com/jmschrei/bam...

I'm sorry Vienna but this weather needs to be made illegal.

I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier. www.biorxiv.org/content/10.1...

why yes I do have a grant under review

just because I didn't work both days of the weekend doesn't mean you have to write an article about me :( www.newscientist.com/article/2232...

The worst part about being a PI is figuring out which meetings and obligations to cancel to fit in 8 hours of Factorio every day. How do others do it?

the saddest part about eRA commons going down is that it doesn't stop me from continuing to check every few minutes

me reviewing cool grants for a Swiss AI initiative that will provide them with lots of resources that i can't apply for

The premier conference on Machine Learning for Computational Biology is Sep 9-10 at the NY Genome Center in NYC! Submission deadline is June 1 for 2-page abstracts and 8-page papers (eligible for proceedings track). Registration is now open! (Link below) Please retweet!

Very happy to see that ISMB has put the outcome of your submissions in the title of their emails now, instead of causing a panic as you try to decipher what the first few words in the preview mean. Anyway, I'll be giving a talk on Ledidi at @iscb-regsys.bsky.social this year! Who else is going?