iiinova — where your digital self keeps evolving

Reposted by Jacob Schreiber

Shenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026

Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41...

35826

Jacob Schreiber @jmschreiber91.bsky.social · 09/03/2026

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

programmable-genomics.github.io

Programmable Genomics Laboratory | Home

1218

Reposted by Jacob Schreiber

Alex Stark @alex-stark.bsky.social · 24/12/2025

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)

biorxiv.org

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...

210448

Jacob Schreiber @jmschreiber91.bsky.social · 10/12/2025

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...

biorxiv.org

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...

26026

Jacob Schreiber @jmschreiber91.bsky.social · 25/11/2025

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!

1120

Jacob Schreiber @jmschreiber91.bsky.social · 20/11/2025

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...

academic.oup.com

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

13514

Reposted by Jacob Schreiber

Pinar Demetci @pinard.bsky.social · 29/10/2025

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...)

052

Jacob Schreiber @jmschreiber91.bsky.social · 13/10/2025

had to land in a nor'eastern storm in boston and i'm ready to move back to the west coast forever

270

Reposted by Jacob Schreiber

Jacob Schreiber @jmschreiber91.bsky.social · 07/10/2025

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.

64326

Jacob Schreiber @jmschreiber91.bsky.social · 07/10/2025

64326

Jacob Schreiber @jmschreiber91.bsky.social · 30/09/2025

is it a good idea to wear a "join, or die!" hat to a big talk in europe? please say yes

130

Jacob Schreiber @jmschreiber91.bsky.social · 22/09/2025

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.

0150

Jacob Schreiber @jmschreiber91.bsky.social · 19/09/2025

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.

0121

Jacob Schreiber @jmschreiber91.bsky.social · 09/09/2025

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

0101

Jacob Schreiber @jmschreiber91.bsky.social · 03/09/2025

stocking up the new apartment with essentials

040

Reposted by Jacob Schreiber

Jacob Schreiber @jmschreiber91.bsky.social · 27/08/2025

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!

14414

Jacob Schreiber @jmschreiber91.bsky.social · 27/08/2025

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?

010

Jacob Schreiber @jmschreiber91.bsky.social · 27/08/2025

14414

Jacob Schreiber @jmschreiber91.bsky.social · 26/08/2025

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...

guangxuanx.com

Why Stacking Sliding Windows Can't See Very Far

Modern LLMs use sliding window attention for efficiency, but why can't stacking sliding windows see as far as theory suggests? A mathematical exploration of information dilution and the exponential ba...

150

Jacob Schreiber @jmschreiber91.bsky.social · 25/08/2025

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

1150

Jacob Schreiber @jmschreiber91.bsky.social · 20/08/2025

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...

0100

Jacob Schreiber @jmschreiber91.bsky.social · 14/08/2025

sitting across the train from a very polite customer

030

Reposted by Jacob Schreiber

Jacob Schreiber @jmschreiber91.bsky.social · 30/06/2025

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:

1205

Jacob Schreiber @jmschreiber91.bsky.social · 30/06/2025

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:

1205

Jacob Schreiber @jmschreiber91.bsky.social · 30/06/2025

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

060

Jacob Schreiber @jmschreiber91.bsky.social · 23/06/2025

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

040

Jacob Schreiber @jmschreiber91.bsky.social · 20/06/2025

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.

090

Jacob Schreiber @jmschreiber91.bsky.social · 18/06/2025

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`

13811

Jacob Schreiber @jmschreiber91.bsky.social · 17/06/2025

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

040

Jacob Schreiber @jmschreiber91.bsky.social · 16/06/2025

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

040

Jacob Schreiber @jmschreiber91.bsky.social · 11/06/2025

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`.

1222

Reposted by Jacob Schreiber

Michael Montgomery @michaeltmont.bsky.social · 11/06/2025

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

0137

Jacob Schreiber @jmschreiber91.bsky.social · 09/06/2025

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`

1294

Jacob Schreiber @jmschreiber91.bsky.social · 05/06/2025

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...

github.com

GitHub - jmschrei/bam2bw: A command-line tool for reading SAM/BAM files and converted them directly to bigwig files.

A command-line tool for reading SAM/BAM files and converted them directly to bigwig files. - jmschrei/bam2bw

4549

Jacob Schreiber @jmschreiber91.bsky.social · 03/06/2025

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

140

Jacob Schreiber @jmschreiber91.bsky.social · 03/06/2025

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...

biorxiv.org

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

Summary Pairwise sequence similarity is a core operation in genomic analysis, yet most attention has been given to sequences made up of discrete characters. With the growing prevalence of machine lear...

25818

Jacob Schreiber @jmschreiber91.bsky.social · 02/06/2025

why yes I do have a grant under review

071

Jacob Schreiber @jmschreiber91.bsky.social · 02/06/2025

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?

5140

Jacob Schreiber @jmschreiber91.bsky.social · 27/05/2025

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

030

Jacob Schreiber @jmschreiber91.bsky.social · 17/05/2025

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

0270

Reposted by Jacob Schreiber

Peter Koo @pkoo562.bsky.social · 16/05/2025

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!

22713