Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind

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`.

We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)

Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics.

Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...

[SAVE THE DATE] MLCB 2025 is happening Sept 10-11 at the NY Genome Center in NYC!

Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!

Submission deadline: June 1
More details: mlcb.github.io

Help spread the word—please RT! #MLCB2025

Super excited to announce our latest flagship model Borzoi: major props to Johannes & David Kelley et al for advancing it. It's been a long journey from our prior Enformer model into this one. A few innovations: i) longer DNA context, ii) adaptation to predict RNA-seq abundance and splice isoforms,

I'm hiring:

1. Research associate (wet-lab w/ phd) to generate mpra perturbation data

2. ML postdoc to build multimodal generative AI for DNA (eg diffusion and LLMs)

3. Bioinformatician (any level) to process and harmonize functional genomics data to train foundation models

DM me if interested!

Just in time for the holidays, we are thrilled to give you the latest preprint from our lab:

Unique nigral and cortical pathways implicated by epigenomic and transcriptional analyses in a rotenone rat model of Parkinson's disease

doi.org/10.1101/2024...

In a big life update, I successfully defended my PhD thesis - massive thanks to my PI Nathan and assessors @steinaerts.bsky.social @proftomellis.bsky.social . Thrilled to share that I will be joining @pkoo562.bsky.social at CSHL in the new year for a post-doc improving genomic deep learning models!

🚨 We’re hiring! 🚨

The Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory is looking for a Research Technician to join our team.

If you’re passionate about genomics, AI, and experimental science, we want to hear from you.

Help us spread the word!

jobrxiv.org/job/cold-spr...

So excited that our work on predicting gene expression from histone modifications using deep learning is out in NAR today. Brilliant to work with lead author @al-murphy.bsky.social and collaborators Aydan Askarova, @borislenhard.bsky.social and Nathan Skene 🧬⭐️🙏
academic.oup.com/nar/advance-...

(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430

My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body.

If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.

Delighted to share our work to develop a genomic DNN, Enformer Celltyping, to accurately predict epigenetic signals in previously unseen cell types has now been published doi.org/10.1038/s414...

Extending pretrained LM-inspired architectures for genome modeling and releasing a tool for predicting epigenetic signals while being cell type-agnostic. Happy to be a co-author on this excellent paper by @Al_Murphy_ , now in Nature Communications. www.nature.com/articles/s41...

Jessica Zhou (@zrcjessica) is a talented postdoc now on the job market looking for ML/data science industry positions in the NY area! If you have an open position reach out!

Please Repost to spread the word! 🙏🏻

🧬 Genomic DNNs can be trained to learn a lot of different aspects of gene regulation, but they're not perfect and we don't know which predictions are reliable and which ones aren't.

We introduce DEGU: Uncertainty-aware Genomic Deep Learning with Knowledge Distillation. 1/n

Perspective on recent developments and challenges in regulatory and systems genomics
arxiv.org/abs/2411.04363

Great perspective piece from an all-star author list on the current state of regulatory genomics and the challenges ahead.