🔥The 9th Round of Easy Loan, Earn $40 Reward is in progress❗️ ⏰ Promotion Period: January 15th - Feburary 15th, 2025 👉 Register now and check more details at gate.io/campaigns/358

🚀 Jenna Lynn Collier in my group is hiring a 2025 Summer Research Intern in AI/ML Genentech! She is SUPER innovative and is pushing the boundaries on how AI is shaping the Genentech drug development pipeline, see posting below! roche.wd3.myworkdayjobs.com/ROG-A2O-GENE/j…

Did you think you were too late for a cool summer internship? Think again! 12 weeks of awesomeness on aging and partial reprogramming working with some great post-docs from the Jasper and Marioni labs at Genentech. roche.wd3.myworkdayjobs.com/ROG-A2O-GENE/j…

[SAVE THE DATE] MLCB 2025 is happening Sep 10-11 at the NY Genome Center—NYC! Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections! Submission deadline: Jun 1 Details: mlcb.github.io Spread the word—please RT!

Many have claimed that AI is struggling to predict genomic function due to the limited & repetitive nature of the training sets. Here's one step towards solving this problem. Congrats André Santos and Matt Maurano. biorxiv.org/content/10.110…

Extremely promising direction! Can’t wait to see what happens when you scale this up to training on many (hundreds of) thousands of rearrangements!

If you don't already put your papers on ArXiv/BioRxiv, you should really start doing it. Pretty soon most interaction with the scientific literature will be via agents, and it's way easier for agents to access things on ArXiv/BioRxiv.

Can DNA sequence models predict mutations affecting human traits? We introduce TraitGym, a curated benchmark of causal regulatory variants for 113 Mendelian & 83 complex traits, and evaluate functional genomics and DNA language models. Joint work w/ gokcen and Yun S. Song 🧵👇

A socratic dialogue over the utility of DNA language models (Part 1 of 2) here's the link: owlposting.com/p/a-socratic-d… and here's a longpost of why i wrote this: i think the effort that went into Evo 2 is very cool and its clearly a very comprehensive paper but the excitement

We are excited to announce the release of the enGenome VarChat track for hg38 and hg19. This track uses AI to search papers for variants, providing information such as its gene, HGVS nomenclature, and dbSNP rsID. Learn more at genome.ucsc.edu/goldenPath/new….

Lab-in-the-loop therapeutic antibody design At Prescient Design Genentech we have spent 3+ years reimagining drug discovery. We built a machine learning system to design and execute experiments. Here's how it works and what we can do 🧵 1/

The peer-reviewed version of our preprint on transfer learning to predict the chromatin response to TF dosage is now out: cell.com/cell-genomics/…

Austin Wang is a fantastic grad student in the lab who will be completing his PhD in the Fall & is looking for research position in AI for bio in industry. austintwang.com 1/

Excited to share a preprint from Howard Chang's lab, co-led w/ Jiaying Li! We combine single-cell multiomics, enhancer mapping, & functional testing of human RPE and choroid to nominate causal variants in macular degeneration. Surag Nair Anshul Kundaje (anshulkundaje@bluesky) biorxiv.org/content/10.110…

📅 Tomorrow: Wednesday, April 2 💬 gokcen Eraslan 🏫 ReLU, BRAID, Genentech 💡 A primer on DNA foundation modeling 💬 Surag Nair 🏫 ReLU, BRAID, Genentech 💡 Nona, a novel multimodal masked modeling framework for functional genomics 🗓️ Add to calendar: events.broadinstitute.org/event/models-i…

I am recruiting a quantitative/computational postdoc to my group at UCLA. This is a great opportunity to work on foundational theory, methods, and software in statistical genetics. Link to apply below. Please repost!

Perspective on recent developments and challenges in regulatory and systems genomics academic.oup.com/bioinformatics… is out, amazing to think about this with Julia Zeitlinger (@[email protected]), Ferhat Ay, Shaun Mahony, Anthony Mathelier, Alejandra Medina-Rivera, Jason Ernst!

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!

Wrapped up Stanford CS336 (Language Models from Scratch), taught with an amazing team Tatsunori Hashimoto Marcel Rød Neil Band Rohith Kuditipudi. Researchers are becoming detached from the technical details of how LMs work. In CS336, we try to fix that by having students build everything:

Sara Mostafavi (Genentech ) & I (Stanford University) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/