Surag Nair

Thanks for sharing- the link isn’t working for me.

[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

Hi Wendy, this internship is for current PhD students only.

We are hiring an intern to work with our team at Genentech next summer, on exciting projects related to deep learning for DNA/RNA sequences. Please share and apply! roche.wd3.myworkdayjobs.com/ROG-A2O-GENE...

An interesting diagnostic application of CRISPR is to activate expression of genes in tissues where they are not normally expressed. This is useful when studying functional consequence of suspect pathogenic variants in genes that are restricted to inaccessible tissues like brain, eyes etc. 1/

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...

Mapping enhancer-gene regulatory interactions from single-cell data Mapping enhancers and their target genes in specific cell types is crucial for understanding gene regulation and human disease genetics. However, accurately predicting enhancer-gene regulatory interac...

Excited to share our latest preprint on scE2G – a new model to link enhancers to target genes using single-cell data – with state-of-the-art performance across multiple perturbation benchmarks.

biorxiv.org/cgi/content/...

Read more below!

1/12

go.bsky.app/PFpnqeM

By demand, I've created the final starter pack in my ML Personality Starter Pack Series.

I'm uncertain who belongs in this starter pack and so if you think you better fit in the Grumpy ML or Unreasonably Upbeat ML starter packs, let me know.

(Self) nominations welcome

go.bsky.app/5Suyk58

A reminder for new folks. BlueSky does not have an algorithm to raise posts of interest. It is incumbent upon you to do so via reposting. Liking things only provides feedback to the poster but does not promote the post. The signal to noise ratio is taking a brief beating, so great to help curate.

1/ Introducing SCimilarity, a new foundation model to explore single-cell RNA-seq data across tissues and diseases! It learns a common measure of cell similarity by training a deep metric learning model on millions of cells from various human tissues and conditions. www.nature.com/articles/s41...

Impressive study from Alex Stark lab identifying 3 new types of silencer elements in Drosophila

New TF binds a particular isolated motif in non-accessible sites to recruit G9a. Deletion of these elements can lead to upregulation of nearby gene

www.sciencedirect.com/science/arti...

Overview of variant effect prediction evaluations that have been performed to date using current genomic deep learning models.

We also review variant effect prediction evaluations that have been performed to date on genomic deep learning models, highlighting strengths and limitations of current models and the need for more comprehensive evaluation. 3/4

Leveraging genomic deep learning models for non-coding variant effect prediction The majority of genetic variants identified in genome-wide association studies of complex traits are non-coding, and characterizing their function remains an important challenge in human genetics. Gen...

Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4

arxiv.org/abs/2411.11158

Really intriguing model of AP-1 driven aging.

@anshulkundaje.bsky.social @suragnair.bsky.social - thinking of your AP1-related results in the ChromBPNet paper here...

Thanks Shaun! The perspective piece did mention our preprint. Our pet hypothesis is that partial reprogramming somehow “resets” somatic TFs and moves them back to their cell identity enhancers. If that’s the case, you may not necessarily need OSK but really any set of potent pioneers at high levels!

Highly recommend if you’re considering a PhD in ML for genomics. Jacob is a phenomenal scientist, knows how to dive deep into the nitty-gritty of things, is incredibly patient, and just a very fun person to work with. His weakness? Incosistent joke quality.

Two BioML starter packs now:

Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc

DM if you want to be included (or nominate people who should be!)

Dusting off this account since it seems like BlueSky is suddenly the place to be!
Here's a couple of resources for anyone interested in gene regulation, chromatin, or genomics:
First, a long list of relevant accounts:
bsky.app/profile/shau...
(will make some starter packs at some point)

Extensive binding of uncharacterized human transcription factors to genomic dark matter Most of the human genome is thought to be non-functional, and includes large segments often referred to as "dark matter" DNA. The genome also encodes hundreds of putative and poorly characterized tran...

Incredible resource for DNA binding protein specificity from the Codebook consortium.

www.biorxiv.org/content/10.1...

www.biorxiv.org/content/10.1...

www.biorxiv.org/content/10.1...

www.biorxiv.org/content/10.1...

Am reading these in detail & will have a lot to say. Stay tuned for thoughts.