Genome-wide rules of transcription factor cooperativity revealed through in silico binding site ablation Transcription factor (TF) cooperativity plays a critical role in gene regulation. However, the underlying genomic rules remain unclear, calling for scalable methods to characterize the TF binding site...

Excited to share DeepCompARE + ISA - a lightweight deep learning model + efficient interpretation method, to uncover rules of TF cooperativity via genome-wide in silico motif ablations!

Preprint: www.biorxiv.org/content/10.1...
Github: github.com/anderssonlab...

Latest from the lab! Led by @xuening-he.bsky.social, establishing a framework for interpretation of the motif syntax of regulatory elements and a quantitative model for transcription factor cooperativity. Plenty of cool stuff revealed, including TF redundancy and synergy, and their regulatory roles!

Symposium on ‘Enhancer Sequences’ at beautiful @collegedefrance.bsky.social in Paris, by April 11th. Open and free, no registration. Come to relax listening to facts #TherapeuticEffects #VillageGauloix Final programme below. Tell your friends! 🙏🤘

Job alert!

We are hiring a postdoc or PhD student focusing on
* developing computational methods to resolve gene regulation in single cells
* investigating the mechanisms and cell-type specific effects of genetic variants

PhD student: bsky.app/profile/jobr...

Postdoc: bsky.app/profile/jobr...

Job alert!

We are hiring a postdoc or PhD student focusing on
* developing computational methods to resolve gene regulation in single cells
* investigating the mechanisms and cell-type specific effects of genetic variants

PhD student: bsky.app/profile/jobr...

Postdoc: bsky.app/profile/jobr...

Enhancer Mechanics and Enhanceropathies Join us for the highly anticipated third EMBO workshop on Enhancer Mechanics and Enhanceropathies! Building on the success of our previous meetings in Santander (2021) and Marseilles (2023), this eve…

Together with @smandrup.bsky.social and Minna Kaikkonen we are happy to announce the 3rd Edition of the EMBO Workshop on #Enhancers and #Enhanceropathies. This time we will meet during the beautiful Danish summer (June 16-21).

Book the dates and register soon!!!

meetings.embo.org/event/25-enh...

Multiscale footprints reveal the organization of cis-regulatory elements - Nature We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.

Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning.
Paper: www.nature.com/articles/s41...

My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.

It’s available on Amazon: tinyurl.com/mx2hewen

This looks great! Just ordered.

Our ChromBPNet preprint out!

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

Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

We are pursuing the wrong applications for AI.

Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪

I'd suggest this starter pack for #epigenetics and #generegulation:
go.bsky.app/TKp9YAn
plus see the description for another 3!

Introducing scE2G: a new model to link enhancers to target genes using single-cell data.

Excited that scE2G will enable building enhancer maps in hundreds of cell types in the human body!

Wonderful collaboration with @randersson.bsky.social @613weilin.bsky.social @mayayayas.bsky.social

Thread👇

Our preprint:

Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart

Multiomic atlas + human genetics = new cell types, genes, and pathways that influence heart development and disease

www.medrxiv.org/content/10.1...

Thread 👇

What cell types drive congenital heart defects (CHD)?

Some new answers in our latest preprint, where we explored:
1). Key cell types contributing to CHD genetics
2). Impact of noncoding variants on CHD risk

www.medrxiv.org/content/10.1101/2024.11....

Check out some highlights of the work here bsky.app/profile/613w...

Check out our latest work, scE2G, for mapping the target genes of enhancers from single cell data! www.biorxiv.org/content/10.1...

Amazing work led by co-first authors @mayayayas.bsky.social and @613weilin.bsky.social in a great collaboration with @jengreitz.bsky.social's lab

See 🧵 by Wei-Lin ⬇️

Insights from complex trait fine-mapping across diverse populations Despite the great success of genome-wide association studies (GWAS) in identifying genetic loci significantly associated with diseases, the vast majority of causal variants underlying disease-associat...

For an idea of how well fine mapping results replicate between biobanks, I would really recommend checking out this preprint from @masakanai.bsky.social
www.medrxiv.org/content/10.1...

Thanks! Glad you liked the talk. Feel free to share as you wish.

Saturday morning: first session, second talk

Looking forward to #cshldata24 meeting starting tonight!

I will present #scE2G, a highly accurate model for mapping enhancer-gene regulatory interactions from single cell data. The model was developed in close collaboration with @jengreitz.bsky.social lab.

Who else is attending the meeting?

Seeing all the excitement from fellow scientists moving from X to here reminds me of academic Twitter 10 years ago. Let’s try out this platform!

I’m a computational genomicist focused on modeling gene regulation.

#firstpost #helloworld #introduction