Big congratulations to Dr. Xuening He, @xuening-he.bsky.social, who yesterday successfully defended her PhD thesis in Bioinformatics 🎉 Genome-wide Rules of Transcription Factor Cooperativity Revealed through Interpretable Deep Learning

Excited to see this preprint out from the lab! Congrats to @heinarsson.bsky.social, Natsuda, @robertkrautz.bsky.social, and all co-authors involved in this major effort on developing nucCAGE and PRIME, and on evaluating transcription initiation-defined regulatory elements for variant interpretation!

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...

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...

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

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 https://www.medrxiv.org/content/10.1101/2024.11.20.24317557v1

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 ⬇️

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...

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