Thrilled to share that our scE2G paper is now published in Nature Genetics! www.nature.com/articles/s41... scE2G predicts enhancer-gene regulatory interactions from single-cell data with state-of-the-art performance. Amazing work led by @mayayayas.bsky.social and @613weilin.bsky.social!

Mapping enhancer–gene regulatory interactions from single-cell data - Nature Genetics

scE2G is a family of models that predict enhancer–gene regulatory interactions from single-cell datasets and enable mapping of these interactions across diverse cell types and tissues.

nature.com

Jesse Engreitz@jengreitz.bsky.social · 2d ago

Update: scE2G is now online at Nature Genetics! Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well nature.com/articles/s41588-026-02695-8 1/

Absolutely thrilled 💣 to share our preprint 🖨️: "Mapping active cis-regulatory elements from transcription initiation events”. www.biorxiv.org/content/10.6... We introduce nucCAGE and PRIME to identify active cis-regulatory elements (CREs) and disease-associated, non-coding variants.

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!

Robert Krautz@robertkrautz.bsky.social · 3mo ago

Absolutely thrilled 💣 to share our preprint 🖨️: "Mapping active cis-regulatory elements from transcription initiation events”. www.biorxiv.org/content/10.6... We introduce nucCAGE and PRIME to identify active cis-regulatory elements (CREs) and disease-associated, non-coding variants.

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...

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...

biorxiv.org

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!

@xuening-he.bsky.social · last yr.

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...

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...

jobRxiv@jobrxiv.org · last yr.

PhD student – Computational modeling of gene regulation in single cells #ScienceJobs #AcademicSky jobrxiv.org/job/univ...

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...

jobRxiv@jobrxiv.org · last yr.

PhD student – Computational modeling of gene regulation in single cells #ScienceJobs #AcademicSky jobrxiv.org/job/univ...

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...

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…

meetings.embo.org

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...

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.

nature.com

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/

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants

Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...

biorxiv.org

Anshul Kundaje@anshulkundaje.bsky.social · 2y ago

Aiming to release our long awaited ChromBPNet preprint by early next week as well. I'm recovering from back to back infections for the past 6 weeks. But we're almost there. We have some solid variant prediction benchmarks in there against large supervised models and lots more. Stay tuned.

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! 🧪

Altmetric@altmetric.com · 2y ago

There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research. A Place of Joy.

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👇

Wei-Lin Qiu@613weilin.bsky.social · 2y ago

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

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 👇

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

Congenital heart defects (CHD) arise in part due to inherited genetic variants that alter genes and noncoding regulatory elements in the human genome. These variants are thought to act during fetal de...

medrxiv.org

Rosa Ma@rosaxma.bsky.social · 2y ago

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

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 ⬇️

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...

biorxiv.org

Wei-Lin Qiu@613weilin.bsky.social · 2y ago

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

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...

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...

medrxiv.org

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