Tessera
Folgen

Alexandra P

@alexanrna.bsky.social

🇸🇰 PhD student @ KU Leuven and VIB 🇧🇪 Genetics, Bioinformatics, and everything in between (she/her)

32 Posts196 Follower505 Folgt
Cas Blaauw@casblaauw.eurosky.social · 3d ago

Excited to show deepSCENIC to the world! GRNs meet sequence-to-function models: explicit TF-region and region-gene links, with the power of enhancer DL models, predicting RNA & ATAC at single-cell resolution. Check out the examples in the paper or try it on your own data: github.com/aertslab/Dee...

GitHub - aertslab/deepSCENIC: Deep learning for single-cell Gene Regulatory Networks

Deep learning for single-cell Gene Regulatory Networks - aertslab/deepSCENIC

github.com

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 3d ago

DeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference https://www.biorxiv.org/content/10.64898/2026.09.18.752607v1

Wendy Bickmore@wbickmor.bsky.social · 2w ago

It was great working with students Kun and Ryan and @hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers. www.nature.com/articles/s41...

Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics

This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...

nature.com

Itai Yanai@itaiyanai.bsky.social · 4w ago

Advice for new PhD students: choose a mentor who is committed to your training, not just your project. The most important product of your PhD - even more important than the science - is YOU, a newly trained scientist.

Jonas Demeulemeester@jdemeul.bsky.social · 8mo ago

🧬 We're hiring a postdoc! Come chart somatic evolution with us using cutting-edge long-read & single-cell tech 🔬 Computational bio background + love for complex cancer genomics = perfect fit 📍 Leuven, Belgium 📧 jobs.vib.be/j/129915/ #postdoc #genomics #hiring

Postdoctoral Researcher in Cancer Genomics - VIB

Chart tumour evolution using cutting-edge long-read and single-cell multiomics Who we are The Integrative Cancer Genomics lab (Jonas Demeulemeester) is embedded within the VIB – KU Leuven Center for ...

jobs.vib.be

Hannah Dickmänken@hannahdckmnkn.bsky.social · 8mo ago

Paper alert! 💻 How many cells do you need to train reliable deep learning models in regulatory genomics? We asked how data quality, sequencing depth, and dataset size affect training of sequence-to-function models from scATAC-seq. Out now www.nature.com/articles/s41... (details below)

Evaluating single-cell ATAC-seq atlasing technologies using sequence-to-function modeling - Nature Communications

Generating high-quality training data for machine learning is costly. Here, authors include sequence-to-function modeling in benchmarking of custom and commercial droplet-based scATAC platforms, and r...

nature.com

Seppe De Winter@seppedewinter.bsky.social · 8mo ago

We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.

scverse@scverse.bsky.social · last yr.

We will have our next community meeting on Tuesday, 2025-09-16 at 18:00 CEST! Niklas Kempynck will be presenting on CREsted, a package for training enhancer models on scATAC-seq data. (Zoom registration link and more information in thread!) 🧵

Dr. Lucky Tran@luckytran.com · last yr.

"This could be the difference whether your child gets cancer. Are you willing for them to die because the therapy for them is delayed?" Powerful video with voices from top US scientists on the very real and devastating impacts of the funding cuts.

FlyBase@flybase.bsky.social · last yr.

We currently have a call for support that has gone out to European labs, to support FlyBase-UK. We are asking our colleagues from labs in the US and other countries to wait for a similar call to them that will go out in the near future, to support the US sites. We thank you for your patience.

Mark A. Hanson@hansonmark.bsky.social · last yr.

URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯 Any lab using @flybase.bsky.social please donate using the link in post below. This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.