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Alexandra P

@alexanrna.bsky.social
196 followers 508 following 32 posts

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

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Astronomer Royal for Scotland | Catherine Heymans @astroroyalscot.bsky.social · 29/09/2026
One additional 'quick fact': if your name is John, the Nobel committee is twice as likely to award you the Prize for Physics, compared to scientists who are female - Number of physics prizes to a John: 10 - Number of female physics Nobel laureates: 5 Best wishes to all the John-hopefuls this yr 👩‍🔬⚛️
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Cas Blaauw @casblaauw.eurosky.social · 22/09/2026
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.com
GitHub - aertslab/deepSCENIC: Deep learning for single-cell Gene Regulatory Networks
Deep learning for single-cell Gene Regulatory Networks - aertslab/deepSCENIC
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 22/09/2026
DeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference www.biorxiv.org/content/10.64898/20…
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Wendy Bickmore @wbickmor.bsky.social · 08/09/2026
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...
nature.com
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...
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Itai Yanai @itaiyanai.bsky.social · 31/08/2026
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.
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Hannah Dickmänken @hannahdckmnkn.bsky.social · 29/06/2026
Looking forward to 5 days of insect science #ECE2026Tours ! Join my talk tomorrow in the insects & society AI session at 18h15 on what genomics and Deep Learning can teach us about fly development 🧬
Photo of title slide at the start of the ECE conference in the main auditorium.
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Aleena M Stolworthy @aleenamolbio.bsky.social · 13/06/2026
Women's forum taking place in G2 #eshg2026 Create a safe and active space for conversation Open and welcome to everyone
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Alexandra P @alexanrna.bsky.social · 12/06/2026
I will be presenting this work at #eshg2026 on Monday during "From Population to Pertubation" session (C31, room F1-F3 @ 10:30)!
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Aligning Science Across Parkinson's @asapresearch.parkinsonsroadmap.org · 18/05/2026
This month’s Discover ASAP features CRN Team Voet's @olgasigalova.bsky.social, Alexandra Pančíková, @juliedeman.bsky.social, & Koen Theunis 🧪 They share a dataset linking non-coding variants to cell type–specific gene regulation in the brain, revealing how genetic risk shapes #PD bit.ly/4trTmmN
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Alexandra P @alexanrna.bsky.social · 16/04/2026
1/ 🧬 Happy to share our new preprint on modeling cis-regulatory variation in human brain enhancers across a large Parkinson’s disease cohort: www.biorxiv.org/content/10.6... Details in the thread below:
biorxiv.org
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Alexandra P @alexanrna.bsky.social · 16/04/2026
1/ 🧬 Happy to share our new preprint on modeling cis-regulatory variation in human brain enhancers across a large Parkinson’s disease cohort: www.biorxiv.org/content/10.6... Details in the thread below:
biorxiv.org
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VIB.AI @vibai.bsky.social · 03/04/2026
The @steinaerts.bsky.social lab published CREsted, an end-to-end modeling framework to 🧬 Train sequence-based enhancer models on large sc datasets 🔍 Decode enhancer logic with nucleotide-level interpretability ⚙️ Design synthetic enhancers with cell-type specificity tinyurl.com/ypurmrw5
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Wouter De Coster @wdecoster.bsky.social · 27/03/2026
The registration deadline for the Flanders Nanopore Day with @nanoporetech.com is quickly approaching, and the program suggests it will be an amazing event! All information is available at nanoporeflanders.be
nanoporeflanders.be
Flanders Nanopore Day 2026 - Flanders Nanopore Day
The Flanders Nanopore Day - April 17th, 2026
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 19/03/2026
Modeling cis-regulatory variation in human brain enhancers across a large Parkinson's Disease cohort www.biorxiv.org/content/10.64898/20…
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Alexandra P @alexanrna.bsky.social · 23/02/2026
Last week to submit an abstract to Flanders Nanopore Day conference!
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Jonas Demeulemeester @jdemeul.bsky.social · 09/02/2026
🧬 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
jobs.vib.be
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 ...
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Hannah Dickmänken @hannahdckmnkn.bsky.social · 29/01/2026
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)
nature.com
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...
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VIB-KU Leuven Center for Neuroscience @vibneuroleuven.bsky.social · 27/01/2026
🚀 Proudly introducing the VIB-KU Leuven Center For Neuroscience, a merger of the two former VIB research centers VIB-KU Leuven Center for Brain & Disease Research and Neuro-Electronics Research Flanders (NERF)! Our new motto: Bold Science, Real Impact. www.youtube.com/watch?v=uhaq...
youtube.com
VIB-KU Leuven Center for Neuroscience
YouTube video by VIB-KU Leuven Center for Neuroscience
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Seppe De Winter @seppedewinter.bsky.social · 15/01/2026
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.
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Wouter De Coster @wdecoster.bsky.social · 13/01/2026
Join us at the Flanders Nanopore Day conference on April 17th in Antwerp, organized together with @nanoporetech.com! Details are available at nanoporeflanders.be, including registration (free), abstract submission, and project prizes with free PromethION sequencing for two selected projects.
nanoporeflanders.be
Flanders Nanopore Day 2026 - Flanders Nanopore Day
The Flanders Nanopore Day - April 17th, 2026
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Alexandra P @alexanrna.bsky.social · 09/01/2026
We are looking for a new colleague in the lab of @jdemeul.bsky.social! If you are looking for a Postdoctoral position in Cancer Genomics,check the position here: jobso.id/pbgr
jobso.id
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 ...
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VSC | Vlaams Supercomputer Centrum @vschpc.bsky.social · 05/01/2026
🧬 How do cancer cells evolve, and become drug resistant during therapy? Researchers at VIB–KU Leuven developed SPLONGGET, a new single-cell method combining long-read sequencing with multi-omics to reveal tumor evolution and CAR-T therapy resistance. 🔗 www.vscentrum.be/post/new-met...
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Stein Aerts @steinaerts.bsky.social · 23/09/2025
We have two open positions for a ML and a LLM engineer to launch a machine learning expertise unit in our center @vibai.bsky.social, see vib.ai/en/opportuni...
vib.ai
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Alexandra P @alexanrna.bsky.social · 10/09/2025
1/ First preprint from @jdemeul.bsky.social lab 🥳! We present our new multi-modal single-cell long-read method SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome)! www.biorxiv.org/content/10.1...
ikea-style logo of splongget
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scverse @scverse.bsky.social · 10/09/2025
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!) 🧵
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Alexandra P @alexanrna.bsky.social · 10/09/2025
1/ First preprint from @jdemeul.bsky.social lab 🥳! We present our new multi-modal single-cell long-read method SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome)! www.biorxiv.org/content/10.1...
ikea-style logo of splongget
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FlyBase @flybase.bsky.social · 15/08/2025
FlyBase needs your help! We ask that European labs continue to contribute to Cambridge, UK FlyBase, whereas US and other non-European labs can contribute to US FlyBase. For more information and how to donate: wiki.flybase.org/wiki/FlyBase...
wiki.flybase.org
FlyBase:Contribute to FlyBase - FlyBase Wiki
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Dr. Lucky Tran @luckytran.com · 24/08/2025
"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.
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FlyBase @flybase.bsky.social · 03/06/2025
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.
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VIB-KU Leuven Center for Neuroscience @vibneuroleuven.bsky.social · 27/05/2025
🤸‍♂️ We once again teamed up with TAJO vzw — an organization combatting early school leaving, and allowing youth from vulnerable home situations to enter society autonomously and prepared — to inspire young people to get interested in neuroscience! Find out more 👉 cbd.sites.vib.be/en/news#/new...
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Oxford Nanopore @nanoporetech.com · 22/05/2025
Our spotlight winner, Ruben Cools, presented his full talk exploring how they are bridging genotype and phenotype through long Oxford Nanopore read, single-molecule multiomics. #NanoporeConf
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VIB.AI @vibai.bsky.social · 06/05/2025
VIB.AI's International PhD call is now open! tinyurl.com/53nc9vnd If you're interested in applying AI to biology, take a look at the PhD projects across our labs. 🗓️ Deadline: June 22nd
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Hannah Dickmänken @hannahdckmnkn.bsky.social · 04/04/2025
Our new preprint is out! We optimized our open-source platform, HyDrop (v2), for scATAC sequencing and generated new atlases for the mouse cortex and Drosophila embryo with 607k cells. Now, we can train sequence-to-function models on data generated with HyDrop v2! www.biorxiv.org/content/10.1...
Data collected with the new sequencing platform HyDrop v2 is shown. First, a schematic overview of the bead batches of the microfluidic beads is followed by a tSNE and a barplot showing the costs in comparison to 10x Genomics. 
Then, a track of mouse data (cortex) is shown together with nucleotide contribution scores in the FIRE enhancer in microglia. Here, the HyDrop and 10x based models show the same contributions. 
On the right, the Drosophila embryo collection is explained; in the paper HyDrop v2 and 10x data are compared to sciATAC data. Then, a nucleotide contribution score is also shown, whereas HyDrop v2 and 10x models show the same contribution, just as in mouse.
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Niklas Kempynck @niklaskemp.bsky.social · 03/04/2025
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
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Seppe De Winter @seppedewinter.bsky.social · 28/02/2025
We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models. From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design! @natrevbioeng.bsky.social www.nature.com/articles/s44...
nature.com
Modelling and design of transcriptional enhancers - Nature Reviews Bioengineering
Enhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to unravel the rules underlying enhancer activit...
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Niklas Kempynck @niklaskemp.bsky.social · 14/02/2025
Just very happy to have our paper out today! A big thanks to all our co-authors, and to Nikolai and @steinaerts.bsky.social for the teamwork over the past years. If you are interested in using our models for cross-species enhancer studies, check out crested.readthedocs.io/en/stable/mo... 🙂
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VIB.AI @vibai.bsky.social · 14/02/2025
In a new study, Nikolai Hecker, Niklas Kempynck et al. in the team of @steinaerts.bsky.social explore 300 million years of brain evolution through the lens of enhancer codes. www.science.org/doi/10.1126/...
science.org
Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium
Combinations of transcription factors govern the identity of cell types, which is reflected by genomic enhancer codes. We used deep learning to characterize these enhancer codes and devised three metr...
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Stephen Curry @scurry.bsky.social · 11/02/2025
An open letter to the President of the @royalsociety.org – time to stand up for your values. occamstypewriter.org/scurry/2025/...
occamstypewriter.org
An open letter to the President of the Royal Society – time to stand up for your values | Reciprocal Space
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Stein Aerts @steinaerts.bsky.social · 12/11/2024
Looking forward to the Inaugural Symposium of the Center for AI & Computational Biology vib.ai with a great line-up of speakers at the interface of AI & biology: D. Kelley, J. Gagneur, Z. Avsec, T. Kortemme, B. Lehner, F. Fraternali, A. Tanay & O. Stegle (20Nov) www.vibconferences.be/events/vibai...
Ziga Avsec (Google DeepMind), Julien Gagneur (TU Munich), Tanja Kortemme (UCSF), David Kelley (Calico), Ben Lehner (Sanger), Franca Fraternali (UCL), Oliver Stegle (EMBL/DKFZ), and Amos Tanay (Weizmann)
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