Alexandra P
@alexanrna.bsky.social
🇸🇰 PhD student @ KU Leuven and VIB 🇧🇪
Genetics, Bioinformatics, and everything in between (she/her)
Genetics, Bioinformatics, and everything in between (she/her)
Reposted by Alexandra P
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
September 23, 2025 at 11:21 AM
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...
Reposted by Alexandra P
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...
September 10, 2025 at 3:48 PM
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...
Reposted by Alexandra P
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!)
🧵
(Zoom registration link and more information in thread!)
🧵
September 10, 2025 at 3:02 PM
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!)
🧵
(Zoom registration link and more information in thread!)
🧵
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...
September 10, 2025 at 3:48 PM
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...
Reposted by Alexandra P
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...
FlyBase:Contribute to FlyBase - FlyBase Wiki
wiki.flybase.org
August 15, 2025 at 12:45 PM
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...
Reposted by Alexandra P
"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.
Powerful video with voices from top US scientists on the very real and devastating impacts of the funding cuts.
August 24, 2025 at 7:25 PM
"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.
Powerful video with voices from top US scientists on the very real and devastating impacts of the funding cuts.
Reposted by Alexandra P
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.
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.
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.
My lab studies bacterial infections. We spend a lot of time looking at (or for) species-specific genetic and genomic databases for hosts and microbes. FlyBase is the best of all—there is literally no comparison. Its existence is under threat. Please donate.
www.philanthropy.cam.ac.uk/give-to-camb...
www.philanthropy.cam.ac.uk/give-to-camb...
June 3, 2025 at 9:17 PM
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.
Reposted by Alexandra P
🤸♂️ 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...
Find out more 👉 cbd.sites.vib.be/en/news#/new...
May 27, 2025 at 8:19 AM
🤸♂️ 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...
Find out more 👉 cbd.sites.vib.be/en/news#/new...
Reposted by Alexandra P
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
May 22, 2025 at 4:02 PM
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
Reposted by Alexandra P
VIB.AI's International PhD call is now open!
https://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
https://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
May 6, 2025 at 12:48 PM
VIB.AI's International PhD call is now open!
https://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
https://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
Reposted by Alexandra P
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...
www.biorxiv.org/content/10.1...
April 4, 2025 at 8:52 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Alexandra P
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...
April 3, 2025 at 2:30 PM
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...
Reposted by Alexandra P
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...
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...
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...
www.nature.com
February 28, 2025 at 2:45 PM
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...
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...
Reposted by Alexandra P
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... 🙂
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/...
www.science.org/doi/10.1126/...
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...
www.science.org
February 14, 2025 at 10:08 AM
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... 🙂
Reposted by Alexandra P
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/...
www.science.org/doi/10.1126/...
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...
www.science.org
February 14, 2025 at 8:28 AM
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/...
www.science.org/doi/10.1126/...
Reposted by Alexandra P
An open letter to the President of the @royalsociety.org – time to stand up for your values. occamstypewriter.org/scurry/2025/...
An open letter to the President of the Royal Society – time to stand up for your values | Reciprocal Space
occamstypewriter.org
February 11, 2025 at 3:26 PM
An open letter to the President of the @royalsociety.org – time to stand up for your values. occamstypewriter.org/scurry/2025/...
Reposted by Alexandra P
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...
November 12, 2024 at 11:26 AM
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...