Stefan Barakat
@stefanbarakat.bsky.social
Associate Professor at Erasmus MC. MD, PhD, Clinical Geneticist, interested in gene regulation and the non-coding genome, bridging research and patient care
Pinned
Stefan Barakat
@stefanbarakat.bsky.social
· Sep 19
It took a while, but finally the Barakat lab is also on Bluesky! Come and follow us if you are interested in our research on genetic causes of neurodevelopmental disorders, the noncoding genome, functional genomics and much more happening in Rotterdam!
Reposted by Stefan Barakat
🧠🧲 BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants
💡 Fantastic initiative from the Barakat Lab
👀 Great to have a sneak peak at #MDC25
🧬 Predicts enhancer activity from DNA sequence
🕵️♂️ Prioritises functional non-coding variants
👇🧵 Check it out
💡 Fantastic initiative from the Barakat Lab
👀 Great to have a sneak peak at #MDC25
🧬 Predicts enhancer activity from DNA sequence
🕵️♂️ Prioritises functional non-coding variants
👇🧵 Check it out
November 20, 2025 at 9:58 AM
🧠🧲 BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants
💡 Fantastic initiative from the Barakat Lab
👀 Great to have a sneak peak at #MDC25
🧬 Predicts enhancer activity from DNA sequence
🕵️♂️ Prioritises functional non-coding variants
👇🧵 Check it out
💡 Fantastic initiative from the Barakat Lab
👀 Great to have a sneak peak at #MDC25
🧬 Predicts enhancer activity from DNA sequence
🕵️♂️ Prioritises functional non-coding variants
👇🧵 Check it out
Reposted by Stefan Barakat
Onderzoekers van Erasmus MC gebruiken kunstmatige intelligentie om verborgen schakelaars te zoeken in het DNA. Die aanpak kan mensen met een zeldzame genetische aandoening alsnog een diagnose bezorgen. amazingerasmusmc.nl/genetica/ai-...
AI speurt naar DNA-schakelaars voor zeldzame genetische aandoeningen - Amazing Erasmus MC
Onderzoekers van Erasmus MC gebruiken kunstmatige intelligentie om verborgen schakelaars te zoeken in het DNA. Die aanpak kan mensen met een zeldzame genetische aandoening alsnog een diagnose bezorgen...
amazingerasmusmc.nl
November 20, 2025 at 8:14 AM
Onderzoekers van Erasmus MC gebruiken kunstmatige intelligentie om verborgen schakelaars te zoeken in het DNA. Die aanpak kan mensen met een zeldzame genetische aandoening alsnog een diagnose bezorgen. amazingerasmusmc.nl/genetica/ai-...
if you would like to read more on BRAIN-MAGNET in the popular press, have a look at the link below!
Onderzoekers van Erasmus MC gebruiken kunstmatige intelligentie om verborgen schakelaars te zoeken in het DNA. Die aanpak kan mensen met een zeldzame genetische aandoening alsnog een diagnose bezorgen. amazingerasmusmc.nl/genetica/ai-...
AI speurt naar DNA-schakelaars voor zeldzame genetische aandoeningen - Amazing Erasmus MC
Onderzoekers van Erasmus MC gebruiken kunstmatige intelligentie om verborgen schakelaars te zoeken in het DNA. Die aanpak kan mensen met een zeldzame genetische aandoening alsnog een diagnose bezorgen...
amazingerasmusmc.nl
November 20, 2025 at 9:45 AM
if you would like to read more on BRAIN-MAGNET in the popular press, have a look at the link below!
Reposted by Stefan Barakat
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants @cellcellpress.bsky.social
www.cell.com/cell/fulltex... @ruizhideng.bsky.social
www.cell.com/cell/fulltex... @ruizhideng.bsky.social
November 20, 2025 at 3:39 AM
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants @cellcellpress.bsky.social
www.cell.com/cell/fulltex... @ruizhideng.bsky.social
www.cell.com/cell/fulltex... @ruizhideng.bsky.social
happy to see our latest paper finally online!
Now online! BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants
BRAIN-MAGNET, a convolutional neural network trained on 148,198 functionally tested non-coding regulatory elements, predicts enhancer activity directly from DNA sequence and identifies nucleotides essential for function. This functional genomic atlas and BRAIN-MAGNET prioritize disease-relevant non-coding variants, advancing functional interpretation of the regulatory genome in neurodevelopment and neurological disease.
dlvr.it
November 20, 2025 at 9:41 AM
happy to see our latest paper finally online!
Very pleased to share our latest paper published in Cell:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants
BRAIN-MAGNET, a convolutional neural network trained on 148,198 functionally tested
non-coding regulatory elements, predicts enhancer activity directly from DNA sequence
and identifies nucleotides ess...
www.cell.com
November 20, 2025 at 9:38 AM
Very pleased to share our latest paper published in Cell:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
Reposted by Stefan Barakat
Now online! Ancient RNA expression profiles from the extinct woolly mammoth
Ancient RNA expression profiles from the extinct woolly mammoth
Ancient RNA profiles from Late Pleistocene woolly mammoths were sequenced from permafrost-preserved mummified tissues, revealing tissue-specific transcriptional functions and gene expression regulatory dynamics. These findings highlight the potential of ancient RNA molecules to provide additional biological information, thus advancing toward integrative paleogenetic research beyond the limits of DNA sequencing alone.
dlvr.it
November 14, 2025 at 7:51 PM
Now online! Ancient RNA expression profiles from the extinct woolly mammoth
Today, we presented at the meeting of the Dutch League against Epilepsy and EpilepsieNL, on some of our work on #ReNU syndrome, #SETD1B and #UGP2. Myrrhe Venema and Michela Maresca for their talks both won a Young Investigator Award for clinical and preclinical research, respectively. #proudPI !
November 7, 2025 at 9:06 PM
New international collaborative work incl. our group on VPS16, just published in Movement Disorders
#dystonia #genetics #raredisease
movementdisorders.onlinelibrary.wiley.com/doi/10.1002/...
#dystonia #genetics #raredisease
movementdisorders.onlinelibrary.wiley.com/doi/10.1002/...
Expanding the Genetic and Phenotypic Spectrum of DYT‐VPS16: The Importance of Splice‐Site Variants
Background DYT-VPS16, an early-onset isolated dystonia caused by variants in the VPS16 gene, has been reported in fewer than 70 patients. Methods We explored the clinical and genotypic spectrum of...
movementdisorders.onlinelibrary.wiley.com
November 7, 2025 at 9:01 PM
New international collaborative work incl. our group on VPS16, just published in Movement Disorders
#dystonia #genetics #raredisease
movementdisorders.onlinelibrary.wiley.com/doi/10.1002/...
#dystonia #genetics #raredisease
movementdisorders.onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Stefan Barakat
📢🧬 Next in the speaker line-up for #Embryo2026 is @eileen-furlong.bsky.social from @embl.org who will present her research on
"Genome regulation during embryogenesis: Going loopy about enhancer regulation"
Register until Oct 31! 👇
www.molgen.mpg.de/embryo2026
Supported by the Weizmann Institute
"Genome regulation during embryogenesis: Going loopy about enhancer regulation"
Register until Oct 31! 👇
www.molgen.mpg.de/embryo2026
Supported by the Weizmann Institute
October 24, 2025 at 11:13 AM
📢🧬 Next in the speaker line-up for #Embryo2026 is @eileen-furlong.bsky.social from @embl.org who will present her research on
"Genome regulation during embryogenesis: Going loopy about enhancer regulation"
Register until Oct 31! 👇
www.molgen.mpg.de/embryo2026
Supported by the Weizmann Institute
"Genome regulation during embryogenesis: Going loopy about enhancer regulation"
Register until Oct 31! 👇
www.molgen.mpg.de/embryo2026
Supported by the Weizmann Institute
New paper from our ultra-rapid WGS project published @ejhg-journal.bsky.social :
"Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making"
#raredisease #WGS @nanoporetech.com @erasmusmc.bsky.social
www.nature.com/articles/s41...
"Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making"
#raredisease #WGS @nanoporetech.com @erasmusmc.bsky.social
www.nature.com/articles/s41...
Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making - European Journal of Human Genetics
European Journal of Human Genetics - Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making
www.nature.com
October 21, 2025 at 2:48 PM
New paper from our ultra-rapid WGS project published @ejhg-journal.bsky.social :
"Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making"
#raredisease #WGS @nanoporetech.com @erasmusmc.bsky.social
www.nature.com/articles/s41...
"Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making"
#raredisease #WGS @nanoporetech.com @erasmusmc.bsky.social
www.nature.com/articles/s41...
Very nice paper showing that many enhancers can function as enhancers even when lacking H3K27ac. Also nice to see lots of our 2018 Cell Stem Cell paper findings confirmed as well! And always nice to see the utility of STARR-seq. More on that to be followed shortly as well from us :)
Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social:
www.biorxiv.org/content/10.1...
🧵 below
www.biorxiv.org/content/10.1...
🧵 below
Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells
Enhancers are key gene regulatory elements that ensure the precise spatiotemporal execution of developmental gene expression programmes. However recent findings indicate that approaches to identify en...
www.biorxiv.org
October 18, 2025 at 9:40 PM
Very nice paper showing that many enhancers can function as enhancers even when lacking H3K27ac. Also nice to see lots of our 2018 Cell Stem Cell paper findings confirmed as well! And always nice to see the utility of STARR-seq. More on that to be followed shortly as well from us :)
Reposted by Stefan Barakat
Come join us in Geneva for everything epigenetics and gene regulation. It will be a great meeting! Please repost!
www.keystonesymposia.org/conferences/...
www.keystonesymposia.org/conferences/...
Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities | Keystone Symposia
Join us at the Keystone Symposia on Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities, March 2026, in Geneva, with field leaders!
www.keystonesymposia.org
October 17, 2025 at 2:36 PM
Come join us in Geneva for everything epigenetics and gene regulation. It will be a great meeting! Please repost!
www.keystonesymposia.org/conferences/...
www.keystonesymposia.org/conferences/...
new international collaborative work incl. our group on EPG5
#genetics, #raredisease #EPG5, #NDD
onlinelibrary.wiley.com/doi/10.1002/...
#genetics, #raredisease #EPG5, #NDD
onlinelibrary.wiley.com/doi/10.1002/...
Mutations in the Key Autophagy Tethering Factor EPG5 Link Neurodevelopmental and Neurodegenerative Disorders Including Early‐Onset Parkinsonism
Objective
Autophagy is a fundamental biological pathway with vital roles in intracellular homeostasis. During autophagy, defective cargoes including mitochondria are targeted to lysosomes for cleara.....
onlinelibrary.wiley.com
October 7, 2025 at 6:22 PM
new international collaborative work incl. our group on EPG5
#genetics, #raredisease #EPG5, #NDD
onlinelibrary.wiley.com/doi/10.1002/...
#genetics, #raredisease #EPG5, #NDD
onlinelibrary.wiley.com/doi/10.1002/...
new recent publication from us in Rotterdam on RNA analysis for rare disease diagnostics #genetics #RNA #raredisease @hggadvances.bsky.social @erasmusmc.bsky.social
🚨Online now!
📄Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools
👉https://tinyurl.com/4wvwf7yy
📄Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools
👉https://tinyurl.com/4wvwf7yy
October 5, 2025 at 11:04 AM
new recent publication from us in Rotterdam on RNA analysis for rare disease diagnostics #genetics #RNA #raredisease @hggadvances.bsky.social @erasmusmc.bsky.social
and some more new work incl. us in @hggadvances.bsky.social
📣New from @deveshp.bsky.social & co!
📄Targeted plasma #proteomics uncover proteins associated with KIF5A-linked SPG10 and ALS spectrum disorders
👉https://tinyurl.com/t53jhthu
📄Targeted plasma #proteomics uncover proteins associated with KIF5A-linked SPG10 and ALS spectrum disorders
👉https://tinyurl.com/t53jhthu
October 5, 2025 at 11:02 AM
and some more new work incl. us in @hggadvances.bsky.social
Reposted by Stefan Barakat
📣New from Ferraro et al!
📄Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome
👉 tinyurl.com/59puc9km
📄Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome
👉 tinyurl.com/59puc9km
September 29, 2025 at 5:34 PM
📣New from Ferraro et al!
📄Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome
👉 tinyurl.com/59puc9km
📄Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome
👉 tinyurl.com/59puc9km
New paper from us in Rotterdam:
"Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome"
www.sciencedirect.com/science/arti...
@hggadvances.bsky.social , Federico Ferraro, Tjakko van Ham, Marieke van Dooren and others #lrWGS
"Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome"
www.sciencedirect.com/science/arti...
@hggadvances.bsky.social , Federico Ferraro, Tjakko van Ham, Marieke van Dooren and others #lrWGS
October 5, 2025 at 10:41 AM
New paper from us in Rotterdam:
"Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome"
www.sciencedirect.com/science/arti...
@hggadvances.bsky.social , Federico Ferraro, Tjakko van Ham, Marieke van Dooren and others #lrWGS
"Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome"
www.sciencedirect.com/science/arti...
@hggadvances.bsky.social , Federico Ferraro, Tjakko van Ham, Marieke van Dooren and others #lrWGS
Join us today at Sept 23rd2025 from 5pm to 6.30 pm (Central European Time) for our ERN ITHACA webinar on the non-coding genome and human disease by @svergult.bsky.social , @mspielmann.bsky.social , Florence Petit and @stefanbarakat.bsky.social
ern-ithaca.eu/events-news/...
ern-ithaca.eu/events-news/...
ERN-ITHACA WEBINAR: NON-CODING GENOME AND HUMAN DISEASE - ERN ITHACA
Recent developments in genomic technologies have enabled the genome-wide identification of regulatory elements and chromatin interactions, controlling the spatiotemporal gene expression. In this webin...
ern-ithaca.eu
September 23, 2025 at 1:23 PM
Join us today at Sept 23rd2025 from 5pm to 6.30 pm (Central European Time) for our ERN ITHACA webinar on the non-coding genome and human disease by @svergult.bsky.social , @mspielmann.bsky.social , Florence Petit and @stefanbarakat.bsky.social
ern-ithaca.eu/events-news/...
ern-ithaca.eu/events-news/...
It took a while, but finally the Barakat lab is also on Bluesky! Come and follow us if you are interested in our research on genetic causes of neurodevelopmental disorders, the noncoding genome, functional genomics and much more happening in Rotterdam!
September 19, 2025 at 7:40 PM
It took a while, but finally the Barakat lab is also on Bluesky! Come and follow us if you are interested in our research on genetic causes of neurodevelopmental disorders, the noncoding genome, functional genomics and much more happening in Rotterdam!
New international collaborative work incl. our group @erasmusmc.bsky.social on MACF1 published @ajhgnews.bsky.social
A clinical and genotype-phenotype analysis of MACF1 variants www.sciencedirect.com/science/arti...
#raredisease #genetics
A clinical and genotype-phenotype analysis of MACF1 variants www.sciencedirect.com/science/arti...
#raredisease #genetics
A clinical and genotype-phenotype analysis of MACF1 variants
Microtubule-actin cross-linking factor 1 (MACF1) is a large protein of the spectraplakin family, which is essential for brain development. MACF1 inter…
www.sciencedirect.com
September 19, 2025 at 7:34 PM
New international collaborative work incl. our group @erasmusmc.bsky.social on MACF1 published @ajhgnews.bsky.social
A clinical and genotype-phenotype analysis of MACF1 variants www.sciencedirect.com/science/arti...
#raredisease #genetics
A clinical and genotype-phenotype analysis of MACF1 variants www.sciencedirect.com/science/arti...
#raredisease #genetics
Thanks for highlighting our recent paper on the clinical utility of DNAmethylation signatures @eshg.bsky.social
#raredisease #genetics #genomics #epigenetics
#raredisease #genetics #genomics #epigenetics
Published in EJHG Journal:
📊 DNAmethylation signatures support VUS reclassification and complement negative genetic tests. This approach boosts diagnostic yield in neurodevelopmental disorders, proving its clinical utility in routine diagnostics. ✅
www.nature.com/articles/s41...
📊 DNAmethylation signatures support VUS reclassification and complement negative genetic tests. This approach boosts diagnostic yield in neurodevelopmental disorders, proving its clinical utility in routine diagnostics. ✅
www.nature.com/articles/s41...
Clinical utility of DNA-methylation signatures in routine diagnostics for neurodevelopmental disorders - European Journal of Human Genetics
European Journal of Human Genetics - Clinical utility of DNA-methylation signatures in routine diagnostics for neurodevelopmental disorders
www.nature.com
September 19, 2025 at 7:15 PM
Thanks for highlighting our recent paper on the clinical utility of DNAmethylation signatures @eshg.bsky.social
#raredisease #genetics #genomics #epigenetics
#raredisease #genetics #genomics #epigenetics
Reposted by Stefan Barakat
Published in EJHG Journal:
📊 DNAmethylation signatures support VUS reclassification and complement negative genetic tests. This approach boosts diagnostic yield in neurodevelopmental disorders, proving its clinical utility in routine diagnostics. ✅
www.nature.com/articles/s41...
📊 DNAmethylation signatures support VUS reclassification and complement negative genetic tests. This approach boosts diagnostic yield in neurodevelopmental disorders, proving its clinical utility in routine diagnostics. ✅
www.nature.com/articles/s41...
Clinical utility of DNA-methylation signatures in routine diagnostics for neurodevelopmental disorders - European Journal of Human Genetics
European Journal of Human Genetics - Clinical utility of DNA-methylation signatures in routine diagnostics for neurodevelopmental disorders
www.nature.com
September 1, 2025 at 8:11 AM
Published in EJHG Journal:
📊 DNAmethylation signatures support VUS reclassification and complement negative genetic tests. This approach boosts diagnostic yield in neurodevelopmental disorders, proving its clinical utility in routine diagnostics. ✅
www.nature.com/articles/s41...
📊 DNAmethylation signatures support VUS reclassification and complement negative genetic tests. This approach boosts diagnostic yield in neurodevelopmental disorders, proving its clinical utility in routine diagnostics. ✅
www.nature.com/articles/s41...