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Stefan Barakat

@stefanbarakat.bsky.social
113 followers 150 following 49 posts

Associate Professor at Erasmus MC. MD, PhD, Clinical Geneticist, interested in gene regulation and the non-coding genome, bridging research and patient care

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Stefan Barakat @stefanbarakat.bsky.social · 23/04/2026
happy with the outcome of the wonderful collaboration with @franciscobustos.bsky.social !
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Stefan Barakat @stefanbarakat.bsky.social · 11/04/2026
And finally for this week, a collaborative review on chromatinopathies www.frontiersin.org/journals/cel...
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Stefan Barakat @stefanbarakat.bsky.social · 11/04/2026
A new paper on KDM2B on chromosome 12q in Clinical Genetics onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Comprehensive Assessment of the KDM2B‐Associated Neurodevelopmental Disorder and the 12q24.31 Microdeletion Syndrome
We set out to characterize genotype–phenotype correlations in the recently delineated KDM2B-associated neurodevelopmental disorder. We observe a highly penetrant CxxC domain-related phenotype with di...
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Stefan Barakat @stefanbarakat.bsky.social · 11/04/2026
Another collaborative paper on CHD3 episignatures in Genome Medicine link.springer.com/article/10.1...
link.springer.com
Identification of an episignature for CHD3-related Snijders Blok-Campeau syndrome reveals heterogeneity in the CHARGE syndrome episignature: towards a better characterisation of chromatinopathies - Genome Medicine
Genome Medicine - Recent advances in sequencing technologies have enhanced patient diagnosis; however, causal pathogenic variants remain unidentified for a significant number of patients due to...
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Stefan Barakat @stefanbarakat.bsky.social · 11/04/2026
Some more international collaborative papers our group could recently contribute to: First in @natgenet.nature.com, Greene et al on an extremely frequent recessive condition caused by variants in the snRNA gene RNU2-2 #noncoding genome remains full of surprises! www.nature.com/articles/s41...
nature.com
Biallelic variants in RNU2-2 cause the most prevalent known recessive neurodevelopmental disorder - Nature Genetics
An analysis of rare disease cohorts from the UK, the USA, Italy and the Netherlands identifies a neurodevelopmental disorder caused by biallelic variants in RNU2-2. Individuals with this disorder have substantially reduced levels of U2-2 small nuclear RNA in blood.
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European Journal of Human Genetics @ejhg-journal.bsky.social · 10/04/2026
📢 Albuainain et al. use transcriptome analysis to diagnose cardiofacioneurodevelopmental syndrome and present two cases with this rare condition. 🧬 @stefanbarakat.bsky.social #RareDisease #RNAseq #GenomicDiagnostics 🔗 Read more: www.nature.com/articles/s41...
nature.com
Two siblings with CCDC32-related cardiofacioneurodevelopmental syndrome diagnosed by clinical RNA-sequencing and review of literature - European Journal of Human Genetics
European Journal of Human Genetics - Two siblings with CCDC32-related cardiofacioneurodevelopmental syndrome diagnosed by clinical RNA-sequencing and review of literature
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Stefan Barakat @stefanbarakat.bsky.social · 25/03/2026
New international collaborative work incl. our group on BLOC1S1 related leukodystrophy www.cell.com/ajhg/abstrac...
cell.com
BLOC1S1 variants cause lysosomal and autophagic defects resulting in a hypomyelinating leukodystrophy with epileptic encephalopathy
We identify bi-allelic BLOC1S1 variants in 11 individuals with severe neurodevelopmental disease, including leukodystrophy, epilepsy, spasticity, and optic atrophy. Functional analyses demonstrate imp...
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Stefan Barakat @stefanbarakat.bsky.social · 13/03/2026
📣We are hiring a computational PhD student, interested in functional genomics and the non-coding genome. To continue developing our BRAIN-MAGNET algorithm recently published in Cell (www.cell.com/cell/fulltex.... See vacancy for details! www.werkenbijerasmusmc.nl/en/vacancy/1...
cell.com
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Stefan Barakat @stefanbarakat.bsky.social · 13/01/2026
Congrats to Eva Medico Salsench from our lab for successfully defending her PhD thesis last week: "Precision Medicine for Rare Neurogenetic Disorders: from aquarium to bedside" #proudPI, #genetics #diseasemodelling @erasmusmc.bsky.social @erasmusuniversity.bsky.social
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Stefan Barakat @stefanbarakat.bsky.social · 09/01/2026
New international collaborative work (incl us) just out in @natgenet.nature.com showing how dominant variants in RNU genes like RNU4-2 can also cause Retinitis Pigmentosa Mathieu Quinodoz, Kim Rodenburg, Susanne Roosing, @carlorivolta.bsky.social & many others www.nature.com/articles/s41...
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Stefan Barakat @stefanbarakat.bsky.social · 23/12/2025
still time to apply till early January, spread the news!
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Stefan Barakat @stefanbarakat.bsky.social · 12/12/2025
Some more media attention yesterday in the Dutch press @pzc.bsky.social about our research into causes of hereditary disease hidden in the noncoding genome. www.pzc.nl/schouwen-dui...
pzc.nl
Zeeuwse topdokter Stefan Barakat doet weer een bijzondere ontdekking en dat is goed nieuws voor hersenpatiënten
Hij boekt succes op succes en je zou er bijna aan gaan wennen, maar het is vergelijkbaar met het winnen van een medaille op de Olympische Spelen. Topdokter Stefan Barakat uit Ouwerkerk en zijn onderzo...
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Stefan Barakat @stefanbarakat.bsky.social · 12/12/2025
Yesterday I explained on the local radio the added value of DNA diagnostics for rare diseases, and how we are now able to find mutations in the dark matter of the human genome that can cause disease. The interview (in Dutch) is available via: www.radiosd.nl/nieuwsberich...
radiosd.nl
Zeeuwse topdokter boekt nieuwe doorbraak in onderzoek naar hersenaandoeningen
Stefan Barakat, klinisch geneticus uit Ouwerkerk en werkzaam bij het Erasmus MC in Rotterdam, heeft opnieuw een belangrijke wetenschappelijke ontdekking gedaan
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Stefan Barakat @stefanbarakat.bsky.social · 08/12/2025
We are hiring! Are you looking for a challenging PhD project studying neurodevelopmental disorders related to chromatin dysfunction, using in vitro stem cell based models, multi-omics and functional studies? Then check out the vacancy! #phd #vacancy www.werkenbijerasmusmc.nl/en/vacancy/1...
werkenbijerasmusmc.nl
Vacature: PhD Position in Neurodevelopmental Disorders
Are you passionate about neurodevelopment and brain diseases? Would you like to work in a highly dynamic environment at the interface of fundamental science and applied human clinical genetics, direct...
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Reposted by Stefan Barakat
James Fasham @jamesfasham.bsky.social · 08/12/2025
Very grateful to colleagues including @rdexeter.bsky.social, @nihrexeterbrc.bsky.social, @stefanbarakat.bsky.social, the NHS Rare & Inherited Disease Genomic Network of Excellence, and to the patients and families who made this work possible. 🙏 Paper: pubmed.ncbi.nlm.nih.gov/41349538/
pubmed.ncbi.nlm.nih.gov
Palindrome-mediated 16p13.3 triplications cause a recognizable neurodegenerative disorder with ataxia - PubMed
Complex neurodegenerative conditions have occasionally been associated with copy-number gains. Using microarray and genome sequencing on DNA samples from eleven individuals from nine unrelated families, we show that copy-number gains at 16p13.3 cause a severe, recognizable disorder characterized by …
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James Fasham @jamesfasham.bsky.social · 08/12/2025
Our new study defines a distinct #neurogenetic condition arising from recurrent structural variants at 16p13.3 palindrome. Individuals show progressive ataxia, cognitive decline, and a characteristic MRI pattern with caudate & cerebellar atrophy. #Genomics #RareDisease 🧵1/3
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Stefan Barakat @stefanbarakat.bsky.social · 06/12/2025
another great international collaboration with our friends in UK and Australia to which we could contribute, describing a very unique disease mechanism for a novel neurodegenerative disorder #genetics #raredisease @ajhgnews.bsky.social @jamesfasham.bsky.social @rdexeter.bsky.social
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Stefan Barakat @stefanbarakat.bsky.social · 30/11/2025
Cool work as usual, @elphegenoralab.bsky.social , congrats!
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Stefan Barakat @stefanbarakat.bsky.social · 28/11/2025
More international collaborative work: Single nucleotide variants in UNC13C associated with neurodevelopmental disorders affect ethanol sensitivity in Drosophila #raredisease #morbidgene #genetics #diseasemodelling www.sciencedirect.com/science/arti...
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Tom Wright @tomwrightuom.bsky.social · 20/11/2025
🧠🧲 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
cell.com
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...
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Erasmus MC @erasmusmc.bsky.social · 20/11/2025
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-...
amazingerasmusmc.nl
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...
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Stefan Barakat @stefanbarakat.bsky.social · 20/11/2025
if you would like to read more on BRAIN-MAGNET in the popular press, have a look at the link below!
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Waggoner Lab @labwaggoner.bsky.social · 20/11/2025
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants @cellcellpress.bsky.social www.cell.com/cell/fulltex... @ruizhideng.bsky.social
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Stefan Barakat @stefanbarakat.bsky.social · 20/11/2025
happy to see our latest paper finally online!
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Stefan Barakat @stefanbarakat.bsky.social · 20/11/2025
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:
cell.com
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...
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Cell - a Cell Press journal @cp-cell.bsky.social · 14/11/2025
Now online! Ancient RNA expression profiles from the extinct woolly mammoth
dlvr.it
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.
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Stefan Barakat @stefanbarakat.bsky.social · 07/11/2025
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 !
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Stefan Barakat @stefanbarakat.bsky.social · 07/11/2025
New international collaborative work incl. our group on VPS16, just published in Movement Disorders #dystonia #genetics #raredisease movementdisorders.onlinelibrary.wiley.com/doi/10.1002/...
movementdisorders.onlinelibrary.wiley.com
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...
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Max Planck Institute for Molecular Genetics @molgen.mpg.de · 24/10/2025
📢🧬 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
SharePic for the contribution of Eileen Furlong from EMBL for the 2nd Meeting on Early embryogenesis & epigenetics organized by the Max Planck Institute for Molecular Genetics in Berlin with support by the Weizmann Institute for Science. The SharePic features the portrait of Eileen and the title of her contritbution "Genome regulation during embryogenesis: Going loopy about enhancer regulation".
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Stefan Barakat @stefanbarakat.bsky.social · 21/10/2025
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...
nature.com
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
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Stefan Barakat @stefanbarakat.bsky.social · 18/10/2025
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 :)
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Rob Klose @robklose.bsky.social · 17/10/2025
Come join us in Geneva for everything epigenetics and gene regulation. It will be a great meeting! Please repost! www.keystonesymposia.org/conferences/...
keystonesymposia.org
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!
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Stefan Barakat @stefanbarakat.bsky.social · 07/10/2025
new international collaborative work incl. our group on EPG5 #genetics, #raredisease #EPG5, #NDD onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
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.....
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Stefan Barakat @stefanbarakat.bsky.social · 05/10/2025
new recent publication from us in Rotterdam on RNA analysis for rare disease diagnostics #genetics #RNA #raredisease @hggadvances.bsky.social @erasmusmc.bsky.social
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Stefan Barakat @stefanbarakat.bsky.social · 05/10/2025
and some more new work incl. us in @hggadvances.bsky.social
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Human Genetics and Genomics Advances @hggadvances.bsky.social · 29/09/2025
📣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
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Stefan Barakat @stefanbarakat.bsky.social · 05/10/2025
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
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Stefan Barakat @stefanbarakat.bsky.social · 23/09/2025
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
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...
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Stefan Barakat @stefanbarakat.bsky.social · 19/09/2025
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!
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Stefan Barakat @stefanbarakat.bsky.social · 19/09/2025
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
sciencedirect.com
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…
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Stefan Barakat @stefanbarakat.bsky.social · 19/09/2025
Thanks for highlighting our recent paper on the clinical utility of DNAmethylation signatures @eshg.bsky.social #raredisease #genetics #genomics #epigenetics
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European Society of Human Genetics @eshg.bsky.social · 01/09/2025
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...
nature.com
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
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