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
happy with the outcome of the wonderful collaboration with @franciscobustos.bsky.social !
Francisco Bustos@franciscobustos.bsky.social · 5mo agoSo happy to see our @cp-iscience.bsky.social paper finally published. Great collaboration with @stefanbarakat.bsky.social spearheaded by our fantastic staff scientist Venky. The reviewers really helped making this paper better www.cell.com/iscience/ful...
And finally for this week, a collaborative review on chromatinopathies www.frontiersin.org/journals/cel...
A new paper on KDM2B on chromosome 12q in Clinical Genetics onlinelibrary.wiley.com/doi/10.1111/...
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...
onlinelibrary.wiley.com
Another collaborative paper on CHD3 episignatures in Genome Medicine link.springer.com/article/10.1...
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...
link.springer.com
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...
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.
nature.com
📢 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...
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
nature.com
New international collaborative work incl. our group on BLOC1S1 related leukodystrophy www.cell.com/ajhg/abstrac...
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...
cell.com
📣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
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
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...
still time to apply till early January, spread the news!
Stefan Barakat@stefanbarakat.bsky.social · 9mo agoWe 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...
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...
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...
pzc.nl
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...
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
radiosd.nl
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...
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...
werkenbijerasmusmc.nl
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/
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 …
pubmed.ncbi.nlm.nih.gov
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
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
The American Journal of Human Genetics@ajhgnews.bsky.social · 9mo ago📣New from @rdexeter.bsky.social 📄Palindrome-mediated 16p13.3 triplications cause a recognizable neurodegenerative disorder with ataxia
Cool work as usual, @elphegenoralab.bsky.social , congrats!
Elphege Nora Lab at UCSF@elphegenoralab.bsky.social · 9mo agoHere is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀 Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function now revised and journal accepted at www.science.org/doi/10.1126/... 🧵👇
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...
🧠🧲 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
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...
cell.com
Stefan Barakat@stefanbarakat.bsky.social · 10mo agoVery 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:
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
if you would like to read more on BRAIN-MAGNET in the popular press, have a look at the link below!
Erasmus MC@erasmusmc.bsky.social · 10mo agoOnderzoekers 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-...
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants @cellcellpress.bsky.social www.cell.com/cell/fulltex... @ruizhideng.bsky.social
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
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...
cell.com
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
New international collaborative work incl. our group on VPS16, just published in Movement Disorders #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
📢🧬 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
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 - 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
nature.com
