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Mihaly Badonyi

@mbadonyi.bsky.social
157 followers 367 following 77 posts

postdoc @mpi-cbg.de computational biology | disease genetics

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Reposted by Mihaly Badonyi
Craig Anderson @craigandersn.bsky.social · 01/10/2026
You can now register for Mutations in time and space 2027 🎉🎉🎉🎉🎉🎉 www.embl.org/about/info/c... 🎉🎉🎉🎉🎉🎉 This time we're in beautiful Heidelberg over 15 - 18 June. Along with a stellar cast of invited speakers, there are a ton of slots for submitted abstracts. Please do come along and take part :-)
embl.org
Mutations in time and space
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Max Planck Institute of Molecular Cell Biology and Genetics @mpi-cbg.de · 07/09/2026
New tool to score AlphaFold-predicted molecular interactions: Mihaly Badonyi @mbadonyi.bsky.social & @tothpetroczylab.bsky.social have developed Pinc, an algorithm to convert AlphaFold's uncertainty into a single number. Publication in Protein Science. onlinelibrary.wiley.com/doi/10.1002/...
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Mihaly Badonyi @mbadonyi.bsky.social · 10/09/2026
AlphaFold can now predict protein complexes at unprecedented scale. But once we have a predicted complex, the core question of how much we should trust the interface remains. Existing confidence scores are useful, but their meaning is not always obvious. #alphafold
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Mihaly Badonyi @mbadonyi.bsky.social · 10/08/2026
This project taught me a lot about the difficulties of mapping genetic variants across hundreds of thousands of alternative transcripts; very grateful to the co-authors for the lessons learnt.
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Reposted by Mihaly Badonyi
Deegan Lab @deeganlab.bsky.social · 01/06/2026
Join us in Nottingham in September for the UK DNA replication meeting 🧬. Super EarlyBird deadline today and abstract deadline in 1 month. www.eventsforce.net/biochemsoc/f...
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Mihaly Badonyi @mbadonyi.bsky.social · 22/05/2026
Having just taken this course, I highly recommend it.
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Reposted by Mihaly Badonyi
Institute of Genetics and Cancer @uoe-igc.bsky.social · 06/05/2026
A study, led by Hasan Çubuk, to identify how to improve diagnosis of the rare condition adenylosuccinate lyase (ADSL) deficiency, has created a framework which could be adapted for other recessive diseases. Read more here 👉 edin.ac/4tf5Zlj
edin.ac
New framework could help diagnose recessive rare diseases | Institute of Genetics and Cancer | Institute of Genetics and Cancer
A study to identify how to improve diagnosis of the rare condition adenylosuccinate lyase (ADSL) deficiency, has created a framework which could be adapted for other recessive diseases.
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Mihaly Badonyi @mbadonyi.bsky.social · 01/04/2026
As we move towards a complete map of human variant effects, evaluating VEP and MAVE scores in clinically meaningful ways becomes essential. In work led by Yifei Shang and @jmarshlab.bsky.social, we explore mean evidence strength (MES) to quantify clinical utility after ACMG/AMP calibration.
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Mihaly Badonyi @mbadonyi.bsky.social · 20/03/2026
Pinc is now available as a C program, eliminating interpreter overhead and substantially speeding up computation for large-scale structural analyses. It’s still under active development, so please reach out with any questions, feedback, or issues. 🔗 git.mpi-cbg.de/tothpetroczy... #alphafold
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Mihaly Badonyi @mbadonyi.bsky.social · 19/03/2026
Great inaugural lecture by Joe. Honoured to see some of our joint work mentioned.
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Mihaly Badonyi @mbadonyi.bsky.social · 04/03/2026
My first manuscript in MPI colours! With @tothpetroczylab.bsky.social, we show that AlphaFold PAE-derived contact probabilities are well calibrated to the fraction of true interface contacts across experimentally determined protein dimers. www.biorxiv.org/content/10.6...
Two-panel calibration plot (two benchmark dimer datasets) comparing predicted interchain contact-probability bins (x-axis) with the observed fraction of native interfacial contacts (y-axis). Points follow the diagonal, indicating close agreement between predicted probabilities and true interface-contact fractions.
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Nezha Benabdallah @nsbenab.bsky.social · 28/01/2026
SS18::SSX activates Polycomb target genes without BAF ❌ Instead, transcription relies on EP300 via the SS18 QPGY domain www.biorxiv.org/content/10.6... ➡️ Coactivator targeting emerges as a new therapeutic strategy in synovial sarcoma 🎯 Team work from @banitolab.bsky.social and @uoe-igc.bsky.social
biorxiv.org
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Reposted by Mihaly Badonyi
Craig Anderson @craigandersn.bsky.social · 13/01/2026
The abstract deadline for Mutations in Time and Space 2026 closes in 3 weeks time. Sign up here: coursesandconferences.wellcomeconnectingscience.org/event/mutati... As well as thrilling science, the programme includes dinner at the beautiful King's College in Cambridge. @eventswcs.bsky.social
coursesandconferences.wellcomeconnectingscience.org
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Reposted by Mihaly Badonyi
Joe Marsh @jmarshlab.bsky.social · 09/01/2026
Our first foray into non-coding variation: structure-guided TF-DNA modelling with AlphaFold 3. Not a replacement for sequence-based predictors, but a complementary way to reason about mechanism. Nice collab with @simonbiddie.bsky.social academic.oup.com/nar/article/...
academic.oup.com
A structure-guided approach to noncoding variant evaluation for transcription factor binding using AlphaFold 3
Abstract. Noncoding single-nucleotide variants (SNVs) that alter transcription factor (TF) binding can affect gene expression and contribute to disease. Se
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Mihaly Badonyi @mbadonyi.bsky.social · 09/12/2025
Can MAVEs and population-free VEPs be combined to improve variant classification? VEPs detect a broad range of pathogenic variants, while MAVEs give more conservative & decisive calls. Combined, they equitably reclassify >90% of VUS. Read more in our study on combining evidence from MAVEs and VEPs:
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Reposted by Mihaly Badonyi
Nezha Benabdallah @nsbenab.bsky.social · 19/11/2025
We have an exciting PhD opportunity through the EASTBIO programme, co-supervised with Diego Oyarzún. This project combines synthetic and systems biology to uncover the gene-regulatory circuitry hijacked in a cancer model. We’re looking for candidates with a strong interest in functional genomics.
findaphd.com
EASTBIO - Dissecting CIC::DUX4 oncogenic circuitry through single-cell perturbation profiling and network inference at University of Edinburgh on FindAPhD.com
PhD Project - EASTBIO - Dissecting CIC::DUX4 oncogenic circuitry through single-cell perturbation profiling and network inference at University of Edinburgh, listed on FindAPhD.com
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Reposted by Mihaly Badonyi
Stephen Turner @stephenturner.us · 14/10/2025
acmgscaler: an R package and Colab for standardized gene-level variant effect score calibration within the ACMG/AMP framework academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/badonyi/acmg... #Rstats
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Mihaly Badonyi @mbadonyi.bsky.social · 05/10/2025
1/3 In this work on RyR1, led by Rolando, we (@marshlab.bsky.social) highlight the limitations of using ROC AUC alone to assess clinical utility. Future approaches should consider classification behaviour across the full score distribution. 📄 onlinelibrary.wiley.com/doi/epdf/10....
onlinelibrary.wiley.com
Complementary Roles of Structure and Variant Effect Predictors in RyR1 Clinical Interpretation
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Reposted by Mihaly Badonyi
Irene Gallego Romero @ee-reh-neh.bsky.social · 02/10/2025
I'm stoked to be organising next year's MSS right here in beautiful Melbourne! We know Australia is very far away, and we're working hard to make sure we can support as many ECRs to attend as possible, so please do register and apply for a travel award!
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Mihaly Badonyi @mbadonyi.bsky.social · 25/09/2025
1/8 Our new paper in Nature Communications explores how often pathogenic missense variants cause disease through loss-of-function (LOF), gain-of-function (GOF), or dominant-negative (DN) effects. 📄 nature.com/articles/s41...
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Mihaly Badonyi @mbadonyi.bsky.social · 24/09/2025
Happy to share that 𝚊𝚌𝚖𝚐𝚜𝚌𝚊𝚕𝚎𝚛 is now on CRAN! 🎉 This means long-term stability and easy installation with: 𝚒𝚗𝚜𝚝𝚊𝚕𝚕.𝚙𝚊𝚌𝚔𝚊𝚐𝚎𝚜('𝚊𝚌𝚖𝚐𝚜𝚌𝚊𝚕𝚎𝚛') 🗞️ doi.org/10.1093/bioi... #rstats #acmg #varianteffect #MAVEs #VEPs #genomics
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Mihaly Badonyi @mbadonyi.bsky.social · 15/08/2025
We’ve updated the acmgscaler manuscript following reviewer and community feedback. The R package now has a single calibrate() function, and the Colab interface is easier to use. 📄 Manuscript: www.biorxiv.org/content/10.1... 🧪 Colab: edin.ac/4mjzijp #rstats @theacmg.bsky.social
biorxiv.org
acmgscaler: An R package and Colab for standardised gene-level variant effect score calibration within the ACMG/AMP framework
A genome-wide variant effect calibration method was recently developed under the guidelines of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/A...
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Reposted by Mihaly Badonyi
bioRxivpreprint @biorxivpreprint.bsky.social · 01/08/2025
Why variant effect predictors and multiplexed assays agree and disagree www.biorxiv.org/content/10.1101/202…
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Reposted by Mihaly Badonyi
Simon Biddie @simonbiddie.bsky.social · 29/07/2025
Congratulations to @gweykopf.bsky.social for her first first author manuscript, now on biorxiv. www.biorxiv.org/content/10.1... Many thanks to all involved - @wbickmor.bsky.social @mbadonyi.bsky.social @eliasfriman.bsky.social, Joe Marsh, Jasmine Nguyen, Mark Gorrell and others.
biorxiv.org
Disease-associated genetic variants can cause mutations in tissue-specific protein isoforms
Genetic variants can cause protein-coding mutations that result in disease. Variants are typically interpreted using the reference transcript for a gene. However, most human multi-exon genes encode al...
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Reposted by Mihaly Badonyi
bioRxivpreprint @biorxivpreprint.bsky.social · 29/07/2025
A knowledge-based distance metric highlights underperformance of variant effect predictors on gain-of-function missense variants www.biorxiv.org/content/10.1101/202…
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Wendy Bickmore @wbickmor.bsky.social · 28/07/2025
GWAS to mechanism: when non-coding is coding. Beautiful insightful science from @gweykopf.bsky.social @simonbiddie.bsky.social Joe Marsh and many colleagues. @uoe-igc.bsky.social @cmvm-edinburghuni.bsky.social www.biorxiv.org/content/10.1...
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Mihaly Badonyi @mbadonyi.bsky.social · 13/06/2025
Thanks to #CCG2025 for the opportunity to present our work on `acmgscaler`, a standardised tool to convert functional scores into ACMG/AMP evidence strengths. #rstats
You can try out the Colab notebook and the R package here: https://github.com/badonyi/acmgscaler
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Mihaly Badonyi @mbadonyi.bsky.social · 22/05/2025
We've developed a method to align genetic variant effect scores with ACMG/AMP classification criteria. It has two key advantages: (1) no assumptions about score distributions, and (2) consistent outputs without user tuning.
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Derek Lowe @dereklowe.bsky.social · 07/05/2025
So, how many genetic diseases come down to good ol’ loss-of-function in the targeted protein? Your estimate is probably too high:
science.org
Mutant Proteins Classified
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Reposted by Mihaly Badonyi
Duncan Sproul @sproullab.bsky.social · 23/04/2025
Want to work with us on DNA methylation and rare genetic disease? Fully funded PhD project with deadline 16th May: www.findaphd.com/phds/project... Excited to collaborate with @hannahlong.bsky.social and Daria Bunina (@uoe-igc.bsky.social/@mdc-berlin.bsky.social). Please share 🙏 #epigenetics
findaphd.com
Fully Funded PhD Studentship in Human Genetics, Genomics and Disease: Dissecting DNMT3B functions in Immunodeficiency-centromeric instability facial anomalies syndrome at University of Edinburgh on Fi...
PhD Project - Fully Funded PhD Studentship in Human Genetics, Genomics and Disease: Dissecting DNMT3B functions in Immunodeficiency-centromeric instability facial anomalies syndrome at University of E...
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Mihaly Badonyi @mbadonyi.bsky.social · 15/04/2025
Happy to have contributed to this work. As variant effect predictors become increasingly integral to genomic medicine, it is essential that their components and blueprints are accessible to researchers and developers.
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medRxivpreprint @medrxivpreprint.bsky.social · 03/04/2025
Structure-informed classification of RyR1 variants highlights limitations of current predictors and enables clinical interpretation www.medrxiv.org/content/10.1101/202…
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the Node @the-node.bsky.social · 27/03/2025
Tamina Lebek @lebektamina.bsky.social is a panellist in the last session of #biologists100. We took a photo of her and her little collaborator! Her key words are #BabiesInScience #PUFFFIN #NeighbourLabelling. Check out this interview with Tamina: thenode.biologists.com/the-sdb-bsdb...
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Mihaly Badonyi @mbadonyi.bsky.social · 17/03/2025
1/ Excited to share our latest work on the "Prevalence of loss-of-function, gain-of-function and dominant-negative mechanisms across genetic disease phenotypes". @marshlab.bsky.social @uoe-igc.bsky.social www.biorxiv.org/content/10.1...
biorxiv.org
Prevalence of loss-of-function, gain-of-function and dominant-negative mechanisms across genetic disease phenotypes
Molecular disease mechanisms caused by mutations in protein-coding regions are diverse, but they can be broadly categorised into loss-of-function (LOF), gain-of-function (GOF), and dominant-negative (...
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Hannah Long @hannahlong.bsky.social · 09/02/2025
Prof Joe Marsh and I have a PhD project as part of the 2025 Edinburgh Doctoral College Scholarship: "Integrating AI, Biophysical Modelling and Experimental Validation for Enhancer Variant Interpretation". Closing date for applications is 25 April 2025. Please get in touch if you are interested! 🧬🧠
institute-genetics-cancer.ed.ac.uk
Edinburgh Doctoral College Scholarship
Applications now open for 2025 intake
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Mihaly Badonyi @mbadonyi.bsky.social · 08/01/2025
Happy to see our predictive scores integrated into DECIPHER! We hope they will help clinicians uncover the molecular mechanisms driving dominant disease. Huge thanks to the team at @deciphergenomics.bsky.social for their support. A follow-up study is underway to improve predictions—stay tuned!
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MRC-LMB Cell Biology Division @cellbiol-mrclmb.bsky.social · 29/12/2024
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
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Mihaly Badonyi @mbadonyi.bsky.social · 07/12/2024
Lagging a day behind, here's my #rstats solution to the day 6 of the 2024 #adventofcode. Part 2 brute forced, super slow, but with a progress bar so people know it's running. I'd really like to know what mathematical trick can speed this up. Link to R Colab: colab.research.google.com/github/badon...
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Mihaly Badonyi @mbadonyi.bsky.social · 05/12/2024
my day 5 #rstats solution to the 2024 #adventofcode I have also created an R Colab for these solutions, so R-curious people can run them without having to install R: github.com/badonyi/adve...
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Mihaly Badonyi @mbadonyi.bsky.social · 04/12/2024
my day 4 #rstat solution of the 2024 #adventofcode
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Mihaly Badonyi @mbadonyi.bsky.social · 03/12/2024
my day 3 #rstats solution of the 2024 #adventofcode
calling paste(collapse = '\n') on the input really got to me
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Mihaly Badonyi @mbadonyi.bsky.social · 02/12/2024
my day 2 #rstat solution of the 2024 #adventofcode
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Mihaly Badonyi @mbadonyi.bsky.social · 01/12/2024
my day1 #rstats solution of the 2024 #adventofcode
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