Mihaly Badonyi
@mbadonyi.bsky.social
π€ 108
π₯ 321
π 50
postdoc
@mpi-cbg.de
computational biology | disease genetics
pinned post!
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. π
nature.com/articles/s41...
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3 months ago
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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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25 days ago
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reposted by
Mihaly Badonyi
Nezha Benabdallah
about 1 month ago
We have an exciting PhD opportunity through the EASTBIO programme, co-supervised with Diego OyarzΓΊn. This project combines synthetic and systems biology to uncover the gene-regulatory circuitry hijacked in a cancer model. Weβre looking for candidates with a strong interest in functional genomics.
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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
https://www.findaphd.com/phds/project/eastbio-dissecting-cic-dux4-oncogenic-circuitry-through-single-cell-perturbation-profiling-and-network-inference/?p191470
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reposted by
Mihaly Badonyi
Stephen Turner
3 months ago
acmgscaler: an R package and Colab for standardized gene-level variant effect score calibration within the ACMG/AMP framework
academic.oup.com/bioinformati...
π§¬π₯οΈπ§ͺ
github.com/badonyi/acmg...
#Rstats
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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. π
onlinelibrary.wiley.com/doi/epdf/10....
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Complementary Roles of Structure and Variant Effect Predictors in RyR1 Clinical Interpretation
You have to enable JavaScript in your browser's settings in order to use the eReader.
https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/1834898
3 months ago
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reposted by
Mihaly Badonyi
Irene Gallego Romero
3 months ago
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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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. π
nature.com/articles/s41...
add a skeleton here at some point
3 months ago
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Happy to share that ππππππππππ is now on CRAN! π This means long-term stability and easy installation with: πππππππ.ππππππππ('ππππππππππ') ποΈ
doi.org/10.1093/bioi...
#rstats
#acmg
#varianteffect
#MAVEs
#VEPs
#genomics
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3 months ago
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Weβve 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. π Manuscript:
www.biorxiv.org/content/10.1...
π§ͺ Colab:
edin.ac/4mjzijp
#rstats
@theacmg.bsky.social
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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...
https://www.biorxiv.org/content/10.1101/2025.05.16.654507v2
5 months ago
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reposted by
Mihaly Badonyi
bioRxivpreprint
5 months ago
Why variant effect predictors and multiplexed assays agree and disagree
https://www.biorxiv.org/content/10.1101/2025.07.31.667868v1
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Mihaly Badonyi
Simon Biddie
5 months ago
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.
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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...
https://www.biorxiv.org/content/10.1101/2025.07.24.666385v3
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reposted by
Mihaly Badonyi
bioRxivpreprint
5 months ago
A knowledge-based distance metric highlights underperformance of variant effect predictors on gain-of-function missense variants
https://www.biorxiv.org/content/10.1101/2025.07.23.666325v1
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reposted by
Mihaly Badonyi
Wendy Bickmore
5 months ago
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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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
7 months ago
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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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8 months ago
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reposted by
Mihaly Badonyi
Derek Lowe
8 months ago
So, how many genetic diseases come down to good olβ loss-of-function in the targeted protein? Your estimate is probably too high:
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Mutant Proteins Classified
https://www.science.org/content/blog-post/mutant-proteins-classified
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reposted by
Mihaly Badonyi
Duncan Sproul
9 months ago
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 π
#epigenetics
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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...
https://www.findaphd.com/phds/project/fully-funded-phd-studentship-in-human-genetics-genomics-and-disease-dissecting-dnmt3b-functions-in-immunodeficiency-centromeric-instability-facial-anomalies-syndrome/?p184520
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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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9 months ago
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reposted by
Mihaly Badonyi
medRxivpreprint
9 months ago
Structure-informed classification of RyR1 variants highlights limitations of current predictors and enables clinical interpretation
https://www.medrxiv.org/content/10.1101/2025.04.02.25325085v1
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reposted by
Mihaly Badonyi
the Node
9 months ago
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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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...
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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 (...
https://www.biorxiv.org/content/10.1101/2025.03.13.642984v1
10 months ago
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reposted by
Mihaly Badonyi
Hannah Long
11 months ago
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! π§¬π§
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Edinburgh Doctoral College Scholarship
Applications now open for 2025 intake
https://institute-genetics-cancer.ed.ac.uk/igc-graduate-research-and-training/edinburgh-college-doctoral-scholarship-projects
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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 predictionsβstay tuned!
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12 months ago
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reposted by
Mihaly Badonyi
MRC-LMB Cell Biology Division
about 1 year ago
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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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...
about 1 year ago
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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...
about 1 year ago
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my day 4
#rstat
solution of the 2024
#adventofcode
about 1 year ago
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my day 3
#rstats
solution of the 2024
#adventofcode
about 1 year ago
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my day 2
#rstat
solution of the 2024
#adventofcode
about 1 year ago
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my day1
#rstats
solution of the 2024
#adventofcode
about 1 year ago
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