Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations Centromeres are among the most diverse and dynamically evolving regions of the human genome and are commonly affected in various human cancers. However, organized into highly repetitive α-satellite hi...

🚨New preprint out!
🧬Short reads can now decode centromeres.
🌍We reveal population-scale centromere haplogroups and their links to disease.
biorxiv.org/content/10.1... (1/n)

Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system - npj Systems Biology and Applications npj Systems Biology and Applications - Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system

If you have questions about our methods or findings, we welcome your feedback and inquiries.

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Thank you for your interest in our work! (8/n)

GitHub - rmateosr/SJ_Classifier_pipeline Contribute to rmateosr/SJ_Classifier_pipeline development by creating an account on GitHub.

Our classifier is freely accessible on GitHub and can be applied to your datasets for KEAP1-NRF2 pathway analysis.
t.ly/S3JUv

When applied to #SRA data, the classifier detected constitutive pathway activation caused not only by known KEAP1-NRF2 alterations in cell lines, but also by previously unreported alterations on the system. (6/n)

The final model was cross-validated, achieving a
Specificity of 96.90%, discovering as well new alterations beyond the original scope of analysis within #TCGA. (5/n)

Our preliminary model helped reclassify ambiguous mutations, enriching our training data.
This iterative approach ensured diverse mutation representation, improving model robustness. (4/n)

We developed a naive Bayes-based classifier trained on #TCGA data to identify constitutive activation of the KEAP1-NRF2 pathway.
It focuses on mutations impacting pathway activity and leverages splicing junction signatures as biomarkers. (3/n)

The KEAP1-NRF2 pathway plays a critical role in cellular stress responses. Its constitutive activation is linked to genomic alterations, often found in cancer.
We explored a novel way to detect these activations using aberrant splicing junctions. (2/n)

Excited to announce that our paper on the use of splicing junction for detecting abnormal constitutive activation of the KEAP1-NRF2 system, led by @friend1ws.bsky.social at NCCRI, is now published in @natureportfolio.bsky.social npj Systems Biology and Applications! (1/n)

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