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Contemporary Genomic Foundation Models (GFMs) rely on a DNA-as-a-string paradigm that employs masked token prediction objectives for pretraining. However, this abstraction does not explicitly model the biochemical, structural, and physical properties essential to biological function. Many molecular properties can be es...
A reference-aligned diploid encoding for single-nucleotide variants (SNVs) and short insertions and deletions (indels) and unphased and phase-retaining tokenizers that accept phased genotypes and convert them to single-sequence diploid representation are introduced.
The results support a dominant-negative mechanism for BRS causing truncating mutations, offering a compelling rationale for allele-specific ASO therapeutic strategy and new venues for treatment.
ASXL3 patient truncations in neurodevelopmental condition Bainbridge-Ropers syndrome are shown to mediates gain-of-function (GOF) by escaping nonsense-mediated decay and Cullin 4-dependent degradation, resulting in aberrant protein accumulation, widespread transcriptional dysregulation, and altered chromatin accessibil...
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