TL;DR
The relationship between DNA sequence and the epigenome relative to RT is dissect and it is suggested that primary DNA sequence instructions exert a powerful baseline control over constitutive and cell-type-specific RT, fine-tuned by regulatory cues beyond the DNA sequence.
This study fine-tune two genome-based pretrained language models, DNABERT and DNABERT-2, to predict replication origins in budding yeast and unravel the DNA base composition behind them, and demonstrates that both models identify replication origin sequences, albeit through different learning strategies.
EpiBinder is presented, a multimodal deep-learning framework for cell-type-specific prediction of TF binding that jointly models DNA sequence with base-resolution epigenetic information, including cytosine methylation from whole-genome bisulfite sequencing and chromatin accessibility from DNase I hypersensitivity data.
This review compares convolutional, Transformer-based and graph architectures used to represent local sequence features, chromatin state and three-dimensional genome organisation to their applications to transcription-factor binding, chromatin accessibility, gene expression, non-coding variant prioritisation and regula...
It is suggested that progress requires reframing seq2func models as continually refined systems, in which targeted perturbation experiments, systematic evaluation and iterative model updates are tightly coupled through artificial intelligence-experiment feedback loops, enabling self-improving models that progressively...
This work developed a scoring-approach for AI-agents to autonomously assess AlphaGenome prediction confidence and accurately differentiate between AlphaGenome’s robust sequence-level recognition across species and its current limitations when interpreting un-fine-mapped regulatory variants.
ContextAware Significance of Cross-gene Attribution for Discovering Elements (CASCADE) is introduced, a positionspecific statistical framework for identifying model-derived candidate regulatory elements from in silico saturation mutagenesis and shifts motif recovery from downstream of the transcription start site towar...
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