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Author

Ethan Pickering

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Jul 2026

Sequence-based modeling of plant epigenomes reveals cell-type-specific cis-regulatory grammar

PEAgent provides a foundational resource for decoding cell-type-specific plant cis-regulatory logic and interpreting noncoding variation in plants, and distinguishes grass-conserved from lineage-specific regulatory sequences better than sequence conservation scores alone.

Jie Yao, Jiaqi Li, Xuan Zhang et al. · 0 citations
Open access Aug 2026

Biology‐informed neural networks learn nonlinear representations from omics data to improve genomic prediction and biological discovery

Here, BINN is extended for genomic prediction and selection in crops by integrating thousands of single‐nucleotide polymorphisms with multi‐omics measurements and prior biological knowledge and substantially reduces prediction error relative to conventional neural nets and correctly identifies the most important nonlin...

Katiana Kontolati, R. J. Gladstone, Ian Davis et al. · 0 citations
Open access Jul 2026

CASCADE recovers promoter-associated regulatory motifs from cell-type-resolved DNA language-model attributions

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...

Ali Farghadan, Robert J. Schmitz, Scott A. Jackson et al. · 0 citations

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