AI Networking Cookbook: Practical recipes for AI-assisted network automation and development
TL;DR
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.
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 argued that CRE function is not only an intrinsic property of DNA sequence alone but also emerges from a multidimensional context, including chromatin accessibility, histone modifications, three-dimensional genome topology, and cell type-specific regulatory landscapes, which promises to transform the ability to r...
This Mini Review summarizes seq2func modelling in plant regulatory genomics, discusses plant-specific challenges and the complementary value of observational and perturbation assays, and proposes evaluation frameworks based on biologically meaningful distribution shifts.
Gene regulatory networks (GRNs) are the maps that plant biologists most want to draw, with arrows pointing from transcription factors to the genes they control, explaining how plants develop and respond to the environment. Since experimental validation of even one arrow can take years, and a single plant genome harbour...
The Vertebrate Regulatory MOdule Detector (VRMOD) provides a universal coordinate reference system for regulatory sequences across 309 vertebrate genomes and enables genome-wide annotation of non-coding regulatory elements in any vertebrate species using genomic sequence alone.
This work proposes a 'collective maintenance' model in which motif vocabularies defining cell type families are evolutionarily stable, while recombination of these motifs generates cell type-specific regulatory programmes.
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