ArticleNAR genomics and bioinformatics2026
Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.
Article in NAR genomics and bioinformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Multiple layers of molecular determinants and mechanisms affect binding specificity between transcription factors (TFs) and DNA. DNA sequence-based deep learning models using convolutional neural networks (CNNs) and self-attention (SA) transformers have improved modeling accuracy and advanced our understanding of TF-DNA binding specificity through network interpretation. However, the systematic evaluation of various strategies for handling DNA sequence orientations in deep learning models-and their interpretation-remains underexplored, especially in the context of learning low-affinity binding site specificity. Using SELEX-seq data for eight Exd-Hox heterodimers in
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