dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility

W Wen, J Zhong, Z Zhang, L Jia, T Chu… - Briefings in …, 2024 - academic.oup.com
Histone modifications (HMs) are pivotal in various biological processes, including
transcription, replication, and DNA repair, significantly impacting chromatin structure. These …

Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data

H Schultheis, M Bentsen, V Heger, M Looso - Scientific Reports, 2024 - nature.com
Transcription factors (TFs) are crucial epigenetic regulators, which enable cells to
dynamically adjust gene expression in response to environmental signals. Computational …

Identification of DNA motif pairs on paired sequences based on composite heterogeneous graph

Q Wu, Y Li, Q Wang, X Zhao, D Sun, B Liu - Frontiers in Genetics, 2024 - frontiersin.org
Motivation The interaction between DNA motifs (DNA motif pairs) influences gene
expression through partnership or competition in the process of gene regulation. Potential …

Discriminative histone imputation using chromatin accessibility

W Wen, J Zhong, Z Zhang, T Chu, N Wang, CG Danko… - bioRxiv, 2024 - biorxiv.org
Abstract Motivation Histone modifications (HMs) play a crucial role in various biological
processes, including transcription, replication, and DNA repair, and they have a significant …