A survey on algorithms to characterize transcription factor binding sites

M Tognon, R Giugno, L Pinello - Briefings in Bioinformatics, 2023 - academic.oup.com
Transcription factors (TFs) are key regulatory proteins that control the transcriptional rate of
cells by binding short DNA sequences called transcription factor binding sites (TFBS) or …

The 2022 Nucleic Acids Research database issue and the online molecular biology database collection

DJ Rigden, XM Fernández - Nucleic acids research, 2022 - academic.oup.com
Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including
87 papers reporting on new databases and 85 updates from resources previously published …

Towards a better understanding of TF-DNA binding prediction from genomic features

Z Wang, M Gong, Y Liu, S **ong, M Wang… - Computers in biology …, 2022 - Elsevier
Transcription factors (TFs) can regulate gene expression by recognizing specific cis-
regulatory elements in DNA sequences. TF-DNA binding prediction has become a …

RBPWorld for exploring functions and disease associations of RNA-binding proteins across species

JY Liao, B Yang, CP Shi, WX Deng… - Nucleic Acids …, 2025 - academic.oup.com
RNA-binding proteins (RBPs) play key roles in a wide range of physiological and
pathological processes. To facilitate the investigation of RBP functions and disease …

TFSyntax: a database of transcription factors binding syntax in mammalian genomes

Y Zhao - Nucleic Acids Research, 2023 - academic.oup.com
In mammals, transcriptional factors (TFs) drive gene expression by binding to regulatory
elements in a cooperative manner. Deciphering the rules of such cooperation is crucial to …

Molecular mechanisms of multi-omic regulation in breast cancer

S Ochoa, E Hernández-Lemus - Frontiers in Oncology, 2023 - frontiersin.org
Breast cancer is a complex disease that is influenced by the concurrent influence of multiple
genetic and environmental factors. Recent advances in genomics and other high throughput …

Transcription Factor-Wide Association Studies to Identify Functional SNPs in Alzheimer's Disease

J Dunn, C Moore, NS Kim, T Gao, Z Cheng… - Journal of …, 2025 - jneurosci.org
Alzheimer's disease (AD) is a progressive neurodegenerative disorder with profound global
impact. While genome-wide association studies (GWAS) have revealed genomic variants …

Molecular regulation of PPARγ/RXRα signaling by the novel cofactor ZFP407

A Charrier, J Ockunzzi, L Main, SV Ghanta… - Plos one, 2024 - journals.plos.org
Cofactors interacting with PPARγ can regulate adipogenesis and adipocyte metabolism by
modulating the transcriptional activity and selectivity of PPARγ signaling. ZFP407 was …

Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4

M Saotome, DB Poduval, SA Grimm… - Nucleic acids …, 2024 - academic.oup.com
Biologically precise enhancer licensing by lineage-determining transcription factors enables
activation of transcripts appropriate to biological demand and prevents deleterious gene …

[HTML][HTML] Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial …

N Jhamat, Y Guo, J Han, P Humblot… - International Journal of …, 2024 - mdpi.com
Endometritis is an inflammatory disease that negatively influences fertility and is common in
milk-producing cows. An in vitro model for bovine endometrial inflammation was used to …