Transcription factor–DNA binding: beyond binding site motifs
S Inukai, KH Kock, ML Bulyk - Current opinion in genetics & development, 2017 - Elsevier
Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
The genetics of transcription factor DNA binding variation
Most complex trait-associated variants are located in non-coding regulatory regions of the
genome, where they have been shown to disrupt transcription factor (TF)-DNA binding …
genome, where they have been shown to disrupt transcription factor (TF)-DNA binding …
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
The complex language of eukaryotic gene expression remains incompletely understood.
Despite the importance suggested by many noncoding variants statistically associated with …
Despite the importance suggested by many noncoding variants statistically associated with …
Mapping genome-wide transcription-factor binding sites using DAP-seq
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any
organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription …
organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription …
A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
The adaptation of the CRISPR-Cas9 system as a genome editing technique has generated
much excitement in recent years owing to its ability to manipulate targeted genes and …
much excitement in recent years owing to its ability to manipulate targeted genes and …
Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome
YG Tak, PJ Farnham - Epigenetics & chromatin, 2015 - Springer
Considerable progress towards an understanding of complex diseases has been made in
recent years due to the development of high-throughput genotyping technologies. Using …
recent years due to the development of high-throughput genotyping technologies. Using …
Genetic determinants and epigenetic effects of pioneer-factor occupancy
Transcription factors (TFs) direct developmental transitions by binding to target DNA
sequences, influencing gene expression and establishing complex gene-regultory networks …
sequences, influencing gene expression and establishing complex gene-regultory networks …
Systematic dissection of genomic features determining transcription factor binding and enhancer function
SR Grossman, X Zhang, L Wang… - Proceedings of the …, 2017 - National Acad Sciences
Enhancers regulate gene expression through the binding of sequence-specific transcription
factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function …
factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function …
[HTML][HTML] Accurate identification of DNA replication origin by fusing epigenomics and chromatin interaction information
DNA replication initiation is a complex process involving various genetic and epigenomic
signatures. The correct identification of replication origins (ORIs) could provide important …
signatures. The correct identification of replication origins (ORIs) could provide important …
DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers
BP de Almeida, F Reiter, M Pagani, A Stark - Nature genetics, 2022 - nature.com
Enhancer sequences control gene expression and comprise binding sites (motifs) for
different transcription factors (TFs). Despite extensive genetic and computational studies, the …
different transcription factors (TFs). Despite extensive genetic and computational studies, the …