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 …
ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions
TS Furey - Nature Reviews Genetics, 2012 - nature.com
Chromatin immunoprecipitation experiments followed by sequencing (ChIP–seq) detect
protein–DNA binding events and chemical modifications of histone proteins. Challenges in …
protein–DNA binding events and chemical modifications of histone proteins. Challenges in …
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
IV Kulakovskiy, IE Vorontsov, IS Yevshin… - Nucleic acids …, 2018 - academic.oup.com
We present a major update of the HOCOMOCO collection that consists of patterns
describing DNA binding specificities for human and mouse transcription factors. In this …
describing DNA binding specificities for human and mouse transcription factors. In this …
[HTML][HTML] Determination and inference of eukaryotic transcription factor sequence specificity
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are
currently known for only∼ 1% of eukaryotic TFs. Broadly sampling DNA-binding domain …
currently known for only∼ 1% of eukaryotic TFs. Broadly sampling DNA-binding domain …
Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning
Knowing the sequence specificities of DNA-and RNA-binding proteins is essential for
developing models of the regulatory processes in biological systems and for identifying …
developing models of the regulatory processes in biological systems and for identifying …
HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors
We present a major update of the HOCOMOCO collection that provides DNA binding
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …
Evaluation of methods for modeling transcription factor sequence specificity
Genomic analyses often involve scanning for potential transcription factor (TF) binding sites
using models of the sequence specificity of DNA binding proteins. Many approaches have …
using models of the sequence specificity of DNA binding proteins. Many approaches have …
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
IV Kulakovskiy, IE Vorontsov, IS Yevshin… - Nucleic acids …, 2016 - academic.oup.com
Abstract Models of transcription factor (TF) binding sites provide a basis for a wide spectrum
of studies in regulatory genomics, from reconstruction of regulatory networks to functional …
of studies in regulatory genomics, from reconstruction of regulatory networks to functional …
[HTML][HTML] Practical guidelines for the comprehensive analysis of ChIP-seq data
Mapping the chromosomal locations of transcription factors, nucleosomes, histone
modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the …
modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the …
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
IV Kulakovskiy, YA Medvedeva, U Schaefer… - Nucleic acids …, 2013 - academic.oup.com
Transcription factor (TF) binding site (TFBS) models are crucial for computational
reconstruction of transcription regulatory networks. In existing repositories, a TF often has …
reconstruction of transcription regulatory networks. In existing repositories, a TF often has …