[HTML][HTML] CLIP and complementary methods
RNA molecules start assembling into ribonucleoprotein (RNP) complexes during
transcription. Dynamic RNP assembly, largely directed by cis-acting elements on the RNA …
transcription. Dynamic RNP assembly, largely directed by cis-acting elements on the RNA …
Low-affinity binding sites and the transcription factor specificity paradox in eukaryotes
JF Kribelbauer, C Rastogi… - Annual review of cell …, 2019 - annualreviews.org
Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA
sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell …
sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell …
Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning
Protein–ligand interactions are increasingly profiled at high throughput using affinity
selection and massively parallel sequencing. However, these assays do not provide the …
selection and massively parallel sequencing. However, these assays do not provide the …
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 …
[HTML][HTML] DNA-binding specificities of human transcription factors
Although the proteins that read the gene regulatory code, transcription factors (TFs), have
been largely identified, it is not well known which sequences TFs can recognize. We have …
been largely identified, it is not well known which sequences TFs can recognize. We have …
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
The gaseous plant hormone ethylene regulates a multitude of growth and developmental
processes. How the numerous growth control pathways are coordinated by the ethylene …
processes. How the numerous growth control pathways are coordinated by the ethylene …
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions
MA Hume, LA Barrera, SS Gisselbrecht… - Nucleic acids …, 2015 - academic.oup.com
Abstract The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE)
serves as a convenient source of information on published data generated using universal …
serves as a convenient source of information on published data generated using universal …
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 …
Quantitative modeling of transcription factor binding specificities using DNA shape
DNA binding specificities of transcription factors (TFs) are a key component of gene
regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs …
regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs …