[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 …
[HTML][HTML] The human transcription factors
Transcription factors (TFs) recognize specific DNA sequences to control chromatin and
transcription, forming a complex system that guides expression of the genome. Despite keen …
transcription, forming a complex system that guides expression of the genome. Despite keen …
JASPAR 2020: update of the open-access database of transcription factor binding profiles
Abstract JASPAR (http://jaspar. genereg. net) is an open-access database of curated, non-
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …
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 …
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
Abstract JASPAR (http://jaspar. genereg. net) is an open-access database of curated, non-
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …
Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
Impact of cytosine methylation on DNA binding specificities of human transcription factors
INTRODUCTION Nearly all cells in the human body share the same primary genome
sequence consisting of four nucleotide bases. One of the bases, cytosine, is commonly …
sequence consisting of four nucleotide bases. One of the bases, cytosine, is commonly …
G-quadruplexes are transcription factor binding hubs in human chromatin
Background The binding of transcription factors (TF) to genomic targets is critical in the
regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely …
regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely …
Short tandem repeats bind transcription factors to tune eukaryotic gene expression
CA Horton, AM Alexandari, MGB Hayes, E Marklund… - Science, 2023 - science.org
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter
gene expression, yet how they regulate transcription remains unknown. We found that STRs …
gene expression, yet how they regulate transcription remains unknown. We found that STRs …
Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch
Fetal hemoglobin (HbF, α 2 γ 2) level is genetically controlled and modifies severity of adult
hemoglobin (HbA, α 2 β 2) disorders, sickle cell disease, and β-thalassemia. Common …
hemoglobin (HbA, α 2 β 2) disorders, sickle cell disease, and β-thalassemia. Common …