Absence of a simple code: how transcription factors read the genome
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
Genome-wide map** of G-quadruplex structures with CUT&Tag
J Lyu, R Shao, PY Kwong Yung… - Nucleic acids …, 2022 - academic.oup.com
Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA: RNA
hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect …
hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect …
Motif-based analysis of large nucleotide data sets using MEME-ChIP
MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can
analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and …
analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and …
Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation
Transcriptional reactivation of TERT, the catalytic subunit of telomerase, is necessary for
cancer progression in about 90% of human cancers. The recent discovery of two prevalent …
cancer progression in about 90% of human cancers. The recent discovery of two prevalent …
A transcription factor network specifying inhibitory versus excitatory neurons in the dorsal spinal cord
The proper balance of excitatory and inhibitory neurons is crucial for normal processing of
somatosensory information in the dorsal spinal cord. Two neural basic helix-loop-helix …
somatosensory information in the dorsal spinal cord. Two neural basic helix-loop-helix …
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences
M Siebert, J Söding - Nucleic acids research, 2016 - academic.oup.com
Position weight matrices (PWMs) are the standard model for DNA and RNA regulatory
motifs. In PWMs nucleotide probabilities are independent of nucleotides at other positions …
motifs. In PWMs nucleotide probabilities are independent of nucleotides at other positions …