[HTML][HTML] Methods for ChIP-seq analysis: A practical workflow and advanced applications
R Nakato, T Sakata - Methods, 2021 - Elsevier
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a central method in
epigenomic research. Genome-wide analysis of histone modifications, such as enhancer …
epigenomic research. Genome-wide analysis of histone modifications, such as enhancer …
A survey on algorithms to characterize transcription factor binding sites
Transcription factors (TFs) are key regulatory proteins that control the transcriptional rate of
cells by binding short DNA sequences called transcription factor binding sites (TFBS) or …
cells by binding short DNA sequences called transcription factor binding sites (TFBS) or …
Meta-4mCpred: a sequence-based meta-predictor for accurate DNA 4mC site prediction using effective feature representation
DNA N4-methylcytosine (4mC) is an important genetic modification and plays crucial roles in
differentiation between self and non-self DNA and in controlling DNA replication, cell cycle …
differentiation between self and non-self DNA and in controlling DNA replication, cell cycle …
Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species
Motivation As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) is
recently shown to play crucial roles in restriction–modification systems. For better …
recently shown to play crucial roles in restriction–modification systems. For better …
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework
The identification of transcription factor binding sites and cis-regulatory motifs is a frontier
whereupon the rules governing protein–DNA binding are being revealed. Here, we …
whereupon the rules governing protein–DNA binding are being revealed. Here, we …
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)
In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic
segmentation of protein sequences into commonly occurring variable-length sub …
segmentation of protein sequences into commonly occurring variable-length sub …
CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq
Sequence motif discovery algorithms enhance the identification of novel deoxyribonucleic
acid sequences with pivotal biological significance, especially transcription factor (TF) …
acid sequences with pivotal biological significance, especially transcription factor (TF) …
AURTHO: Autoregulation of transcription factors as facilitator of cis-acting element discovery
S Anderssen, A Naômé, C Jadot, A Brans… - … et Biophysica Acta (BBA …, 2022 - Elsevier
Transcriptional regulation is key in bacteria for providing an adequate response in time and
space to changing environmental conditions. However, despite decades of research, the …
space to changing environmental conditions. However, despite decades of research, the …
De novo sequencing of proteins by mass spectrometry
Introduction Proteins are crucial for every cellular activity and unraveling their sequence and
structure is a crucial step to fully understand their biology. Early methods of protein …
structure is a crucial step to fully understand their biology. Early methods of protein …
A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package
V Levitsky, E Zemlyanskaya, D Oshchepkov… - Nucleic acids …, 2019 - academic.oup.com
Recognition of composite elements consisting of two transcription factor binding sites gets
behind the studies of tissue-, stage-and condition-specific transcription. Genome-wide data …
behind the studies of tissue-, stage-and condition-specific transcription. Genome-wide data …