[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 …

A survey on algorithms to characterize transcription factor binding sites

M Tognon, R Giugno, L Pinello - Briefings in Bioinformatics, 2023 - academic.oup.com
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 …

Meta-4mCpred: a sequence-based meta-predictor for accurate DNA 4mC site prediction using effective feature representation

B Manavalan, S Basith, TH Shin, L Wei… - Molecular Therapy-Nucleic …, 2019 - cell.com
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 …

Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species

L Wei, S Luan, LAE Nagai, R Su, Q Zou - Bioinformatics, 2019 - academic.oup.com
Motivation As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) is
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

J Yang, A Ma, AD Hoppe, C Wang, Y Li… - Nucleic acids …, 2019 - academic.oup.com
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 …

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

E Asgari, AC McHardy, MRK Mofrad - Scientific reports, 2019 - nature.com
In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic
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

Y Wang, Y Li, C Wang, CWJ Lio, Q Ma… - Briefings in …, 2024 - academic.oup.com
Sequence motif discovery algorithms enhance the identification of novel deoxyribonucleic
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 …

De novo sequencing of proteins by mass spectrometry

R Vitorino, S Guedes, F Trindade, I Correia… - Expert review of …, 2020 - Taylor & Francis
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 …

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 …