AIMC Topic: Nucleotide Motifs

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A machine learning-based framework for modeling transcription elongation.

Proceedings of the National Academy of Sciences of the United States of America Feb 9, 2021
RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gen...
Histones Binding Sites Base Sequence Genome, Human RNA Splicing RNA Splice Sites Transcription Elongation, Genetic RNA Polymerase II Nucleotide Motifs DNA Methylation Protein Processing, Post-Translational HeLa Cells HEK293 Cells Models, Biological Machine Learning Epigenesis, Genetic Humans
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DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning.

Nucleic acids research Jul 27, 2020
Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling...
Computational Biology RNA-Binding Proteins Protein Binding Mice Base Sequence Nucleic Acid Conformation Binding Sites Mutation RNA Humans Computer Simulation Animals Deep Learning Nucleotide Motifs
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Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework.

Nucleic acids research Sep 5, 2019
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 developed a new method (DEep Sequence and Shape mOtif or DESSO) for cis-re...
Binding Sites Nucleotide Motifs Gene Expression Regulation K562 Cells Deep Learning Protein Binding Transcription Factors Humans DNA Computational Biology
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DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.

Bioinformatics (Oxford, England) Oct 1, 2017
MOTIVATION: Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of ...
Software Transcription Factors Sequence Analysis, DNA Nucleotide Motifs Support Vector Machine DNA-Binding Proteins Protein Array Analysis Nucleic Acid Conformation Binding Sites Protein Binding DNA Genomics
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A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data.

Nucleic acids research Aug 21, 2017
Characterizing the binding behaviors of RNA-binding proteins (RBPs) is important for understanding their functional roles in gene expression regulation. However, current high-throughput experimental methods for identifying RBP targets, such as CLIP-s...
Gene Expression Regulation Protein Binding Computational Biology Base Sequence Humans Binding, Competitive Algorithms Internet RNA-Binding Proteins Binding Sites Machine Learning 3' Untranslated Regions Reproducibility of Results High-Throughput Nucleotide Sequencing Mutation Nucleotide Motifs
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