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DNA Binding Site Characterization by Means of RÉnyi Entropy Measures on Nucleotide Transitions
2008 Edition, Volume 7, June 1, 2008 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

In this work, parametric information-theory measures for the characterization of binding sites in DNA are extended with the use of transitional probabilities on the sequence. We propose the use of parametric uncertainty...

DNA Binding Sites Characterization by Means of Rényi Entropy Measures on Nucleotide Transitions
2006 Edition, August 1, 2006 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

In this work, parametric information-theory measures for the characterization of binding sites in DNA are extended with the use of transitional probabilities on the sequence. We propose the use of parametric uncertainty...

Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction
Volume PP - IEEE - Institute of Electrical and Electronics Engineers, Inc.

Through sequence-based classification, this paper tries to accurately predict the DNA binding sites of transcription factors (TFs) in an unannotated cellular context. Related methods in the literature fail to perform such predictions accurately, since they do not...

Sequence-based prediction of putative transcription factor binding sites in DNA sequences of any length
Volume PP - IEEE - Institute of Electrical and Electronics Engineers, Inc.

A transcription factor (TF) is a protein that regulates gene expression by binding to specific DNA sequences. Despite the recent advances in experimental techniques for identifying transcription factor binding sites (TFBS) in DNA sequences, a large number...

Fast and Accurate Genome-Scale Identification of DNA-Binding Sites
2018 Edition, December 1, 2018 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

Discovering DNA binding sites in genome sequences is crucial for understanding genomic regulation. Currently available computational tools for finding binding sites with Position Weight Matrices of known motifs are often used in restricted genomic regions...

TargetDBP: Accurate DNA-Binding Protein Prediction via Sequence-based Multi-View Feature Learning
Volume PP - IEEE - Institute of Electrical and Electronics Engineers, Inc.

Accurately identifying DNA-binding proteins (DBPs) from protein sequence information is an important but challenging task for protein function annotations. In this paper, we establish a novel computational method, named TargetDBP, for accurately targeting DBPs from primary sequences....

DeeperBind: Enhancing prediction of sequence specificities of DNA binding proteins
2016 Edition, December 1, 2016 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

Transcription factors (TFs) are macromolecules that bind to cis-regulatory specific sub-regions of DNA promoters and initiate transcription. Finding the exact location of these binding sites (aka motifs) is important in a variety of domains such as drug...

High-Order Convolutional Neural Network Architecture for Predicting DNA-Protein Binding Sites
Volume PP - IEEE - Institute of Electrical and Electronics Engineers, Inc.

Although Deep learning algorithms have outperformed conventional methods in predicting the sequence specificities of DNA-protein binding, they lack to consider the dependencies among nucleotides and the diverse binding lengths for different transcription factors...

MotifMark: Finding regulatory motifs in DNA sequences
2017 Edition, July 1, 2017 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the...

Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering
2017 Edition, Volume 14, March 1, 2017 - IEEE - Institute of Electrical and Electronics Engineers, Inc.

Understanding binding cores is of fundamental importance in deciphering Protein-DNA (TF-TFBS) binding and gene regulation. Limited by expensive experiments, it is promising to discover them with variations directly from sequence data. Although existing...

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