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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...

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...

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...

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...

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...

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...

Sequence-Based Prediction of Putative Transcription Factor Binding Sites in DNA Sequences of Any Length
2018 Edition, Volume 15, September 1, 2018 - 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 recent advances in experimental techniques for identifying transcription factor binding sites (TFBS) in DNA sequences, a large number...

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....

Oligo Design with Single Primer Binding Site for High Capacity DNA-Based Data Storage
Volume PP - IEEE - Institute of Electrical and Electronics Engineers, Inc.

DNA has become an attractive medium for long-term data archiving due to its extremely high storage density and longevity. Short single-stranded DNAs, called oligonucleotides (oligos), have been designed and synthesized to store digital data. Previous works designed the oligos with a...

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...

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