Information theory applications for biological sequence analysis
S Vinga - Briefings in bioinformatics, 2014 - academic.oup.com
Abstract Information theory (IT) addresses the analysis of communication systems and has
been widely applied in molecular biology. In particular, alignment-free sequence analysis …
been widely applied in molecular biology. In particular, alignment-free sequence analysis …
Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella
The food industry is facing a major transition regarding methods for confirmation,
characterization, and subtyping of Salmonella. Whole-genome sequencing (WGS) is rapidly …
characterization, and subtyping of Salmonella. Whole-genome sequencing (WGS) is rapidly …
Normalized feature vectors: a novel alignment-free sequence comparison method based on the numbers of adjacent amino acids
DS Huang, HJ Yu - IEEE/ACM Transactions on Computational …, 2013 - ieeexplore.ieee.org
Based on all kinds of adjacent amino acids (AAA), we map each protein primary sequence
into a 400 by (L-1) matrix M. In addition, we further derive a normalized 400-tuple …
into a 400 by (L-1) matrix M. In addition, we further derive a normalized 400-tuple …
Survey on encoding schemes for genomic data representation and feature learning—from signal processing to machine learning
N Yu, Z Li, Z Yu - Big Data Mining and Analytics, 2018 - ieeexplore.ieee.org
Data-driven machine learning, especially deep learning technology, is becoming an
important tool for handling big data issues in bioinformatics. In machine learning, DNA …
important tool for handling big data issues in bioinformatics. In machine learning, DNA …
Genomic signature in evolutionary biology: A review
Simple Summary In a broad sense, genomic signature refers to characteristics associated to
DNA sequences. Many studies analyze genotype–phenotype patterns in a group of genes …
DNA sequences. Many studies analyze genotype–phenotype patterns in a group of genes …
A new method to cluster DNA sequences using Fourier power spectrum
A novel clustering method is proposed to classify genes and genomes. For a given DNA
sequence, a binary indicator sequence of each nucleotide is constructed, and Discrete …
sequence, a binary indicator sequence of each nucleotide is constructed, and Discrete …
Comparative study of encoded and alignment-based methods for virus taxonomy classification
The emergence of viruses and their variants has made virus taxonomy more important than
ever before in controlling the spread of diseases. The creation of efficient treatments and …
ever before in controlling the spread of diseases. The creation of efficient treatments and …
[HTML][HTML] New approaches in the systematics of rickettsiae
SN Shpynov, PE Fournier, NN Pozdnichenko… - New Microbes and New …, 2018 - Elsevier
The development of a formal order analysis (FOA) allowed constructing a classification of 49
genomes of Rickettsiaceae family representatives. Recently FOA has been extended with …
genomes of Rickettsiaceae family representatives. Recently FOA has been extended with …
Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping
P Kolekar, M Kale, U Kulkarni-Kale - Molecular phylogenetics and evolution, 2012 - Elsevier
The data deluge in post-genomic era demands development of novel data mining tools.
Existing molecular phylogeny analyses (MPAs) developed for individual gene/protein …
Existing molecular phylogeny analyses (MPAs) developed for individual gene/protein …
Prediction of the tetramer protein complex interaction based on CNN and SVM
Y Lyu, R He, J Hu, C Wang, X Gong - Frontiers in Genetics, 2023 - frontiersin.org
Protein-protein interactions play an important role in life activities. The study of protein-
protein interactions helps to better understand the mechanism of protein complex …
protein interactions helps to better understand the mechanism of protein complex …