Alignment-free sequence comparison: benefits, applications, and tools
Alignment-free sequence analyses have been applied to problems ranging from whole-
genome phylogeny to the classification of protein families, identification of horizontally …
genome phylogeny to the classification of protein families, identification of horizontally …
Time-series data mining
P Esling, C Agon - ACM Computing Surveys (CSUR), 2012 - dl.acm.org
In almost every scientific field, measurements are performed over time. These observations
lead to a collection of organized data called time series. The purpose of time-series data …
lead to a collection of organized data called time series. The purpose of time-series data …
A normalized Levenshtein distance metric
L Yujian, L Bo - IEEE transactions on pattern analysis and …, 2007 - ieeexplore.ieee.org
Although a number of normalized edit distances presented so far may offer good
performance in some applications, none of them can be regarded as a genuine metric …
performance in some applications, none of them can be regarded as a genuine metric …
Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in
a phylogeny. It shows excellent performance in estimating divergence times for both …
a phylogeny. It shows excellent performance in estimating divergence times for both …
Topological network alignment uncovers biological function and phylogeny
Sequence comparison and alignment has had an enormous impact on our understanding of
evolution, biology and disease. Comparison and alignment of biological networks will …
evolution, biology and disease. Comparison and alignment of biological networks will …
Interpretation of the Lempel-Ziv complexity measure in the context of biomedical signal analysis
Lempel-Ziv complexity (LZ) and derived LZ algorithms have been extensively used to solve
information theoretic problems such as coding and lossless data compression. In recent …
information theoretic problems such as coding and lossless data compression. In recent …
Enhanced genome assembly and a new official gene set for Tribolium castaneum
N Herndon, J Shelton, L Gerischer, P Ioannidis… - BMC genomics, 2020 - Springer
Background The red flour beetle Tribolium castaneum has emerged as an important model
organism for the study of gene function in development and physiology, for ecological and …
organism for the study of gene function in development and physiology, for ecological and …
Optimal network alignment with graphlet degree vectors
Important biological information is encoded in the topology of biological networks.
Comparative analyses of biological networks are proving to be valuable, as they can lead to …
Comparative analyses of biological networks are proving to be valuable, as they can lead to …
[LIBRO][B] Multiscale analysis of complex time series: integration of chaos and random fractal theory, and beyond
The only integrative approach to chaos and random fractal theory Chaos and random fractal
theory are two of the most important theories developed for data analysis. Until now, there …
theory are two of the most important theories developed for data analysis. Until now, there …
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 …