Use of wavelet-packet transforms to develop an engineering model for multifractal characterization of mutation dynamics in pathological and nonpathological gene sequences

This study uses dynamical analysis to examine in a quantitative fashion the information coding mechanism in DNA sequences. This exceeds the simple dichotomy of either modeling the mechanism by comparing DNA sequence walks as Fractal Brownian Motion (fbm) processes. The 2-D mappings of the DNA sequences for this research are from Iterated Function System (IFS) (Also known as the Chaos Game Representation (CGR)) mappings of the DNA sequences. This technique converts a 1-D sequence into a 2-D representation that preserves subsequence structure and provides a visual representation. The second step of this analysis involves the application of Wavelet Packet Transforms, a recently developed technique from the field of signal processing. A multi-fractal model is built by using wavelet transforms to estimate the Hurst exponent, H. The Hurst exponent is a non-parametric measurement of the dynamism of a system. This procedure is used to evaluate gene-coding events in the DNA sequence of cystic fibrosis mutations. The H exponent is calculated for various mutation sites in this gene. The results of this study indicate the presence of anti-persistent, random walks and persistent sub-periods in the sequence. This indicates the hypothesis of a multi-fractal model of DNA information encoding warrants further consideration.;This work examines the model\u27s behavior in both pathological (mutations) and non-pathological (healthy) base pair sequences of the cystic fibrosis gene. These mutations both natural and synthetic were introduced by computer manipulation of the original base pair text files. The results show that disease severity and system information dynamics correlate. These results have implications for genetic engineering as well as in mathematical biology. They suggest that there is scope for more multi-fractal models to be developed

Latitude, longitude, and beyond:mining mobile objects' behavior

Rapid advancements in Micro-Electro-Mechanical Systems (MEMS), and wireless communications, have resulted in a surge in data generation. Mobility data is one of the various forms of data, which are ubiquitously collected by different location sensing devices. Extensive knowledge about the behavior of humans and wildlife is buried in raw mobility data. This knowledge can be used for realizing numerous viable applications ranging from wildlife movement analysis, to various location-based recommendation systems, urban planning, and disaster relief. With respect to what mentioned above, in this thesis, we mainly focus on providing data analytics for understanding the behavior and interaction of mobile entities (humans and animals). To this end, the main research question to be addressed is: How can behaviors and interactions of mobile entities be determined from mobility data acquired by (mobile) wireless sensor nodes in an accurate and efficient manner? To answer the above-mentioned question, both application requirements and technological constraints are considered in this thesis. On the one hand, applications requirements call for accurate data analytics to uncover hidden information about individual behavior and social interaction of mobile entities, and to deal with the uncertainties in mobility data. Technological constraints, on the other hand, require these data analytics to be efficient in terms of their energy consumption and to have low memory footprint, and processing complexity

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward