Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 31 for “"Sequence evolution"”.
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Stochastic modeling of biological sequence evolution
Markov models of sequence evolution are a fundamental building block for making inferences in biological research. This thesis reviews several major techniques developed to estimate parameters of Markov models of sequence evolution and presents a new approach for evaluating and comparing estimation …
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Using a complex model of sequence evolution to evaluate and improve phylogenetic methods
… variety of tree shapes under a complex model of sequence evolution based on the work of Aaron Halpern and William Bruno. Parameters of the model were estimated by maximum likelihood techniques applied to a phylogeny of 1,610 sequences of mammalian cytochrome b genes. These simulations represent a …
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Relationships in slow motion. How sequence evolution can be exploited to predict functional relationships between proteins
Contains fulltext : 117568.pdf (Publisher’s version ) (Open Access)
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The Formation Of Massive Stars: A 30 Mo Case Study
… core throughout the whole of their pre-main sequence phase.;Pre-main sequence evolution has been calculated under the accretion paradigm: beginning with a collapsed core, mass is accreted until a final stellar mass is reached. The calculations begin with a one solar mass core.;The initial 1 …
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Modeling evolution of protein coding DNA sequences
… models for statistical analysis of genetic sequence evolution and inference of properties of the underlying substitution processes in the context of maximum likelihood framework. Existing models for evolution of protein coding sequences allow site to site variation in non-synonymous …
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Rotation and magnetism in massive stars
Rotation has a number of important effects on the evolution of stars. Apart from structural changes because of the centrifugal force, turbulent mixing and meridional circulation can dramatically affect a star's chemical evolution. This leads to changes in the surface temperature and luminosity as …
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Last Call for Life: Habitability of Terrestrial Planets Orbiting Red Giants and White Dwarfs
… properties are relatively stable on the main sequence, post-main sequence evolution of a star involves significant changes in stellar temperature and radius, which is reflected in the changing irradiation at a specific orbital distance when the star becomes a red giant, and then later a white …
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Comparative gene identification in mammalian, fly, and fungal genomes
… by natural selection over millions of years of evolution. I develop general computational methods that combine statistical analysis of genome sequence alignments with classification algorithms in order to detect the distinctive signatures of protein-coding DNA sequence evolution. I implement …
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The Evolution of Planetary Nebula Nuclei
The evolution of planetary nebula nuclei (PNNs) is examined with the aid of the most recent available stellar evolution calculations and new observations of these objects. Their expected distribution in the log L-log T plane is calculated based upon the stellar evolutionary models of Paczynski, …
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Language Models Predict Drug Resistance from Complex Sequence Variation
… neural language models trained on viral protein sequence evolution have shown promise in their ability to predict viral escape mutations, potentially enabling more intelligent therapeutic design [6]. Hie et al.’s work puts forth the key conceptual advance that viral escape from human immunity …
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THE ROLE OF COMPLEX EVOLUTIONARY DYNAMICS IN MOLECULAR SEQUENCE ANALYSIS
… used to quantify selective pressure on molecular sequences. The work contained within this dissertation represents my efforts to create, validate, and test codon models, and to apply them to biologically diverse data sets. Specifically, my objective is to determine the impact and consequences of …
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Statistical analysis of protein interaction network topology
… the relationship between interaction and sequence evolution, functional class, phylogenetic class, and expression profiles. On the global level, we focused on large-scale properties like small-world, scale-free, and attack tolerance. Major differences were discovered between viral and …
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Learning the language of biomolecular interactions
… language models trained on amino acid sequences, namely protein language models, learn patterns in sequence evolution that encode protein structure and function. These protein language models are thus a powerful tool for extracting features of proteins, enabling the adoption of …
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Evolutionary analysis of mammalian genomes and associations to human disease
Statistical models of DNA sequence evolution for analysing protein-coding genes can be used to estimate rates of molecular evolution and to detect signals of natural selection. Genes that have undergone positive selection during evolution are indicative of functional adaptations that drive species …
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The Influence of Structural Constraints on Protein Evolution
Few mathematical models of sequence evolution incorporate parameters describingprotein structure, despite its high conservation, essential functional role and the increasingavailability of structural data. The primary goal of my PhD project was to create astructurally aware amino acid substitution …
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Dynamic accident sequence analysis using dynamic flowgraph method and Markov/cell-to-cell mapping technique
… system interactions and time-dependent accident sequence evolution. Subsequently there is an interest within the PSA community to complement the classical techniques with dynamic methodologies; driven in addition by a goal to eventually develop a framework for integrated safety assessment. The …
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Probabilistic Model-Based Approach to Evolutionary Analysis of Non-Coding Sequences
Non-coding sequences, constituting a large fraction of genomic DNA, are of great importance because (i) they harbor functional elements that are involved in the regulation of gene expression and (ii) they are essential for the study of genome structure and evolution. The availability of genome …
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Alignment- and Alignment-refining Algorithms: Effects on Branch-length Estimation and Selection Pattern Analyses
… First, I investigated the effects of multiple-sequence alignment quality on branch-length estimation, which can influence downstream bioinformatic analyses such as estimating rates of evolution and divergence times. To quantify the accuracy of branch-length estimates, I devised a scale-free …
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Molecular adaptation to low-temperature in New Zealand stick insects
… lifestyles, is a complex interaction between DNA sequence evolution and gene expression changes, which can evolve differentially in isolated species and populations.
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Reassessment of species limits and diversification process in the Cape grass genus Ehrharta Thunb
… age estimates. Comparisons of morphological evolutionary rates, as well as rates of nonsynonymous to synonymous sequence evolution (��), provide little evidence to support the hypothesis that non-ecological processes have been more important at high elevations. Both the low- and …
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