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 22 for “"fitness landscapes"”.
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An Exploration of Fitness Landscapes: Theory and Experiments
Genotypes, phenotypes, and fitness are the ultimate determinants of evolution. The relationship between these three components is collectively referred to as the fitness landscape. Evolutionary biologists have been working to understand the mechanisms and processes governing the fitness landscape …
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Exploring protein fitness landscapes with new high-throughput technologies
The concept of a protein’s fitness landscape – an abstract space in which related sequences are close together and matched with their fitness – is a useful tool to visualize core principles of protein evolution. Acquiring a new function, for example the laboratory evolution of an enzyme to convert …
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Strategies to Roam Enzymatic Fitness Landscapes in Ultrahigh-Throughput
… protein function. Each theoretical enzyme has a fitness value; peaks for high activity variants, and valleys for inactive enzymes that together shape the topological features of a fitness landscape. Enzyme function is as of yet virtually impossible to predict from sequence alone and finding …
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Fitness Landscapes, Genetic Interactions, and the Fitness of Hybrids
… re-arranged into novel combinations. The fitness of these hybrids is central to the evolution of reproductive isolation, but also plays an important role in conservation policy, and in crop and animal breeding. Fitness landscapes are simple mathematical models that generate a rich variety …
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Characterising fitness landscapes of protein evolution by next-generation sequencing
… is still incompletely understood. Protein fitness landscapes powerfully describe the sequence-function relationship by dividing sequence space into functional hills and valleys. This representation is often invoked yet lacks experimental evidence; the immense vastness of possible sequence …
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High-throughput protein engineering tools for efficient exploration and quantitative mapping of protein fitness landscapes
… of the measurements and thus the derived fitness function (e.g. stochastic noise in single-cell experiments, variability in expression levels in cell-based and lysate assays, use of proxy reaction substrates, discrepancies between assay reaction conditions and final application …
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Engineering TEV Protease Specificity: An Exploration of Machine Learning and High-Throughput Experimentation for Protein Design
… portion of this thesis focuses on generating fitness landscapes from high-throughput experiments. Most machine learning models do not account for experimental noise, harming model performance and changing model rankings in benchmarking studies. Here we develop FLIGHTED, a Bayesian method of …
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Evolution, Evolvability, Expression and Engineering
… sequence→function problems by building ‘Complete Fitness Landscapes’ in sequence space. This framework for measuring, modelling and designing biological sequences is built around the idea of learning an ‘oracle’ (typically a deep neural network model that takes a sequence as input and predicts its …
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Genetic algorithms with implicit memory
… in dynamic optimisation problems where fitness landscapes materialise that are identical to, or resemble in some way, landscapes previously encountered. The objective is to appraise the performances of the various approaches offered by the GAs. Approaches specifically tailored for …
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In silico vaccine design for hepatitis C: A computational platform for fighting disease
… high-performance computing to define empirical fitness landscapes and conduct viral dynamics simulations to determine vulnerable viral targets and rationally design vaccine immunogens. This computational design protocol will guide and accelerate vaccine development efforts by massively reducing …
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Multiscale dissection of bacterial proteome optimization
… quantitative relationship between expression and fitness for specific translation factors in the Gram-positive species Bacillus subtilis. These precision measurements confirmed that endogenous expression maximizes growth rate. Idiosyncratic transcriptional changes in regulons were however observed …
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Determining The Genotype-Phenotype Connection In Synthetic Inducible Gene Expression Systems
… the speed with which cells explored their fitness landscapes due to noisy gene expression.</p> <p><strong>Conclusions</strong> Models incorporating noisy gene expression and cell division were necessary to design, understand, and predict the behaviors of synthetic gene expression systems. …
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Modeling and Measuring Affordability as Fitness
… a broader concept of affordability – one of fitness to perform at the level of quality required by the consumer, to perform at that level whenever the product or service is used, and to do so with minimum consumption of resources. This concept of affordability is applied to technological …
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Scheduling and Resource Efficiency Balancing: Discrete Species Conserving Cuckoo Search for Scheduling in an Uncertain Execution Environment
… these kind of problems have complex multimodal fitness landscapes, which are characterised by a wide solution search spaces and presence of multiple local and global optima. The main goal of this thesis is twofold. Firstly, it presents a variation of the RCPSP that considers optimisation of …
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Methods to study protein folding and evolution in vivo
… to conveniently explore protein folding and fitness landscapes on the laboratory timescale has hindered the study of evolution in higher eukaryotes. Thus, my later work sought to overcome this limitation by creating new evolution platforms. Though the inspiration for my work stemmed from a …
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Graph-Based Computational Approaches for Modeling Viral Evolution
… graph-centered frameworks that integrate viral fitness, mutational distance, and mutational dynamics to model viral evolution from algorithmic and data-driven perspectives. First, ViraFit introduces a proof-of-concept model that couples epidemiological spread on contact networks with …
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Using signal processing, evolutionary computation, and machine learning to identify transposable elements in genomes
… detailed analysis of the genetic algorithm, its fitness functions, and its fitness landscapes is performed. The features are used, together with features used in existing exon finding algorithms, to build classifiers that distinguish TE's from other genomic sequences in humans, fruit flies, and …
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Bayesian network structure learning using characteristic properties of permutation representations with applications to prostate cancer treatment.
… Using selected benchmarks, rugged and plateaued fitness landscapes are identified that result in a loss of population diversity throughout the search. The thesis proposes two approaches to handle the loss of diversity. First, the benefits of introducing the Island Model (IM) paradigm are studied, …
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Design in the Modern Age: Investigating the Role of Complexity in the Performance of Collaborative Engineering Design Teams
… collaboration as it explores theoretical design fitness landscapes with various degrees of ruggedness.
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Fitness Landscape Analysis for the Differential Evolution Algorithm
… of its control parameters; the influence of fitness landscape characteristics (FLCs) on both algorithmic performance and search behavior; and the recurring failure patterns, which illuminate key vulnerabilities and inform the development of robust adaptive strategies. The first part of this …
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