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 23 for “"Biological sequences"”.
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Molecular evolution of biological sequences
… we combined statistical analyses of genomic sequences, mathematical models of evolutionary dynamics and experiments in molecular evolution to advance our understanding of rapid adaptation. Our results open new avenues in our understanding of population dynamics that can be translated to a …
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Function-based Algorithms for Biological Sequences
… Carbondale. TITLE: FUNCTION-BASED ALGORITHMS FOR BIOLOGICAL SEQUENCES MAJOR PROFESSOR: Dr. Spyros Tragoudas Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene …
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Toward Structural and Functional Predictions from Biological Sequences
Biological sequences, including DNA and protein sequences, are believed to encode sufficient information to determine the structure and function of biological molecules, which in turn decide the phenotypic traits of animals. Deciphering the biological sequences is an important and multiscale …
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Entropy Measurements and Ball Cover Construction for Biological Sequences
… is making it easier to select or engineer DNA sequences that produce dangerous proteins, it is important to be able to predict whether a novel DNA sequence is potentially dangerous by determining its taxonomic identity and functional characteristics. These tasks can be facilitated by the ever …
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Insights on Serology, CRISPR Diagnostics, and Machine Learning Architectures for Biological Sequences
… space model designed to efficiently handle large biological sequences. Janus demonstrates superior performance in genomics and proteomics tasks, outperforming existing models with significantly fewer parameters, thus paving the way for more efficient and accurate modeling of protein behavior and …
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Evolution, Evolvability, Expression and Engineering
… a framework for understanding and engineering biological sequences, and solving 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’ …
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A sequence-length sensitive approach to learning biological grammars using inductive logic programming.
… can help us to improve the process of learning biological grammars from protein sequences using Inductive Logic Programming (ILP). Contrary to most traditional ILP learning problems, biological sequences often have a high variation in their length. This variation in length is an important …
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Mathematical Models, Algorithms, and Statistics of Sequence Alignment
<p>The problem of biological sequence comparison arises naturally in an attempt to explain many biological phenomena. Due to the combinatorial structure and pattern preserving properties of the sequences it attracted not only biologists, but also mathematicians, statisticians and computer …
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Motif Mining On Structured And Semi-structured Biological Data
Motif discovery in biological data is very important to biologists becausethey are conjectured to have biological significance. Despite the considerateeffort put in this topic, it remains a challenging and difficult problem.There are several advances in biology such that the data is structured …
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DNA Phonology: Investigating the Codon Space
… to the compositional constraints of coding sequences. The heterogeneity of codon usage in the coding sequences of each genome was examined and presented, noting the consistency of intra-genomic distributions of codon similarity and atypicality. Such distributions provide the grounds on which …
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Machine Aided Biological Discovery and Design
… explore, understand, and engineer via iterative biological experimentation. Next-generation sequencing technologies have made it possible to measure biology in high-throughput, giving observational insight into these complexities. Further, in recent years, it has become possible to both …
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Knowledge discovery in biological databases : a neural network approach
… neural network approach to finding knowledge in biological databases. Specifically, we propose new methods to process biological sequences in two case studies: the classification of protein sequences and the prediction of E. Coli promoters in DNA sequences. Our proposed methods, based oil neural …
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MCAT: Motif Combining and Association Tool
De novo motif discovery in biological sequences is an important and computationally challenging problem. A myriad of algorithms have been developed to solve this problem with varying success, but it can be difficult for even a small number of these tools to reach a consensus. Because individual …
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Statistical physics and biological information : hydrophobicity patterns in protein design and differential motif finding in DNA
… identification of DNA motifs--short patterns in biological sequences--is essential. Common examples of motifs include transcription factor binding sites in promoter regions of co-regulated genes and exonic and intronic splicing enhancers ...
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Probabilistic arithmetic automata : applications of a stochastic computational framework in biological sequence analysis
The immense amount of biological sequence data available these days requires efficient and sensitive analysis in order to provide e.g. the identification of unknown proteins, or information about the similarity between DNA sequences. Furthermore, new challenges to computational sequence analysis …
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A distributed CPU-GPU framework for large-scale pairwise alignment
… comparisons of tens of thousands of individual biological sequences. Each such comparison can be performed with the well-known Needleman-Wunsch alignment algorithm. However, with the rapid growth of biological databases, performing all possible comparisons with this algorithm in serial becomes …
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Computational methods for splice site prediction
… each gene, as well as non-coding and regulatory sequences. In spite of the extensive research done in the area, the production of genomic data remains far ahead of the ability to reliably predict such features computationally. Eukaryotic genes consist predominantly of exons and introns; while the …
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Efficient Substring Discovery Using Suffix, LCP Array and Algorithm-Architecture Interaction
… to extract information from large databases like biological sequences of gene or protein. Discovery of patterns becomes very time efficient when we preprocess the database in the form suffix array. Due to inherent organization of data in suffix array and it’s secondary data structure longest …
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Controlling Neural Language Generation
… such as the generation of images, molecules, and biological sequences. We begin by presenting a class of sequence models called blank language models (BLMs), which generate sequences by dynamically creating and filling in blanks. Given partially specified text with one or more blanks, BLM will …
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Analysis and Abstraction of Parallel Sequence Search
The ability to compare two biological sequences is extremely valuable, as matches can suggest evolutionary origins of genes or the purposes of particular amino acids. Results of such comparisons can be used in the creation of drugs, can help combat newly discovered viruses, or can assist in …
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