Relevant bibliographies by topics / Bioinformatics / Dissertations / Theses
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Dissertations / Theses on the topic 'Bioinformatics'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 July 2025

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1

Hvidsten, Torgeir R. "Predicting Function of Genes and Proteins from Sequence, Structure and Expression Data." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4490.

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2

Hooper, Sean. "Dynamics of Microbial Genome Evolution." Doctoral thesis, Uppsala University, Molecular Evolution, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3283.

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<p>The success of microbial life on Earth can be attributed not only to environmental factors, but also to the surprising hardiness, adaptability and flexibility of the microbes themselves. They are able to quickly adapt to new niches or circumstances through gene evolution and also by sheer strength of numbers, where statistics favor otherwise rare events.</p><p>An integral part of adaptation is the plasticity of the genome; losing and acquiring genes depending on whether they are needed or not. Genomes can also be the birthplace of new gene functions, by duplicating and modifying existing ge
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3

Snøve, Jr Ola. "Hardware-accelerated analysis of non-protein-coding RNAs." Doctoral thesis, Norwegian University of Science and Technology, Faculty of Information Technology, Mathematics and Electrical Engineering, 2005. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-713.

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<p>A tremendous amount of genomic sequence data of relatively high quality has become publicly available due to the human genome sequencing projects that were completed a few years ago. Despite considerable efforts, we do not yet know everything that is to know about the various parts of the genome, what all the regions code for, and how their gene products contribute in the myriad of biological processes that are performed within the cells. New high-performance methods are needed to extract knowledge from this vast amount of information.</p><p>Furthermore, the traditional view that DNA codes
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Björkholm, Patrik. "Method for recognizing local descriptors of protein structures using Hidden Markov Models." Thesis, Linköping University, The Department of Physics, Chemistry and Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-11408.

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<p>Being able to predict the sequence-structure relationship in proteins will extend the scope of many bioinformatics tools relying on structure information. Here we use Hidden Markov models (HMM) to recognize and pinpoint the location in target sequences of local structural motifs (local descriptors of protein structure, LDPS) These substructures are composed of three or more segments of amino acid backbone structures that are in proximity with each other in space but not necessarily along the amino acid sequence. We were able to align descriptors to their proper locations in 41.1% of the cas
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Keller, Jens. "Clustering biological data using a hybrid approach : Composition of clusterings from different features." Thesis, University of Skövde, School of Humanities and Informatics, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-1078.

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<p>Clustering of data is a well-researched topic in computer sciences. Many approaches have been designed for different tasks. In biology many of these approaches are hierarchical and the result is usually represented in dendrograms, e.g. phylogenetic trees. However, many non-hierarchical clustering algorithms are also well-established in biology. The approach in this thesis is based on such common algorithms. The algorithm which was implemented as part of this thesis uses a non-hierarchical graph clustering algorithm to compute a hierarchical clustering in a top-down fashion. It performs the
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Chawade, Aakash. "Inferring Gene Regulatory Networks in Cold-Acclimated Plants by Combinatorial Analysis of mRNA Expression Levels and Promoter Regions." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-20.

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<p>Understanding the cold acclimation process in plants may help us develop genetically engineered plants that are resistant to cold. The key factor in understanding this process is to study the genes and thus the gene regulatory network that is involved in the cold acclimation process. Most of the existing approaches1-8 in deriving regulatory networks rely only on the gene expression data. Since the expression data is usually noisy and sparse the networks generated by these approaches are usually incoherent and incomplete. Hence a new approach is proposed here that analyzes the promoter regio
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Muhammad, Ashfaq. "Design and Development of a Database for the Classification of Corynebacterium glutamicum Genes, Proteins, Mutants and Experimental Protocols." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-23.

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<p>Coryneform bacteria are largely distributed in nature and are rod like, aerobic soil bacteria capable of growing on a variety of sugars and organic acids. Corynebacterium glutamicum is a nonpathogenic species of Coryneform bacteria used for industrial production of amino acids. There are three main publicly available genome annotations, Cg, Cgl and NCgl for C. glutamicum. All these three annotations have different numbers of protein coding genes and varying numbers of overlaps of similar genes. The original data is only available in text files. In this format of genome data, it was not easy
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Chen, Lei. "Construction of Evolutionary Tree Models for Oncogenesis of Endometrial Adenocarcinoma." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-25.

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<p>Endometrial adenocarcinoma (EAC) is the fourth leading cause of carcinoma in woman worldwide, but not much is known about genetic factors involved in this complex disease. During the EAC process, it is well known that losses and gains of chromosomal regions do not occur completely at random, but partly through some flow of causality. In this work, we used three different algorithms based on frequency of genomic alterations to construct 27 tree models of oncogenesis. So far, no study about applying pathway models to microsatellite marker data had been reported. Data from genome–wide scans wi
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Dodda, Srinivasa Rao. "Improvements and extensions of a web-tool for finding candidate genes associated with rheumatoid arthritis." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-26.

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<p>QuantitativeTraitLocus (QTL) is a statistical method used to restrict genomic regions contributing to specific phenotypes. To further localize genes in such regions a web tool called “Candidate Gene Capture” (CGC) was developed by Andersson et al. (2005). The CGC tool was based on the textual description of genes defined in the human phenotype database OMIM. Even though the CGC tool works well, the tool was limited by a number of inconsistencies in the underlying database structure, static web pages and some gene descriptions without properly defined function in the OMIM database. Hence, in
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Huque, Enamul. "Shape Analysis and Measurement for the HeLa cell classification of cultured cells in high throughput screening." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-27.

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<p>Feature extraction by digital image analysis and cell classification is an important task for cell culture automation. In High Throughput Screening (HTS) where thousands of data points are generated and processed at once, features will be extracted and cells will be classified to make a decision whether the cell-culture is going on smoothly or not. The culture is restarted if a problem is detected. In this thesis project HeLa cells, which are human epithelial cancer cells, are selected for the experiment. The purpose is to classify two types of HeLa cells in culture: Cells in cleavage that
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Naswa, Sudhir. "Representation of Biochemical Pathway Models : Issues relating conversion of model representation from SBML to a commercial tool." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-28.

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<p>Background: Computational simulation of complex biological networks lies at the heart of systems biology since it can confirm the conclusions drawn by experimental studies of biological networks and guide researchers to produce fresh hypotheses for further experimental validation. Since this iterative process helps in development of more realistic system models a variety of computational tools have been developed. In the absence of a common format for representation of models these tools were developed in different formats. As a result these tools became unable to exchange models amongst th
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Poudel, Sagar. "GPCR-Directed Libraries for High Throughput Screening." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-29.

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<p>Guanine nucleotide binding protein (G-protein) coupled receptors (GPCRs), the largest receptor family, is enormously important for the pharmaceutical industry as they are the target of 50-60% of all existing medicines. Discovery of many new GPCR receptors by the “human genome project”, open up new opportunities for developing novel therapeutics. High throughput screening (HTS) of chemical libraries is a well established method for finding new lead compounds in drug discovery. Despite some success this approach has suffered from the near absence of more focused and specific targeted librarie
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Anders, Patrizia. "A bioinformaticians view on the evolution of smell perception." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-30.

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<p>Background:</p><p>The origin of vertebrate sensory systems still contains many mysteries and thus challenges to bioinformatics. Especially the evolution of the sense of smell maintains important puzzles, namely the question whether or not the vomeronasal system is older than the main olfactory system. Here I compare receptor sequences of the two distinct systems in a phylogenetic study, to determine their relationships among several different species of the vertebrates.</p><p>Results:</p><p>Receptors of the two olfactory systems share little sequence similarity and prove to be a challenge i
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Pohl, Matin. "Using an ontology to enhance metabolic or signaling pathway comparisions by biological and chemical knowledge." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-32.

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<p>Motivation:</p><p>As genome-scale efforts are ongoing to investigate metabolic networks of miscellaneous organisms the amount of pathway data is growing. Simultaneously an increasing amount of gene expression data from micro arrays becomes available for reverse engineering, delivering e.g. hypothetical regulatory pathway data. To avoid outgrowing of data and keep control of real new informations the need of analysis tools arises. One vital task is the comparison of pathways for detection of similar functionalities, overlaps, or in case of reverse engineering, detection of known data corrobo
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Sentausa, Erwin. "Time course simulation replicability of SBML-supporting biochemical network simulation tools." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-33.

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<p>Background: Modelling and simulation are important tools for understanding biological systems. Numerous modelling and simulation software tools have been developed for integrating knowledge regarding the behaviour of a dynamic biological system described in mathematical form. The Systems Biology Markup Language (SBML) was created as a standard format for exchanging biochemical network models among tools. However, it is not certain yet whether actual usage and exchange of SBML models among the tools of different purpose and interfaces is assessable. Particularly, it is not clear whether dyna
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Simu, Tiberiu. "A method for extracting pathways from Scansite-predicted protein-protein interactions." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-34.

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<p>Protein interaction is an important mechanism for cellular functionality. Predicting protein interactions is available in many cases as computational methods in publicly available resources (for example Scansite). These predictions can be further combined with other information sources to generate hypothetical pathways. However, when using computational methods for building pathways, the process may become time consuming, as it requires multiple iterations and consolidating data from different sources. We have tested whether it is possible to generate graphs of protein-protein interaction b
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Mathew, Sumi. "A method to identify the non-coding RNA gene for U1 RNA in species in which it has not yet been found." Thesis, University of Skövde, School of Humanities and Informatics, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-37.

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<p>Background</p><p>Non coding RNAs are the RNA molecules that do not code for proteins but play structural, catalytic or regulatory roles in the organisms in which they are found. These RNAs generally conserve their secondary structure more than their primary sequence. It is possible to look for protein coding genes using sequence signals like promoters, terminators, start and stop codons etc. However, this is not the case with non coding RNAs since these signals are weakly conserved in them. Hence the situation with non coding RNAs is more challenging. Therefore a protocol is devised to iden
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Rao, Aditya. "Tarfetpf: A Plasmodium faciparum protein localization predictor." Thesis, University of Skövde, School of Humanities and Informatics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-24.

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Wakadkar, Sachin. "Analysis of transmembrane and globular protein depending on their solvent energy." Thesis, University of Skövde, School of Life Sciences, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-2971.

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<p>The number of experimentally determined protein structures in the protein data bank (PDB) is continuously increasing. The common features like; cellular location, function, topology, primary structure, secondary structure, tertiary structure, domains or fold are used to classify them. Therefore, there are various methods available for classification of proteins. In this work we are attempting an additional method for making appropriate classification, i.e. solvent energy. Solvation is one of the most important properties of macromolecules and biological membranes by which they remain stabil
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Birkmeier, Bettina. "Integrating Prior Knowledge into the Fitness Function of an Evolutionary Algorithm for Deriving Gene Regulatory Networks." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-31.

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<p>The topic of gene regulation is a major research area in the bioinformatics community. In this thesis prior knowledge from Gene Ontology in the form of templates is integrated into the fitness function of an evolutionary algorithm to predict gene regulatory networks. The resulting multi-objective fitness functions are then tested with MAPK network data taken from KEGG to evaluate their respective performances. The results are presented and analyzed. However, a clear tendency cannot be observed. The results are nevertheless promising and can provide motivation for further research in that di
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Rao, Aditya. "TargetPf: A Plasmodium falciparum protein localization predictor." Thesis, University of Skövde, School of Humanities and Informatics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-914.

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<p>Background: In P. falciparum a similarity between the transit peptides of apicoplast and mitochondrial proteins in the context of net positive charge has previously been observed in few proteins. Existing P. falciparum protein localization prediction tools were leveraged in this study to study this similarity in larger sets of these proteins.</p><p>Results: The online public-domain malarial repository PlasmoDB was utilized as the source of apicoplast and mitochondrial protein sequences for the similarity study of the two types of transit peptides. It was found that</p><p>many of the 551 api
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Truvé, Katarina. "Using combined methods to reveal the dynamic organization of protein networks." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-962.

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<p>Proteins combine in various ways to execute different essential functions. Cellular processes are enormously complex and it is a great challenge to explain the underlying organization. Various methods have been applied in attempt to reveal the organization of the cell. Gene expression analysis uses the mRNA levels in the cell to predict which proteins are present in the cell simultaneously. This method is useful but also known to sometimes fail. Proteins that are known to be functionally related do not always show a significant correlation in gene expression. This fact might be explained by
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Orzechowski, Westholm Jakub. "Genome-wide Studies of Transcriptional Regulation in Yeast." Doctoral thesis, Uppsala universitet, Institutionen för cell- och molekylärbiologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-99205.

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In this thesis, nutrient signalling in yeast is used as a model to study several features of gene regulation, such as combinatorial gene regulation, the role of motif context and chromatin modifications. The nutrient signalling system in yeast consists of several pathways that transmit signals about the availability of key nutrients, and regulate the transcription of a large part of the genome. Some of the signalling pathways are also conserved in other eukaryotic species where they are implicated in processes such as aging and in human disease.   Combinatorial gene regulation is examined in p
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Besnier, Francois. "Development of Variance Component Methods for Genetic Dissection of Complex Traits." Doctoral thesis, Uppsala universitet, Centrum för bioinformatik, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-101399.

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This thesis presents several developments on Variance component (VC) approach for Quantitative Trait Locus (QTL) mapping. The first part consists of methodological improvements: a new fast and efficient method for estimating IBD matrices, have been developed. The new method makes a better use of the computer resources in terms of computational power and storage memory, facilitating further improvements by resolving methodological bottlenecks in algorithms to scan multiple QTL. A new VC model have also been developed in order to consider and evaluate the correlation of the allelic effects withi
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Hennerdal, Aron, and Arne Elofsson. "Rapid membrane protein topology prediction." Stockholms universitet, Institutionen för biokemi och biofysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-61921.

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State-of-the-art methods for topology of α-helical membrane proteins are based on the use of time-consuming multiple sequence alignments obtained from PSI-BLAST or other sources. Here, we examine if it is possible to use the consensus of topology prediction methods that are based on single sequences to obtain a similar accuracy as the more accurate multiple sequence-based methods. Here, we show that TOPCONS-single performs better than any of the other topology prediction methods tested here, but ~6% worse than the best method that is utilizing multiple sequence alignments. AVAILABILITY AND IMP
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Csaba, Gergely. "Context based bioinformatics." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-157252.

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The goal of bioinformatics is to develop innovative and practical methods and algorithms for bio- logical questions. In many cases, these questions are driven by new biotechnological techniques, especially by genome and cell wide high throughput experiment studies. In principle there are two approaches: 1. Reduction and abstraction of the question to a clearly defined optimization problem, which can be solved with appropriate and efficient algorithms. 2. Development of context based methods, incorporating as much contextual knowledge as possible in the algorithms, and derivation of practi
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Cingolani, Pablo. "Bioinformatics for epigenomics." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=40820.

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Epigenetics refers to reversible, heritable changes in gene regulation that occur without a change in DNA sequence. These changes are usually due to methylation of cytosine bases in DNA. In this work we review existing method- ologies and propose new ones for their use in epigenomics. High throughtput methods to estimate methylation levels were developed as well as methods to make a biological interpretation of the data based on gene sets enrichment. High correlation was obtained between our methylation estimations and ex- perimental data from MeDIP experiments. Our proposed methods for
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LEMOS, MELISSA. "WORKFLOW FOR BIOINFORMATICS." PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 2004. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=5928@1.

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CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO<br>Os projetos para estudo de genomas partem de uma fase de sequenciamento onde são gerados em laboratório dados brutos, ou seja, sequências de DNA sem significado biológico. As sequências de DNA possuem códigos responsáveis pela produção de proteínas e RNAs, enquanto que as proteínas participam de todos os fenômenos biológicos, como a replicação celular, produção de energia, defesa imunológica, contração muscular, atividade neurológica e reprodução. As sequências de DNA, RNA e proteínas são chamadas nesta tese de biossequê
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Gnad, Florian. "Bioinformatics of phosphoproteomics." Diss., kostenfrei, 2008. http://edoc.ub.uni-muenchen.de/9303/.

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Jauhiainen, Alexandra. "Evaluation and Development of Methods for Identification of Biochemical Networks." Thesis, Linköping University, The Department of Physics, Chemistry and Biology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-2811.

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<p>Systems biology is an area concerned with understanding biology on a systems level, where structure and dynamics of the system is in focus. Knowledge about structure and dynamics of biological systems is fundamental information about cells and interactions within cells and also play an increasingly important role in medical applications. </p><p>System identification deals with the problem of constructing a model of a system from data and an extensive theory of particularly identification of linear systems exists. </p><p>This is a master thesis in systems biology treating identification of b
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Andrade, Jorge. "Grid and High-Performance Computing for Applied Bioinformatics." Doctoral thesis, Stockholm : Bioteknologi, Kungliga Tekniska högskolan, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4573.

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Bresell, Anders. "Characterization of protein families, sequence patterns, and functional annotations in large data sets." Doctoral thesis, Linköping : Department of Physics, Chemistry and Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-10565.

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Gold, David L. "Bayesian learning in bioinformatics." [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-1624.

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Peng, Zeshan. "Structure comparison in bioinformatics." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B36271299.

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Baladandayuthapani, Veerabhadran. "Bayesian methods in bioinformatics." Texas A&M University, 2005. http://hdl.handle.net/1969.1/4856.

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This work is directed towards developing flexible Bayesian statistical methods in the semi- and nonparamteric regression modeling framework with special focus on analyzing data from biological and genetic experiments. This dissertation attempts to solve two such problems in this area. In the first part, we study penalized regression splines (P-splines), which are low-order basis splines with a penalty to avoid under- smoothing. Such P-splines are typically not spatially adaptive, and hence can have trouble when functions are varying rapidly. We model the penalty parameter inherent in the P-spl
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French, Leon Hayes. "Bioinformatics for neuroanatomical connectivity." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/40369.

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Neuroscience research is increasingly dependent on bringing together large amounts of data collected at the molecular, anatomical, functional and behavioural levels. This data is disseminated in scientific articles and large online databases. I utilized these large resources to study the wiring diagram of the brain or ‘connectome’. The aims of this thesis were to automatically collect large amounts of connectivity knowledge and to characterize relationships between connectivity and gene expression in the rodent brain. To extract the knowledge embedded in the neuroscience literature I created t
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Peng, Zeshan, and 彭澤山. "Structure comparison in bioinformatics." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B36271299.

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GOMES, LUCIANA DA SILVA ALMENDRA. "PROVENANCE FOR BIOINFORMATICS WORKFLOWS." PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 2011. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=18566@1.

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CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO<br>Muitos experimentos científicos são elaborados como fluxos de tarefas computacionais, que podem ser implementados através do uso de linguagens de programação. Na área de bioinformática é muito comum o uso de scripts ad-hoc para construir fluxos de tarefas. Os Sistemas de Gerência de Workflow Científico (SGWC) surgiram como uma alternativa a estes scripts. Uma das funcionalidades desses sistemas que têm recebido bastante atenção pela comunidade científica é a captura automática de dados de proveniência. Estes permitem averiguar qu
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Birney, Ewan. "Sequence alignment in bioinformatics." Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621653.

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Mumtaz, Shahzad. "Visualisation of bioinformatics datasets." Thesis, Aston University, 2015. http://publications.aston.ac.uk/25261/.

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Analysing the molecular polymorphism and interactions of DNA, RNA and proteins is of fundamental importance in biology. Predicting functions of polymorphic molecules is important in order to design more effective medicines. Analysing major histocompatibility complex (MHC) polymorphism is important for mate choice, epitope-based vaccine design and transplantation rejection etc. Most of the existing exploratory approaches cannot analyse these datasets because of the large number of molecules with a high number of descriptors per molecule. This thesis develops novel methods for data projection in
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Petty, Emma Marie. "Shape analysis in bioinformatics." Thesis, University of Leeds, 2009. http://etheses.whiterose.ac.uk/822/.

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In this thesis we explore two main themes, both of which involve proteins. The first area of research focuses on the analyses of proteins displayed as spots on 2-dimensional planes. The second area of research focuses on a specific protein and how interactions with this protein can naturally prevent or, in the presence of a pesticide, cause toxicity. The first area of research builds on previously developed EM methodology to infer the matching and transformation necessary to superimpose two partially labelled point configurations, focusing on the application to 2D protein images. We modify the
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Profiti, Giuseppe <1980&gt. "Graph algorithms for bioinformatics." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6914/1/profiti_giuseppe_tesi.pdf.

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Biological data are inherently interconnected: protein sequences are connected to their annotations, the annotations are structured into ontologies, and so on. While protein-protein interactions are already represented by graphs, in this work I am presenting how a graph structure can be used to enrich the annotation of protein sequences thanks to algorithms that analyze the graph topology. We also describe a novel solution to restrict the data generation needed for building such a graph, thanks to constraints on the data and dynamic programming. The proposed algorithm ideally improves the gene
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Profiti, Giuseppe <1980&gt. "Graph algorithms for bioinformatics." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6914/.

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Biological data are inherently interconnected: protein sequences are connected to their annotations, the annotations are structured into ontologies, and so on. While protein-protein interactions are already represented by graphs, in this work I am presenting how a graph structure can be used to enrich the annotation of protein sequences thanks to algorithms that analyze the graph topology. We also describe a novel solution to restrict the data generation needed for building such a graph, thanks to constraints on the data and dynamic programming. The proposed algorithm ideally improves the gene
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44

Bertoldi, Loris. "Bioinformatics for personal genomics: development and application of bioinformatic procedures for the analysis of genomic data." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421950.

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In the last decade, the huge decreasing of sequencing cost due to the development of high-throughput technologies completely changed the way for approaching the genetic problems. In particular, whole exome and whole genome sequencing are contributing to the extraordinary progress in the study of human variants opening up new perspectives in personalized medicine. Being a relatively new and fast developing field, appropriate tools and specialized knowledge are required for an efficient data production and analysis. In line with the times, in 2014, the University of Padua funded the BioInfoGen
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45

Malm, Patrik. "Development of a hierarchical k-selecting clustering algorithm – application to allergy." Thesis, Linköping University, The Department of Physics, Chemistry and Biology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-10273.

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<p>The objective with this Master’s thesis was to develop, implement and evaluate an iterative procedure for hierarchical clustering with good overall performance which also merges features of certain already described algorithms into a single integrated package. An accordingly built tool was then applied to an allergen IgE-reactivity data set. The finally implemented algorithm uses a hierarchical approach which illustrates the emergence of patterns in the data. At each level of the hierarchical tree a partitional clustering method is used to divide data into k groups, where the number k is de
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46

Enroth, Stefan. "The Nucleosome as a Signal Carrying Unit : From Experimental Data to Combinatorial Models of Transcriptional Control." Doctoral thesis, Uppsala universitet, Centrum för bioinformatik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129181.

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The human genome consists of over 3 billion nucleotides and would be around 2 meters long if uncoiled and laid out. Each human somatic cell contains all this in their nucleus which is only around 5 µm across. This extreme compaction is largely achieved by wrapping the DNA around a histone octamer, the nucleosome. Still, the DNA is accessible to the transcriptional machinery and this regulation is highly dynamic and change rapidly with, e.g. exposure to drugs. The individual histone proteins can carry specific modifications such as methylations and acetylations. These modifications are a major
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47

Lindskog, Mats. "Computational analyses of biological sequences -applications to antibody-based proteomics and gene family characterization." Doctoral thesis, KTH, School of Biotechnology (BIO), 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-527.

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<p>Following the completion of the human genome sequence, post-genomic efforts have shifted the focus towards the analysis of the encoded proteome. Several different systematic proteomics approaches have emerged, for instance, antibody-based proteomics initiatives, where antibodies are used to functionally explore the human proteome. One such effort is HPR (the Swedish Human Proteome Resource), where affinity-purified polyclonal antibodies are generated and subsequently used for protein expression and localization studies in normal and diseased tissues. The antibodies are directed towards prot
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Lysholm, Fredrik. "Structural characterization of overrepresented." Thesis, Linköping University, The Department of Physics, Chemistry and Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-12325.

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<p>Background: Through the last decades vast amount of sequence information have been produced by various protein sequencing projects, which enables studies of sequential patterns. One of the bestknown efforts to chart short peptide sequences is the Prosite pattern data bank. While sequential patterns like those of Prosite have proved very useful for classifying protein families, functions etc. structural analysis may provide more information and possible crucial clues linked to protein folding. Today PDB, which is the main repository for protein structure, contains more than 50’000 entries wh
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Lingemark, Maria. "A Lexicon for Gene Normalization." Thesis, Department of Computer and Information Science, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-20250.

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<p>Researchers tend to use their own or favourite gene names in scientific literature, even though there are official names. Some names may even be used for more than one gene. This leads to problems with ambiguity when automatically mining biological literature. To disambiguate the gene names, gene normalization is used. In this thesis, we look into an existing gene normalization system, and develop a new method to find gene candidates for the ambiguous genes. For the new method a lexicon is created, using information about the gene names, symbols and synonyms from three different databases.
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50

Viklund, Håkan. "Formalizing life : Towards an improved understanding of the sequence-structure relationship in alpha-helical transmembrane proteins." Doctoral thesis, Stockholm University, Department of Biochemistry and Biophysics, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-7144.

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<p>Genes coding for alpha-helical transmembrane proteins constitute roughly 25% of the total number of genes in a typical organism. As these proteins are vital parts of many biological processes, an improved understanding of them is important for achieving a better understanding of the mechanisms that constitute life.</p><p>All proteins consist of an amino acid sequence that fold into a three-dimensional structure in order to perform its biological function. The work presented in this thesis is directed towards improving the understanding of the relationship between sequence and structure for
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