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Dissertations / Theses on the topic 'Bioinformatic analyses'

Author: Grafiati

Published: 7 June 2025

Last updated: 16 July 2025

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1

Al, Haj Baddar Nour W. "BIOINFORMATIC AND EXPERIMENTAL ANALYSES OF AXOLOTL REGENERATION." UKnowledge, 2019. https://uknowledge.uky.edu/biology_etds/61.

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Salamanders have an extraordinary ability to regenerate appendages after loss or amputation, irrespective of age. My dissertation research explored the possibility that regenerative ability is associated with the evolution of novel, salamander-specific genes. I utilized transcriptional and genomic databases for the axolotl to discover previously unidentified genes, to the exclusion of other vertebrate taxa. Among the genes identified were multiple mmps (Matrix metalloproteases) and a jnk1/mapk8 (c-jun-N-terminal kinase) paralog. MMPs function in extracellular matrix remodeling (ECM) and tissue

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2

Algothmi, Khloud Mubarak. "Some bioinformatic analyses of human GDAP1 gene expression." Doctoral thesis, importedStudentThesis, 2015. https://researchprofiles.canberra.edu.au/en/studentTheses/7bb52323-1539-490e-850a-4f7265cd0fff.

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Poluri, Raghavendra Tejo Karthik. "Using bioinformatic analyses to understand prostate cancer cell biology." Master's thesis, Université Laval, 2020. http://hdl.handle.net/20.500.11794/66803.

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Le cancer de la prostate (CaP) affecte 1 homme sur 7 au cours de sa vie. C’est le cancer numéro un diagnostiqué chez l'homme. Il s'agit du quatrième cancer le plus fréquent au Canada. Le CaP est une maladie hormonodépendante diagnostiquée chez l'homme. Les androgènes jouent un rôle vital dans la progression de la maladie. La première ligne de traitement, suivant une intervention chirurgicale ou un traitement de radiothérapie, est la thérapie de déprivation aux androgènes. Malgré une réponse initiale positive à l'inhibition des androgènes, la progression de la maladie vers un cancer de la prost

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4

Acar, Hande. "Bioinformatic Analyses In Microsatellite-based Genetic Diversity Of Turkish Sheep Breeds." Master's thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12612585/index.pdf.

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In the present study, within and among breed genetic diversity in thirteen Turkish sheep breeds (Sakiz, Karag&uuml<br>l, Hemsin, &Ccedil<br>ine &Ccedil<br>apari, Norduz, Herik, Akkaraman, Dagli&ccedil<br>, G&ouml<br>k&ccedil<br>eada, Ivesi, Karayaka, Kivircik and Morkaraman<br>in total represented by 628 individuals) were analyzed based on 20 microsatellite loci. Loci were amplified by Polymerase Chain Reactions and products were electronically recorded and converted into [628 x 20] matrix representing genotypes of individuals. Reliability of the genotyping and genetic diversity analyses were

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Kirk, Michael School of Biotechnology &amp Biomolecular Science UNSW. "Bioinformatic analyses of microarray experiments on genetic control of gene expression level." Awarded by:University of New South Wales. School of Biotechnology and Biomolecular Science, 2006. http://handle.unsw.edu.au/1959.4/25986.

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The advent of microarray technology, allowing measurement of gene expression levels for thousands of genes in parallel, has made possible experiments designed to investigate the genetic control of variation in gene expression level (described in the literature as ???genetical genomics??? or ???eQTL??? experiments). Published results from these studies, in yeast and in mice, show that genetic variation is an important factor in gene regulation, and furthermore that individual polymorphisms modify the expression level of many genes. The concern of this thesis is the bioinformatic analyses of the

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Eves-van, den Akker Sebastian. "Molecular and bioinformatic analyses of nematode-derived proteins involved in plant-parasitism." Thesis, University of Leeds, 2014. http://etheses.whiterose.ac.uk/7421/.

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Plant parasitic nematodes comprise several groups; the most economically damaging of these are the sedentary endoparasites. Sedentary endoparasitic nematodes modify host root tissues, using a suite of effector proteins to create and maintain a feeding site that is their sole source of nutrition. Ultrastructural studies of plant-nematode interactions, and in particular those of the feeding sites, have identified two key feeding structures; feeding tubes and feeding plugs. Sedentary plant-parasitic nematodes feed by withdrawing host cell assimilate from the feeding site though a feeding tube. Th

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Kröger, Stefan. "Bioinformatic analyses for T helper cell subtypes discrimination and gene regulatory network reconstruction." Doctoral thesis, Humboldt-Universität zu Berlin, 2017. http://dx.doi.org/10.18452/18122.

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Die Etablierung von Hochdurchsatz-Technologien zur Durchführung von Genexpressionsmessungen führte in den letzten 20 Jahren zu einer stetig wachsende Menge an verfügbaren Daten. Sie ermöglichen durch Kombination einzelner Experimente neue Vergleichsstudien zu kombinieren oder Experimente aus verschiedenen Studien zu großen Datensätzen zu vereinen. Dieses Vorgehen wird als Meta-Analyse bezeichnet und in dieser Arbeit verwendet, um einen großen Genexpressionsdatensatz aus öffentlich zugänglichen T-Zell Experimenten zu erstellen. T-Zellen sind Immunzellen, die eine Vielzahl von unterschiedlichen

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MOZZICAFREDDO, MATTEO. "Structural bioinformatic analyses of (macro)molecular interactions of biomedical relevance: an experimental validation." Doctoral thesis, Università degli Studi di Camerino, 2014. http://hdl.handle.net/11581/401775.

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Structural bioinformatics, like many other subdisciplines within bioinformatics, is characterized by the establishment of general purpose methods for manipulating information about biological macromolecules, and the application of these methods to solving problems in biology and creating new knowledge. Among its capabilities, structural bioinformatics can analyse the feasible (macro)molecular interactions and assists, or sometimes anticipates, the experimental approaches in biological research, even starting from a prediction analysis of the three-dimensional structures of the partners. This t

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9

Rajaonarifara, Elinambinina. "A bioinformatic study on the feasibility of a cross-species proteomics analyses of mycobacteria." Master's thesis, University of Cape Town, 2013. http://hdl.handle.net/11427/3073.

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10

Li, Yu. "Functional genomic and bioinformatic analyses of host responses to chronic AIDS and hepatitis RNA virus infections /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/11530.

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11

Piatkowski, Bryan. "Axillary hair developmental ultrastructure and mucilage composition in the moss Physcomitrella patens: Microscopic and bioinformatic analyses." OpenSIUC, 2015. https://opensiuc.lib.siu.edu/theses/1841.

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Physcomitrella patens, a haploid-dominant land plant, has increasingly become useful in molecular genetic studies and is a model for early land plant evolution. This thesis work explores the mucilage secretory hair ontology, development, and ultrastructure with microscopic methods. Axillary hair development parallels that of secretory tissues found in other mosses and ultrastructure shares important similarities with liverwort mucilage papillae. These mucilage secretory structures cover the developing apex and young leaves with mucilage for protection. Changes in the hair cell wall and mucilag

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Bermúdez, Mei-Ling. "Carnosine as a Mechanism-based Intervention in the Thy1-aSyn Mouse Model of Parkinson’s Disease: Neurobehavioral, Biochemical, and Bioinformatic Analyses." University of Cincinnati / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1543839362404126.

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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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Kröger, Stefan [Verfasser], Ulf [Gutachter] Leser, Joachim [Gutachter] Selbig, and Nils [Gutachter] Blüthgen. "Bioinformatic analyses for T helper cell subtypes discrimination and gene regulatory network reconstruction / Stefan Kröger ; Gutachter: Ulf Leser, Joachim Selbig, Nils Blüthgen." Berlin : Humboldt-Universität zu Berlin, 2017. http://d-nb.info/118933108X/34.

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Wehking, Jörn [Verfasser]. "Bioinformatic analyses of biogenic aerosol particles by classical and high-throughput sequencing : diversity, seasonal dynamics, and characterization of airborne microbial communities / Jörn Wehking." Mainz : Universitätsbibliothek Mainz, 2018. http://d-nb.info/117135861X/34.

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Werner, Johannes [Verfasser], Frank Oliver [Akademischer Betreuer] Glöckner, Matthias [Akademischer Betreuer] Ullrich, Rudolf I. [Akademischer Betreuer] Amann, and Hanno [Akademischer Betreuer] Teeling. "Bioinformatic analyses of marine microorganisms from contrasting habitats / Johannes Werner. Betreuer: Frank Oliver Glöckner. Gutachter: Frank Oliver Glöckner ; Matthias Ullrich ; Rudolf I. Amann ; Hanno Teeling." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2014. http://d-nb.info/1087295181/34.

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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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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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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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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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Mann, Alexander J. [Verfasser], Frank Oliver [Akademischer Betreuer] Glöckner, Matthias [Akademischer Betreuer] Ullrich, Rudolf I. [Akademischer Betreuer] Amann, and Hanno [Akademischer Betreuer] Teeling. "Bioinformatic analyses of genomes, metagenomes and expression data of polysaccharide-degrading marine microbes / Alexander J. Mann. Betreuer: Frank Oliver Glöckner. Gutachter: Frank Oliver Glöckner ; Matthias Ullrich ; Rudolf I. Amann ; Hanno Teeling." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2013. http://d-nb.info/1087285046/34.

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22

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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23

Odelgard, Anna. "Coverage Analysis in Clinical Next-Generation Sequencing." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-379228.

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With the new way of sequencing by NGS new tools had to be developed to be able to work with new data formats and to handle the larger data sizes compared to the previous techniques but also to check the accuracy of the data. Coverage analysis is one important quality control for NGS data, the coverage indicates how many times each base pair has been sequenced and thus how trustworthy each base call is. For clinical purposes every base of interest must be quality controlled as one wrong base call could affect the patient negatively. The softwares used for coverage analysis with enough accuracy

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Stenerlöw, Oskar. "Artefact detection in microstructures using image analysis." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-417342.

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Gyros Protein Technologies AB produce instruments designed to perform automated immunoassaying on plastic CDs with microstructures. While generally being a very robust process, the company had noticed that some runs on the instruments encountered problems. They hypothesised it had to do with the chamber on the CD in which the sample is added to. It was believed that the chamber was not being filled properly, leaving it completely empty or contained with a small amount of air, rather than liquid. This project aimed to investigate this hypothesis and to develop an image analysis solution that co

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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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Dafalla, Israa Yahia Al Hag Ibrahim. "Improving SARS-CoV-2 analyses from wastewater." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-20237.

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Wastewater-based epidemiology (WBE) analyzes wastewater for the presence of biological and chemical substances to make public health conclusions. COVID-19 disease is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that infected individuals shed also in their feces, making WBE an alternative way to track SARS-CoV-2 in populations. There are many limitations to the detection and quantification of SARS-CoV-2 from wastewater, such as sample quality, storage conditions or viral concentration. This thesis aims to determine the extent of these limitations and the factors that c

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Thelander, Tilia. "Optimisation of ForenSeq STR data analysis with FDSTools and comparative analysis with UAS." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-20053.

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DNA profiling with short tandem repeat data generated with massively parallel sequencing is associated with several challenges. FDSTools is an open-source software which applies correction models based on a reference database to correct DNA profiles. The correction models aim to provide an accurate representation of the true DNA profile and associated artefacts. Low analytical thresholds in FDSTools are suggested to improve detection of minor profiles in complex mixtures. The objective was to optimise FDSTools analysis for ForenSeq data, and to establish a Swedish reference database. The FDSTo

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Stenberg, Johan. "Software Tools for Design of Reagents for Multiplex Genetic Analyses." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6832.

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Jadhav, Trishul. "Knowledge Based Gene Set analysis (KB-GSA) : A novel method for gene expression analysis." Thesis, University of Skövde, School of Life Sciences, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-4352.

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<p>Microarray technology allows measurement of the expression levels of thousand of genes simultaneously. Several gene set analysis (GSA) methods are widely used for extracting useful information from microarrays, for example identifying differentially expressed pathways associated with a particular biological process or disease phenotype. Though GSA methods like Gene Set Enrichment Analysis (GSEA) are widely used for pathway analysis, these methods are solely based on statistics. Such methods can be awkward to use if knowledge of specific pathways involved in particular biological processes a

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Bogaerts, Márquez María 1991. "Identification of environmental variables in Drosophila melanogaster natural populations." Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2022. http://hdl.handle.net/10803/673159.

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Entender cómo las especies se adaptan al ambiente es aún una pregunta sin resolver en el campo de la Biología Evolutiva. Mientras el foco principal siempre ha estado en la base genética, los factores ambientales responsables de dichos procesos adaptativos se quedan por detrás. Nuestro objetivo principal es identificar las principales variables ambientales que contribuyen a la adaptación. Utilizamos poblaciones naturales de D. melanogaster de Europa y Norte América, y analizamos tanto SNPs como elementos transponibles (TEs). Para detectar y estimar las frecuencias de una población con pr

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Weinstein, Earl G. 1974. "MicroRNA cloning and bioinformatic analysis." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/8390.

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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Biology, 2002.<br>Includes bibliographical references.<br>Part I. Two gene-regulatory noncoding RNAs (ncRNAs), let-7 RNA and lin-4 RNA, were previously discovered in the C. elegans genome. The let-7 gene is conserved across a wide range of genomes, suggesting that these ncRNAs represent a wider class of gene-regulatory RNAs. Both lin-4 and let-7 RNAs are generated from stem-loop precursor RNAs, and share a common biochemical signature, namely 5'-terminal phosphate and 3'-terminal hydroxyl groups. We refer to ncRNAs that share the

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Leonardi, Emanuela. "Bioinformatic Analysis of Protein Mutations." Doctoral thesis, Università degli studi di Padova, 2012. http://hdl.handle.net/11577/3426280.

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Many gene defects have been associated to genetic disorders, but the details of molecular mechanisms by which they contribute to the disease are often unclear. The study of mutation effects at the protein level can help elucidate the biological processes involved in the disease and the role of the protein in it. Bioinformatics can help to address this problem, being the connection between different disciplines including clinical, genetics, structural biology, and biochemistry. By using a computational approach I tackled the analysis of some examples of biomedical interesting proteins integrati

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Freyhult, Eva. "A Study in RNA Bioinformatics : Identification, Prediction and Analysis." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8305.

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Alborgeba, Zainab. "Development and evaluation of a cost-effectiveness analysis model for sepsis diagnosis." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19155.

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Sepsis is a life-threatening organ dysfunction that is caused by a dysregulated host response to infection. Sepsis is a substantial health care and economic burden worldwide and is one of the most common reasons for admission to the hospital and intensive care unit. Early diagnosis and targeted treatment of sepsis are the bases to reduce the mortality and morbidity. Conventional blood culturing is the gold standard method for sepsis diagnostics. However, blood culturing is a time consuming method, requiring at least 48 to 72 hours to get the first results with very low sensitivity and specific

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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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Ishak, Helena. "Developing a ChIP-seq pipeline that analyzes the human genome and its repetitive sequences." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-335914.

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Chatzou, Maria 1985. "Large-scale comparative bioinformatics analyses." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/587086.

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One of the main and most recent challenges of modern biology is to keep-up with growing amount of biological data coming from next generation sequencing technologies. Keeping up with the growing volumes of experiments will be the only way to make sense of the data and extract actionable biological insights. Large-scale comparative bioinformatics analyses are an integral part of this procedure. When doing comparative bioinformatics, multiple sequence alignments (MSAs) are by far the most widely used models as they provide a unique insight into the accurate measure of sequence similaritie

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Reddy, Joseph. "Identification and Analysis of Important Proteins in Protein Interaction Networks Using Functional and Topological Information." Thesis, University of Skövde, School of Life Sciences, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-2395.

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<p>Studying protein interaction networks using functional and topological information is important for understanding cellular organization and functionality. This study deals with identifying important proteins in protein interaction networks using SWEMODE (Lubovac, et al, 2006) and analyzing topological and functional properties of these proteins with the help of information derived from modular organization in protein interaction networks as well as information available in public resources, in this case, annotation sources describing the functionality of proteins. Multi-modular proteins are

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Tangruksa, Benyapa. "Extracellular vesicles (EVs):roles in cell proliferation and transcriptomic analysis of HUVEC receiving cancerderived EVs." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-20593.

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Extracellular vesicles (EVs) are released by almost all types of cells. EVs play an important role in cell-to-cell communication by sending biomolecules such as mRNAs to other cells via endocytosis. This project aims to understand the roles of EVs and their potential application as mRNA delivery vehicles by completing two objectives. One objective was to investigate the EVs’ roles in cell proliferation by routinely removing EVs from cell-conditioned media, transferring stress-induced EVs to recipient epithelial cells, and examining their cell number. Another objective was to

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Oguchi, Chizoba. "A Comparison of Sensitive Splice Aware Aligners in RNA Sequence Data Analysis in Leaping towards Benchmarking." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-18513.

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Bioinformatics, as a field, rapidly develops and such development requires the design ofalgorithms and software. RNA-seq provides robust information on RNAs, both alreadyknown and new, hence the increased study of the RNA. Alignment is an important step indownstream analyses and the ability to map reads across splice junctions is a requirement ofan aligner to be suitable for mapping RNA-seq reads. Therefore, the necessity for a standardsplice-aware aligner. STAR, Rsubread and HISAT2 have not been singly studied for thepurpose of benchmarking one of them as a standard aligner for spliced RNA-se

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Lember, Geivi. "Sepsis-associated Escherichia coli whole-genome sequencing analysis using in-house developed pipeline and 1928 diagnostics tool." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19841.

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Sepsis is a life-threatening condition that is caused by a dysregulated host response to infection. Timely detection of sepsis and antibiotic treatment is important for the patient’s recovery from sepsis. Usually, when sepsis is detected, immediate antibiotic treatment is started with broad-spectrum antibiotics as it takes time to determine the correct antibiotic susceptibility. To overcome this problem, next-generation sequencing is seen as one possible development in clinical diagnostics in the future. Automated bioinformatics pipelines could be used initially for surveillance purposes but e

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Cova, Marta Alexandra Mendonça Nóbrega. "Bioinformatic analysis of the neuronal phosphoproteome." Master's thesis, Universidade de Aveiro, 2013. http://hdl.handle.net/10773/11623.

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Mestrado em Biomedicina Molecular<br>A fosforilação anormal de proteínas é uma das características chave da Doença de Alzheimer (DA) que pode estar envolvida tanto na patogénese como na progressão da doença. A fosforilação reversível de proteínas representa um importante mecanismo regulador que envolve a atividade de fosfoproteínas fosfatases (FPF) e proteínas cinases (PC). Um desequilíbrio intracelular entre a actividade de FPF e PC pode alterar a atividade, localização subcelular e interacções de proteínas, contribuindo para a desregulação da função e sinalização neuronal e, consequen

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Reddy, Veena K. "Analysis of single cell RNA seq data to identify markers for subtyping of non-small cell lung cancer." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-18514.

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Single cell RNA technology is a recent technical advancement used to understand the cancertumorgenicity at single cell resolution. In this study we have analyzed the scRNA data from thenon-small cell lung cancer (NSCLC) dataset to facilitate the early identification of NSCLCsubtypes namely, squamous cell carcinoma (SCC) and adenocarcinoma (AC). Non-immunecells, have a major role in tumorigenesis of the malignant tumors, in early stages. Therefore,we have analyzed the major non-immune cells, namely endothelial cells and fibroblast cellsfrom the GSE127465 dataset using SEURAT pipeline. Dimension

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Bakhtiyari, Elnaz. "Analysis of differentially expressed genes (DEGs) in neuronal cells from the cerebral cortex of Alzheimer’s disease mouse model." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19218.

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Alzheimer’s disease (AD) is an aging-related neurodegenerative disorder with large implications for society and individuals. AD is a multi-factor disorder, with these factors having a direct or indirect correlation with each other. Despite many studies with different aspects on molecular and cellular pathways, there is still no specific treatment for AD. Identification of potential pathogenic factors can be done by transcriptomic studies of differentially expressed genes (DEGs), but the outcomes have been contradictory. Using both bioinformatics and meta-analysis methods can be useful for remo

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Fasold, Mario. "Hybridization biases of microarray expression data - A model-based analysis of RNA quality and sequence effects." Doctoral thesis, Universitätsbibliothek Leipzig, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-116957.

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Modern high-throughput technologies like DNA microarrays are powerful tools that are widely used in biomedical research. They target a variety of genomics applications ranging from gene expression profiling over DNA genotyping to gene regulation studies. However, the recent discovery of false positives among prominent research findings indicates a lack of awareness or understanding of the non-biological factors negatively affecting the accuracy of data produced using these technologies. The aim of this thesis is to study the origins, effects and potential correction methods for selected method

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Gunnarsson, Ida. "Deriving Protein Networks by Combining Gene Expression and Protein Chip Analysis." Thesis, University of Skövde, Department of Computer Science, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-706.

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<p>In order to derive reliable protein networks it has recently been suggested that the combination of information from both gene and protein level is required. In this thesis a combination of gene expression and protein chip analysis was performed when constructing protein networks. Proteins with high affinity to the same substrates and encoded by genes with high correlation is here thought to constitute reliable protein networks. The protein networks derived are unfortunately not as reliable as were hoped for. According to the tests performed, the method derived in this thesis does not perfo

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Mbah-Mbole, Georgia Fru. "Comparative study of topology based pathway enrichment analysis methods for cardiac hypertrophy from a stem cell model using : ToPASeq and EnrichmentBrowser packages." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19465.

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Pathway enrichment analysis is an approach extensively used when analyzing high throughput data to identify pathways enriched within a group of differentially expressed genes. Furthermore, different methods utilizing the topology of the pathway offer a unique way of analyzing and interpreting gene expression data. These methods usually offer pathway topologies with a limited number of methods and visualization of results. Also, the use of different methods individually and comparison of their results can be very cumbersome, time-consuming and prone to errors due to the need for repeated data c

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Lythgow, Kieren. "Bioinformatics analysis of mitochondrial disease." Thesis, University of Newcastle Upon Tyne, 2011. http://hdl.handle.net/10443/1174.

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Several bioinformatic methods have been developed to aid the identification of novel nuclear-mitochondrial genes involved in disease. Previous research has aimed to increase the sensitivity and specificity of these predictions through a combination of available techniques. This investigation shows the optimum sensitivity and specificity can be achieved by carefully selecting seven specific classifiers in combination. The results also show that increasing the number of classifiers even further can paradoxically decrease the sensitivity and specificity of a prediction. Additionally, text mining

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Akman, Kemal. "Bioinformatics of DNA Methylation analysis." Diss., Ludwig-Maximilians-Universität München, 2014. http://nbn-resolving.de/urn:nbn:de:bvb:19-182873.

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Benaim, Jalfon Carlos 1966. "Analysis of the bioinformatics industry." Thesis, Massachusetts Institute of Technology, 2001. http://hdl.handle.net/1721.1/8882.

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Thesis (S.M.M.O.T.)--Massachusetts Institute of Technology, Sloan School of Management, Management of Technology Program, 2001.<br>Includes bibliographical references (leaf 76).<br>The rise of the commercial genomic industry and the broadening application of genomic techniques in biology and medicine together with the growing availability of DNA sequence information have created a new industry: The Bioinformatics Industry. This thesis analyzes technologies, applications market and competitors in this industry and explores potential changes to the business models that are being used today. The

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