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Relevant bibliographies by topics / Systems Bioinformatics / Dissertations / Theses

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Dissertations / Theses on the topic 'Systems Bioinformatics'

Author: Grafiati

Published: 3 June 2025

Last updated: 20 July 2025

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1

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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Ohler, Nathaniel Tobias. "Metaprogramming bioinformatics in the postgenomic era." Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/ohler/OhlerN0506.pdf.

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mattei, gianluca. "Tumor Microenvironment: Bioinformatics and Systems Biology Approaches." Doctoral thesis, Università di Siena, 2019. http://hdl.handle.net/11365/1070301.

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Cancers develop in complex microenvironments whose importance was emerging during last years. In fact, cancer microenvironment influences tumor progression and leads to the raising of chemotherapics resistance. Thus, a shift of the focus from cancer cells to cancer cells in their environment is crucial for studying the molecular and metabolic features of tumors in physiological contexts. Within the microenvironment, cancer associated fibroblasts (CAF) are attracting the attention of scientific community since, up to date, it is clear that they are the main component involved in the organizatio

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Hayes, John A. "A Framework for Implementing Bioinformatics Knowledge-Exploration Systems." W&M ScholarWorks, 2004. https://scholarworks.wm.edu/etd/1539626830.

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Malatras, Apostolos. "Bioinformatics tools for the systems biology of dysferlin deficiency." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066627/document.

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Le but de mon projet est de créer et d’appliquer des outils pour l’analyse de la biologie des systèmes musculaires en utilisant différentes données OMICS. Ce projet s’intéresse plus particulièrement à la dysferlinopathie due la déficience d’une protéine appelée dysferline qui est exprimée principalement dans les muscles squelettiques et cardiaque. La perte du dysferline due à la mutation (autosomique-récessive) du gène DYSF entraîne une dystrophie musculaire progressive (LGMD2B, MM, DMAT). Nous avons déjà développé des outils bio-informatiques qui peuvent être utilisés pour l’analyse fonctionn

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Malatras, Apostolos. "Bioinformatics tools for the systems biology of dysferlin deficiency." Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066627.pdf.

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Le but de mon projet est de créer et d’appliquer des outils pour l’analyse de la biologie des systèmes musculaires en utilisant différentes données OMICS. Ce projet s’intéresse plus particulièrement à la dysferlinopathie due la déficience d’une protéine appelée dysferline qui est exprimée principalement dans les muscles squelettiques et cardiaque. La perte du dysferline due à la mutation (autosomique-récessive) du gène DYSF entraîne une dystrophie musculaire progressive (LGMD2B, MM, DMAT). Nous avons déjà développé des outils bio-informatiques qui peuvent être utilisés pour l’analyse fonctionn

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Markstedt, Olof. "Kubernetes as an approach for solving bioinformatic problems." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-330217.

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The cluster orchestration tool Kubernetes enables easy deployment and reproducibility of life science research by utilizing the advantages of the container technology. The container technology allows for easy tool creation, sharing and runs on any Linux system once it has been built. The applicability of Kubernetes as an approach to run bioinformatic workflows was evaluated and resulted in some examples of how Kubernetes and containers could be used within the field of life science and how they should not be used. The resulting examples serves as proof of concepts and the general idea of how i

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Niklasson, Markus. "Coding to cure : NMR and thermodynamic software applied to congenital heart disease research." Doctoral thesis, Linköpings universitet, Kemi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-142785.

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Regardless of scientific field computers have become pivotal tools for data analysis and the field of structural biology is not an exception. Here, computers are the main tools used for tasks including structural calculations of proteins, spectral analysis of nuclear magnetic resonance (NMR) spectroscopy data and fitting mathematical models to data. As results reported in papers heavily rely on software and scripts it is of key importance that the employed computational methods are robust and yield reliable results. However, as many scientific fields are niched and possess a small potential us

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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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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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Lutimba, Stuart. "Determination of specificity and affinity of the Lactose permease (LacY) protein of Escherichia coli through application of molecular dynamics simulation." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-15933.

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Proteins are essential in all living organisms. They are involved in various critical activities and are also structural components of cells and tissues. Lactose permease a membrane protein has become a prototype for the major facilitator super family and utilises an existing electrochemical proton gradient to shuttle galactoside sugars to the cell. Therefore it exists in two principle states exposing the internal binding site to either side of the membrane. From previous studies it has been suggested that protonation precedes substrate binding but it is still unclear why this has to occur in

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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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Telele, Nigus Fikrie. "Predicting interspecies transmission and pandemic risks of coronaviruses." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19495.

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Bajalan, Amanj. "Improved methods for virus detection and discovery in metagenomic sequence data." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-412478.

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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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Nilsson, Grimstad Kristoffer. "Evaluation of the Oxford Nanopore Minion for the identification and differentiation of MRSA and non-MRSA isolates." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-18528.

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Staphylococcus aureus are bacterial pathogens causing infectious diseases. Methicillin-resistant S. aureus, or MRSA, carry the mecA or mecC genes generating resistance to β-lactam antibiotics. MRSA is problematic to treat and crucial to rapidly detect while current diagnostic workflows are time-consuming. DNA sequencing offers an alternative to existing methods. Illumina, the leading sequencing platform, is time-consuming and generates short reads. The Oxford Nanopore Technologies MinION presents rapid sequencing protocols, generating long reads at reduced accuracy. Here, the MinION device was

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Saloum, Alaa. "Bridging inflammatory bowel diseases and hepatobiliary disorders through pathway enrichment and module-based approach." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-18597.

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Inflammatory bowel diseases (IBD) including Crohn’s disease (CD) and ulcerative colitis (UC) are associated with various hepatobiliary disorders. Two of the chronic hepatobiliary disorders that may coexist with inflammatory bowel diseases are: primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). Previous studies have hypothesized that IBD, PBC, and PSC might share an underlying mechanism which contributes to the pathogenesis of the three conditions. In this study, a module-based network analysis and pathway enrichment analysis was applied on IBD, PSC, and PBC differentia

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Sparring, Leonard. "Conquering Chemical Space : Optimization of Docking Libraries through Interconnected Molecular Features." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416977.

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Copied selected text to selection primary: The development of new pharmaceuticals is a long and ardous process that typically requires more than 10 years from target identification to approved drug. This process often relies on high throughput screening of molecular libraries. However, this is a costly and time-intensive approach and the selection of molecules to screen is not obvious, especially in relation to the size of chemical space, which has been estimated to consist of 10 60 compounds. To accelerate this exploration, molecules can be obtained from virtual chemical libraries and tested

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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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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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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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Marzec-Schmidt, Katarzyna. "Deep convolutional neural networks accurately predict the differentiation status of human induced pluripotent stem cells." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19420.

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Rapid progress of AI technology in the life science area is observed in recent years. Convolutionalneural network (CNN) models were successfully applied for the localization and classification of cellson microscopic images. Induced pluripotent stem cells are one of the most important innovations inbiomedical research and are widely used, e.g. in regenerative medicine, drug screening, and diseasemodeling. However, assessment of cell cultures’ quality requires trained personnel, is timeconsumingand hence expensive. Fluorescence microscope images of human induced pluripotentstem‐hepatocytes (hiPS

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Shahid, Hira. "Association between neuroticism and risk of incident cardiovascular disease in UK Biobank cohort." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19330.

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Myocardial infarction (MI) and stroke are the major causes of cardiovascular related morbidities and mortalities around the world. The prevalence of cardiovascular diseases has been increased in last decades and it is vital need of time to investigate this global problem with focus on risk population stratification. The aim of the present study is to investigate the association between individualized personality trait that is neuroticism and risk of MI and stroke has been investigated in a large population-based cohort of UK biobank.375,713 individuals (mean age: 56.24 ± 8.06) were investigate

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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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Mahmoud, Nada. "Next-generation diagnostics of escherichia coli from community-onset sepsis patients in sweden : Studying the biodiversity of escherichia coli genomes." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19893.

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Escherichia coli (E. coli) is among the gram-negative bacteria that can cause several infections including sepsis. Confirmed sepsis patients must show a sequential organ failure assessment (SOFA) score of ≥2 with verified infection. Understanding the genotypic characteristics of E. coliclinical isolates from sepsis patients can help directing treatment strategies, tracking antibiotic resistance, and monitoring acquired virulence factors that can contribute to the severity of sepsis. The isolates included in this thesis were collected from confirmed sepsis patients (SOFA 2-3)during a prospectiv

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Lodhi, Saad Salman Khan. "Unraveling gene gene interactions in rheumatoid arthritis." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19908.

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Rheumatoid arthritis (RA) is a systematic autoimmune disorder characterized by a persistent joint inflammation. A subset of HLA-DRB1 alleles known as shared epitope (SE) are the strongest genetic risk factors to develop anti-citrullinated protein antibody positive (ACPA-positive) RA. A strong enrichment of interactions exists between ACPA-positive RA-associated genetic variants and HLA-DRB1 SE alleles in disease development. Pathway analysis was performed to investigate how the interactions between risk variants (SNPs) with HLA-DRB1 from a previous study related to ACPA-positive RA. Gene-gene

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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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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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Öhman, Caroline. "Studie av fladdermusförekomst och hur den påverkas av habitattyper : I Vara, Alingsås, Vårgårda och Borås kommuner." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-20495.

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Insectivorous bats face fragmentation and loss of suitable habitats. Bats numbers are declining in several parts of the world and scientists aim to construct distribution models that can predict occurrence, in order to understand species habitat requirements. Significant correlation has been found between species and habitat attributes but conditions differ across the world and between species. A predictive model will not work as well somewhere else. Bat occurrence in Vara, Alingsås, Vårgårda and Borås municipalities is only briefly inventoried. The aim of this study is to investigate if chose

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Tahseen, Yahia Keelani Ahlam. "Genes involved in inflammation are within celiac disease risk loci show differential mRNA expression." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-16292.

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Celiac disease (CD) is a chronic autoimmune disease, caused by the consumption of gluten in genetically predisposed individuals. Celiac patients develop many clinical features include; weight loss, diarrhea, and Intestinal damage, and if left untreated, CD patient may face an increased risk of malignancies. Materials and methods403 patient were admitted to the study. These patients were divided into three groups; celiac cases, controls, and latent celiac cases. Gene expression analysis was performed for intestinal biopsies and blood samples (leukocytes) using a quantitative PCR technique. The

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Pour, Akaber Shirin. "Identification of DEGs in B cells of patients with common variable immunodeficiency and healthy donors." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-18370.

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Common variable immunodeficiency (CVID) is a rare primary immune deficiency (1:25000) in which patients have a reduction in antibody production and very low titres in one or more of their Ig isotypes, (IgG, IgA and sometimes IgM). This disease can cause different symptoms such as: bronchiectasis, chronic lung disease and even autoimmunity, polyclonal lymphocytic infiltration, lymphoma and death. The underlying causes of CVID are still largely unknown but studies show that different factors like primary B-cell dysfunctions, defects in T cells and antigen-presenting cells are involved. Quantitat

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Fakhry, Charbel Bader. "Exploring Strategies to Integrate Disparate Bioinformatics Datasets." ScholarWorks, 2019. https://scholarworks.waldenu.edu/dissertations/7472.

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Distinct bioinformatics datasets make it challenging for bioinformatics specialists to locate the required datasets and unify their format for result extraction. The purpose of this single case study was to explore strategies to integrate distinct bioinformatics datasets. The technology acceptance model was used as the conceptual framework to understand the perceived usefulness and ease of use of integrating bioinformatics datasets. The population of this study included bioinformatics specialists of a research institution in Lebanon that has strategies to integrate distinct bioinformatics data

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Falin, Lee J. "Systems Uncertainty in Systems Biology & Gene Function Prediction." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/26634.

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The widespread use of high-throughput experimental assays designed to measure the entire complement of a cells genes or gene products has led to vast stores of data which are extremely plentiful in terms of the number of items they can measure in a single sample, yet often sparse in the number of samples per experiment due to their high cost. This often leads to datasets where the number of treatment levels or time points sampled is limited, or where there are very small numbers of technical and/or biological replicates. If the goal is to use this data to infer network models, these sparse dat

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Persson, Emma. "Developing a web based tool for identification of disease modules." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-16479.

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Complex diseases such as cancer or obesity are thought to be caused by abnormalities in multiple genes and cannot be derived to one specific location in the genome. It has been shown that identification of disease associated genes can be made through looking at interaction patterns in a protein‐protein interaction network, where the disease associated genes are represented in clusters, or disease modules. There are several algorithms developed to infer these disease modules, but studies have shown that the reliability of the results increase if multiple algorithms are used and a consensu

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Veanes, Margus. "Identification of novel loss of heterozygosity collateral lethality genes for potential applications in cancer." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-433768.

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Over the course of this project, I demonstrate the utility of a 4-phase analysis pipeline in the context of cancer therapy and the associated search for antineoplastic drug candidates. I showcase a repeatable means for generating lists of potential targets which may be used in conjunction with methods like small molecule screening as part of a search for broadly effective antineoplastic agents. By using publicly available variant call format (VCF) data sourced from the 1000 genomes project, global human population-wide data for non-sex chromosomes was filtered and transformed in a 4-phase pro

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Wiredja, Danica. "Phosphoproteomic Characterization of Systems-Wide Differential Signaling Induced by Small Molecule PP2A Activation." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1511288772792226.

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Malatras, Apostolos [Verfasser]. "Bioinformatics tools for the systems biology of dysferlin deficiency / Apostolos Malatras." Berlin : Freie Universität Berlin, 2018. http://d-nb.info/1171431333/34.

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Haughey, Caitlin, Lauri Mesilaakso, Erik Berner-Wik, Emma Östlund, Jonatan Ulfsparre, and Hampus Olin. "Probes for ESBL : A Method for Production of Probe Targets in Antibiotic Resistant Genes." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-323686.

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This project aimed to find a method for producing potential probe targets for identification of ESBL (Extended Spectrum Beta Lactamase) genes in bacteria. ESBLs are a type of enzymes responsible for antibiotic resistance in many bacteria. The result we developed was a semi-automated pipeline that utilises several Perl scripts to download gene sequences, identify sequence subgroups based on sequence similarity, find common target sequences among them and screen the target sequences against a background database. These target sequences should work with padlock probes and therefore had specific r

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Wu, Xi. "Ontology-driven Web-based Medical Image Sharing Interface for Epilepsy Research." Case Western Reserve University School of Graduate Studies / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=case1496660866436638.

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Peterson, Rickard. "Enkel navigering i webbdatabaser inom bioinformatik: En implementation av moduler för ett urval av databaser." Thesis, Linköping University, Department of Computer and Information Science, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-58928.

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<p>Detta examensarbete är framtaget för att utforma moduler till programmet BioSpider som utvecklats vid ADIT avdelningen vid IDA institutionen Linköping Universitet med syfte att förenkla för biologer när de söker information om andra forskares resultat.</p><p>Det finns ett stort antal databaser som innehåller forskningsdata kring proteiner, reaktioner, signalvägar etc. Exempel på databaser är UniProt, Reactome, IntAct, BioModels och KEGG. Det uppstår problem med att dessa databaser är uppbyggda på olika sätt och ej kan användas på ett universellt sätt, utan kräver individuellt utformning och

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Ram, Shri, and Sanjay Kataria. "Facilitating access and use of Bioinformatics Information Resources through Digital Library Systems." Society for Advancement of Library and Information Science, 2006. http://hdl.handle.net/10150/106089.

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As the Recombinant DNA, Gene Cloning and DNA sequencing technologies improved in 1970s the scientists began to think about the possibilities of sequencing the 3x109 nucleotide pairs in human genome. This led to the launch of the Human Genome Project (1990), and the greatest discovery in the field of life sciences, is near to completion. Vast and ever expanding diverse information on bioinformatics resources are being developed. These include databases of biological information, software tools etc. Advances in Internet Technology have largely affected to the bioinformatics resources as heterog

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Shateri, Najafabadi Hamed. "A systems approach towards a functional annotation of the genome of Trypanosoma brucei." Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=106493.

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The pathogenic species of trypanosomatids, including Trypanosoma brucei, T. cruzi, and Leishmania spp, cause serious human as well as animal diseases, with a very high incidence and mortality rate if untreated. Although the genome sequences of several trypanosomatids have been known for several years, many aspects of gene function and gene regulation are still unclear in these organisms. Most importantly, the lack of similarity between the majority of their genes and characterized genes of other organisms has limited our understanding of the gene functions in trypanosomatids. Not only the func

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Palma, Daniela. "Analysis of metatranscriptomes from an acidophilic electricity generating community treating acidic mining wastewaters." Thesis, Linnéuniversitetet, Institutionen för biologi och miljö (BOM), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-75933.

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Human ́s constant need for metals requires unsustainable mining and refining of metalore. As a result, highly contaminated wastewaters are discharged in the environmentcompromising the nearby habitat together with all its life forms. Microbial fuel cells arebioelectrochemical systems (BES’s) that use microorganisms to convert organic andinorganic matter, producing electricity as the final product. This technology has shownto have great potential for application for bioremediation of wastewaters. This thesisdescribes the gene expression and the taxonomical abundance of an acidophilic,electricit

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Nibbe, Rod K. "Systems Biology of Human Colorectal Cancer." Case Western Reserve University School of Graduate Studies / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=case1264179836.

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Desai, Amruta. "Design support for biomolecular systems." Cincinnati, Ohio : University of Cincinnati, 2010. http://rave.ohiolink.edu/etdc/view.cgi?acc_num=ucin1265986863.

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Thesis (M.S.)--University of Cincinnati, 2010.<br>Advisor: Carla Purdy. Title from electronic thesis title page (viewed Apr. 19, 2010). Includes abstract. Keywords: Biological pathways; weighted gate; BMDL; pyrimidine. Includes bibliographical references.

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Patel, Vishal N. "Colon Cancer and its Molecular Subsystems: Network Approaches to Dissecting Driver Gene Biology." Case Western Reserve University School of Graduate Studies / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=case1310087563.

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Gosline, Sara. "A systems biology approach to understanding the role of the endoplasmic reticulum in human disease." Thesis, McGill University, 2010. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=94997.

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The endoplasmic reticulum (ER) is a cellular organelle responsible for lipid biosynthesis, protein folding, drug detoxification and regulation of cellular calcium levels. One third of all cellular proteins are folded and assembled in the ER, including most membrane-bound and secreted proteins that are responsible for inter-cellular signaling. As such, the ER has evolved a series of pathways collectively called Endoplasmic Reticulum Quality Control (ERQC) that ensure proteins that are properly folded, as errantly folded proteins can be toxic to the cell. These pathways play a diverse role in m

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Hudson, Corey M. "Informatic approaches to evolutionary systems biology." Thesis, University of Missouri - Columbia, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3577951.

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<p> The sheer complexity of evolutionary systems biology requires us to develop more sophisticated tools for analysis, as well as more probing and biologically relevant representations of the data. My research has focused on three aspects of evolutionary systems biology. I ask whether a gene’s position in the human metabolic network affects the degree to which natural selection prunes variation in that gene. Using a novel orthology inference tool that uses both sequence similarity and gene synteny, I inferred orthologous groups of genes for the full genomes of 8 mammals. With these ortho

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Calderhead, Ben. "A study of Population MCMC for estimating Bayes Factors over nonlinear ODE models." Connect to e-thesis, 2007. http://theses.gla.ac.uk/304/.

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Thesis (MSc(R)) - University of Glasgow, 2007.<br>MSc(R) thesis submitted to the Faculty of Information and Mathematical Sciences, Department of Computing Science, University of Glasgow, 2007. Includes bibliographical references. Print version also available.

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Leung, Shuen-yi. "Predicting metabolic pathways from metabolic networks." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B42664317.

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