Browsing NTNU Open by Author "Almaas, Eivind"
Now showing items 1-20 of 42
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A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma
Voigt, Andre; Nowick, Katja; Almaas, Eivind (Journal article; Peer reviewed, 2017)Differential co-expression network analyses have recently become an important step in the investigation of cellular differentiation and dysfunctional gene-regulation in cell and tissue disease-states. The resulting networks ... -
A method for dynamic flux balance analysis with global constraints
Karlsen, Emil (Master thesis, 2017)Nytteverdien til modellering i biologi øker stadig. Maskinvare og programvare blir stadig mer sofistikert, og i møte med den stadig voksende strømmen av data fra høy-volum eksperimentelle teknikker vokser også modellers ... -
A Simulated Annealing Based Method for Generating Random Metabolic Networks
Overn, Siri Haftun (Master thesis, 2017)A new method for randomization of metabolic networks was developed. The method was based on a Simulated Annealing algorithm, which is a well known technique for approximating optimal solutions to optimization problems. By ... -
A song of Host and Virus: Studying Phage Plaque Development on Bacterial Lawns
Todal, Aslak (Master thesis, 2020)I denne masteroppgaven presenteres nye metoder, utstyr og en matematisk modell for undersøkelse av utviklingen av bakteriofagplakk i semisolid agar fylt med bakterier. Cellfiebooth-systemet, opprinnelig utviklet og introdusert ... -
A study of the interactions and dynamics of microbial communties
Pettersen, Jakob Peder (Master thesis, 2019)De seneste årene har strukturen, sammensetningen og interaksjonene i mikrobielle samfunn vært et hett tema i de vitenskapelig miljøene. En rekke næringer som havbruk, vannbehandling og helse har mye å tjene dersom en utvidet ... -
An adjustable algal chloroplast plug-and-play model for genome-scale metabolic models
Røkke, Gunvor Bjerkelund; Hohmann-Marriott, Martin Frank; Almaas, Eivind (Peer reviewed; Journal article, 2020)The chloroplast is a central part of plant cells, as this is the organelle where the photosynthesis, fixation of inorganic carbon, and other key functions related to fatty acid synthesis and amino acid synthesis occur. ... -
Agent-Based Modelling of Bee Communication Networks
Rem, Vetle (Master thesis, 2020)I denne avhandlingen ble det laget en agentbasert modell som skulle gjenskape det sosiale interaksjonsnettverket i en bikube basert på et empirisk datasett med registrerte kommunikasjonstilfeller mellom honningbier. ... -
Alginate Biosynthesis Factories in Pseudomonas fluorescens : Localization and Correlation with Alginate Production Level
Maleki, Susan; Almaas, Eivind; Zotchev, Sergey; Valla, Svein; Ertesvåg, Helga (Journal article; Peer reviewed, 2016)Pseudomonas fluorescens is able to produce the medically and industrially important exopolysaccharide alginate. The proteins involved in alginate biosynthesis and secretion form a multiprotein complex spanning the inner ... -
An integrated systems biology approach to investigate transcriptomic data of thyroid carcinoma
Gulla, Marie (Master thesis, 2019)Som følge av store framskritt i teknologi og innovativ tenkning har det blitt mulig å måle uttrykk av gener og hvordan dette uttrykket varierer over store grupper mennesker. Sammenligning av genuttrykk gjør det mulig å ... -
Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks
Voigt, Andre; Almaas, Eivind (Journal article; Peer reviewed, 2019)Background For more than a decade, gene expression data sets have been used as basis for the construction of co-expression networks used in systems biology investigations, leading to many important discoveries in a wide ... -
Automated generation of genome-scale metabolic draft reconstructions based on KEGG
Karlsen, Emil; Schulz, Christian; Almaas, Eivind (Journal article; Peer reviewed, 2018)Background Constraint-based modeling is a widely used and powerful methodology to assess the metabolic phenotypes and capabilities of an organism. The starting point and cornerstone of all such modeling is a genome-scale ... -
Comparative analysis of weighted gene co-expression networks in human and mouse
Eidsaa, Marius; Stubbs, Lisa; Almaas, Eivind (Journal article; Peer reviewed, 2017)The application of complex network modeling to analyze large co-expression data sets has gained traction during the last decade. In particular, the use of the weighted gene co-expression network analysis framework has ... -
Computational SIS Modeling of the Spread of Antibiotic Resistance within Bacterial Metapopulation Networks
Finstad, Nora Rosvoll (Master thesis, 2018)The world faces a continually ongoing emergence of antibiotic resistance, and an almost non-existent development of new antibiotics to fight resistant bacteria. This leads to a substantial need for new and effective methods ... -
Conservation and Evolution of Pairwise Gene Co-Expression Correlations in HIV and TB Co-infected Individuals - A Network-based Analysis of Whole-Blood RNA samples
Borud, Martin (Master thesis, 2014)Network analysis of gene co-expression data has been shown to be a strong tool to elucidate biological information from large datasets. In this analysis the goal has been to see if the method developed by Voigt, Nowick & ... -
Core Decomposition Analysis of Weighted Biological Networks
Eidsaa, Marius (Doctoral thesis at NTNU;2016:162, Doctoral thesis, 2016)Summary of thesis: English version: In biology, advanced, high-throughput experimental methods are becoming faster, cheaper and more accessible. Effective network analysis tools applicable to a broad range of networks ... -
Development of an Internally Constrained Flux Balance Analysis Method for Saccharomyces cerevisiae
Røynestad, Pål (Master thesis, 2016)One of the most successful applications of the principles of systems biology has been the development of genome-scale metabolic models (GSMs). GSMs are models where every known metabolic reaction taking place in a cell is ... -
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production
Sulheim, Snorre; Kumelj, Tjasa; van Dissel, Dino; Salehzadeh-Yazdi, Ali; Chao, Du; Van Wezel, Gilles P.; Nieselt, Kay; Almaas, Eivind; Wentzel, Alexander; Kerkhoven, Eduard J (Journal article; Peer reviewed, 2020)Many biosynthetic gene clusters (BGCs) require heterologous expression to realize their genetic potential, including silent and metagenomic BGCs. Although the engineered Streptomyces coelicolor M1152 is a widely used host ... -
Epidemic Network Modeling for the Prediction of the Transmission of Gonorrhea in Norway
Solnes, Sofie Grefsrud (Master thesis, 2018)The number of gonorrhea infections among men who have sex with men (MSM) in Norway continues to rise, and in 2017 the number of infections increased with more than 50 % relative to 2016. This has resulted in various campaigns ... -
ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models
Martyushenko, Nikolay; Almaas, Eivind (Journal article; Peer reviewed, 2019)Motivation: The number and complexity of genome-scale metabolic models is steadily increasing, empowered by automated model-generation algorithms. The quality control of the models, however, has always remained a significant ... -
Fluorescent Reporters for investigating the Bacterial Stringent Response
Pahr, Jarle Magnus Ribe (Master thesis, 2013)The ``stringent response'' is a bacterial physiological adaptation to nutritional stress most well studied in the model organism \textit{Escherichia coli}. It is a research topic of interest both for increasing our ...