Blar i NTNU Open på forfatter "Almaas, Eivind"
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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 ... -
Automatic Reconstruction of Metabolic Pathways for Ribosomally Synthesized and Post-translationally Modified Peptides
Thorsplass, Adrian (Master thesis, 2023)Biosyntetiske genkluster (BGC-er) fasiliterer produksjonen av sekundære metabolitter i organismer. Disse forbindelsene er kjent for å ha nyttige egenskaper som antibiotisk, antiviral eller anti-tumor aktivitet. Imidlertid ... -
Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters
Sulheim, Snorre; Fossheim, Fredrik A.; Wentzel, Alexander; Almaas, Eivind (Peer reviewed; Journal article, 2021)Background A wide range of bioactive compounds is produced by enzymes and enzymatic complexes encoded in biosynthetic gene clusters (BGCs). These BGCs can be identified and functionally annotated based on their DNA ... -
Comparative analysis of cancers and identification of novel anticancer drug targets using genome-scale metabolic modeling
Sandtrøen, Rebecca Madeleine Gilbert (Master thesis, 2022)Mange av dagens kreftmedisiner har som mål å hemme cellulære prosesser i kreftvev, noe som uungåelig også påvirker de samme prosessene i friskt vev. Dette resulterer i uønskede og langsiktige bivirkninger for pasienten, ... -
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 ... -
Comparing the impact of vaccination strategies on the spread of COVID-19, including a novel household-targeted vaccination strategy
Voigt, Andre; Omholt, Stig William; Almaas, Eivind (Peer reviewed; Journal article, 2022)With limited availability of vaccines, an efficient use of the limited supply of vaccines in order to achieve herd immunity will be an important tool to combat the wide-spread prevalence of COVID-19. Here, we compare a ... -
Comparison of volatile compounds in five hop (Humulus lupulus) varieties and the effect of solvent and temperature on retainment using Headspace Gas Chromatography-Mass Spectrometry
Jondal, Maren Sigbjørnsen (Master thesis, 2021)Humle (Humulus lupulus) er en viktig ingrediens i øl. For å få den typiske bitre smaken, samt en attraktiv aroma, har humle vært en del av produksjonen av øl i århundrer. Det er spesielt humlearomaen, som stammer fra ... -
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 & ... -
Constructing Metabolic Pathways from Identified Biosynthetic Gene Clusters
Fossheim, Fredrik Aunaas (Master thesis, 2020)Vi har i dette arbeidet utviklet og implementert en algoritme som konverterer informasjon om predikerte biosyntetiske genklustere (BGC'er) som gitt av antiSMASH til metabolske reaksjonsveier for bruk i genomskalamodeller ... -
Containing pandemics through targeted testing of households
Voigt, Andre; Martyushenko, Nikolay; Karlsen, Emil; Hall, Martina; Nyhamar, Kristen; Omholt, Stig William; Almaas, Eivind (Peer reviewed; Journal article, 2021)Background While invasive social distancing measures have proven efficient to control the spread of pandemics failing wide-scale deployment of vaccines, they carry vast societal costs. The development of a diagnostic ... -
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 ... -
csdR, an R package for differential co-expression analysis
Pettersen, Jakob Peder; Almaas, Eivind (Peer reviewed; Journal article, 2022)Background Differential co-expression network analysis has become an important tool to gain understanding of biological phenotypes and diseases. The CSD algorithm is a method to generate differential co-expression 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 ... -
Differential Gene Co-expression Analysis of Bipolar Disorder Using a Consensus Network Approach
Hessevik, Anna Sunniva (Master thesis, 2022)Analyser av differensielle gen-samuttrykksnettverk har nylig blitt utviklet som en viktig strategi for identifisering og undersøkelse av potensielt dysregulerte gener og spor i sykdommer og andre tilstander. CSD-metoden, ... -
Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus
Ofaim, Shany; Sulheim, Snorre; Almaas, Eivind; Sher, Daniel; Segrè, Daniel (Peer reviewed; Journal article, 2021)Microbial life in the oceans impacts the entire marine ecosystem, global biogeochemistry and climate. The marine cyanobacterium Prochlorococcus, an abundant component of this ecosystem, releases a significant fraction of ... -
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 ...