Blar i Institutt for bioteknologi og matvitenskap på tidsskrift "BMC Bioinformatics"
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Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks
(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
(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 from identified biosynthetic gene clusters
(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 ... -
csdR, an R package for differential co-expression analysis
(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 ... -
Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts
(Peer reviewed; Journal article, 2023)Background - Use of alternative non-Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce ... -
ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions
(Journal article; Peer reviewed, 2019)Background Genome-scale metabolic network reconstructions are low level chemical representations of biological organisms. These models allow the system-level investigation of metabolic phenotypes using a variety of ... -
wTO: An R package for computing weighted topological overlap and a consensus network with integrated visualization tool
(Journal article; Peer reviewed, 2018)Background Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exist ...