Trygve Almøy

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BACKGROUND The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter approach by using statistical ideas developed for(More)
Gene expression microarray experiments generate data sets with multiple missing expression values. In some cases, analysis of gene expression requires a complete matrix as input. Either genes with missing values can be removed, or the missing values can be replaced using prediction. We propose six imputation methods. A comparative study of the methods was(More)
A Wiener process is a Brownian-motion process initiated in a certain state in a state space, and the first passage time is defined as the time of the process to reach a predefined absorbing state where the process stops. Time from 31 d prepartum to first treatment of clinical mastitis (CM) was modeled as first passage times of such Wiener processes. Two(More)
Baselines are often chosen by visual inspection of their effect on selected spectra. A more objective procedure for choosing baseline correction algorithms and their parameter values for use in statistical analysis is presented. When the goal of the baseline correction is spectra with a pleasing appearance, visual inspection can be a satisfactory approach.(More)
Comparative genomic hybridization (CGH) using microarrays is performed on bacteria in order to test for genomic diversity within various bacterial species. The microarrays used for CGH are based on the genome of a fully sequenced bacterium strain, denoted reference strain. Labelled DNA fragments from a sample strain of interest and from the reference strain(More)
China is the world's largest producer and consumer of fertilizer N, and decades of overuse has caused nitrate leaching and possibly soil acidification. We hypothesized that this would enhance the soils' propensity to emit N(2) O from denitrification by reducing the expression of the enzyme N(2) O reductase. We investigated this by standardized oxic/anoxic(More)
The need for precise and stable taxonomic classification is highly relevant in modern microbiology. Parallel to the explosion in the amount of sequence data accessible, there has also been a shift in focus for classification methods. Previously, alignment-based methods were the most applicable tools. Now, methods based on counting K-mers by sliding windows(More)
The 16S rRNA is by far the most common genomic marker used for prokaryotic classification, and has been used extensively in metagenomic studies over recent years. Along the 16S gene there are regions with more or less variation across the kingdom of bacteria. Nine variable regions have been identified, flanked by more conserved parts of the sequence. It has(More)
In microarray studies several statistical methods have been proposed with the purpose of identifying differentially expressed genes in two varieties. A commonly used method is an analysis of variance model where only the effect of interaction between variety and gene is tested. In this paper we argue that in addition to the interaction effects, the main(More)
Comparative genomic hybridizations (CGH) using microarrays are performed with bacteria in order to determine the level of genomic similarity between various strains. The microarrays applied in CGH experiments are constructed on the basis of the genome sequence of one strain, which is used as a control, or reference, in each experiment. A strain being(More)