Blar i Department of Informatics på forfatter "Jonassen, Inge"
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RASflow: an RNA-Seq analysis workflow with Snakemake
Zhang, Xiaokang; Jonassen, Inge (Journal article; Peer reviewed, 2020)Background With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq ... -
ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species
Hanna, Eileen Marie; Zhang, Xiaokang; Eide, Marta; Fallahi, Shirin; Furmanek, Tomasz; Yadetie, Fekadu; Zielinski, Daniel Craig; Goksøyr, Anders; Jonassen, Inge (Journal article; Peer reviewed, 2020-11)The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in ... -
Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Xue, Yaxin; Lanzén, Anders; Jonassen, Inge (Journal article; Peer reviewed, 2020-03-13)Motivation Technological advances in meta-transcriptomics have enabled a deeper understanding of the structure and function of microbial communities. ‘Total RNA’ meta-transcriptomics, sequencing of total reverse transcribed ... -
Repeats and EST analysis for new organisms
Malde, Ketil; Jonassen, Inge (Journal article, 2008-01-18)Background Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask ... -
Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis
Eichner, Christiane; Frost, Petter; Dysvik, Bjarte; Jonassen, Inge; Kristiansen, Bjørn; Nilsen, Frank (Peer reviewed; Journal article, 2008-03-10)Background Lepeophtheirus salmonis is an ectoparasitic copepod feeding on skin, mucus and blood from salmonid hosts. Initial analysis of EST sequences from pre adult and adult stages of L. salmonis revealed a large proportion ... -
SeeCiTe: a method to assess CNV calls from SNP arrays using trio data
Lavrichenko, Ksenia; Helgeland, Øyvind; Njølstad, Pål Rasmus; Jonassen, Inge; Johansson, Stefan (Journal article; Peer reviewed, 2021)Motivation Single nucleotide polymorphism (SNP) genotyping arrays remain an attractive platform for assaying copy number variants (CNVs) in large population-wide cohorts. However, current tools for calling CNVs are still ... -
Systematic exploration of error sources in pyrosequencing flowgram data
Balzer, Susanne Mignon; Malde, Ketil; Jonassen, Inge (Peer reviewed; Journal article, 2011)Motivation: 454 pyrosequencing, by Roche Diagnostics, has emerged as an alternative to Sanger sequencing when it comes to read lengths, performance and cost, but shows higher per-base error rates. Although there are several ... -
TMM@: a web application for the analysis of transmembrane helix mobility
Skjærven, Lars; Jonassen, Inge; Reuter, Nathalie (Peer reviewed; Journal article, 2007-07-02)Background: To understand the mechanism by which a protein transmits a signal through the cell membrane, an understanding of the flexibility of its transmembrane (TM) region is essential. Normal Mode Analysis (NMA) has ... -
Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity
Sridhar, Settu; Sharma, Animesh; Kongshaug, Heidi; Nilsen, Frank; Jonassen, Inge (Peer reviewed; Journal article, 2012-11-06)Background: Francisella is a genus of gram-negative bacterium highly virulent in fishes and human where F. tularensis is causing the serious disease tularaemia in human. Recently Francisella species have been reported to ... -
XHM: A system for detection of potential cross hybridizations in DNA microarrays
Flikka, Kristian; Yadetie, Fekadu; Lægreid, Astrid; Jonassen, Inge (Peer reviewed; Journal article, 2004-08-27)Background: Microarrays have emerged as the preferred platform for high throughput gene expression analysis. Cross-hybridization among genes with high sequence similarities can be a source of error reducing the reliability ...