Inge Jonassen

Inge Jonassen
University of Bergen | UiB · Department of Informatics

Professor, PhD

About

285
Publications
34,761
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Introduction
I am professor in bioinformatics at the Department of Informatics and heading the Computational Biology Unit, both at the University of Bergen. I am heading a National research infrastructure project aimed at building a Norwegian Node in the pan-European ELIXIR research infrastructure for bioinformatics. I am partner in the Sea Lice Research Centre and associated with the Centre for Cancer Biomarkers under establishment at the University of Bergen.
Additional affiliations
January 2011 - present
January 2006 - December 2008
Haukeland universitetssjukehus - Helse Bergen
January 1999 - December 2009
MRC National Institute for Medical Research
Education
August 2003 - June 2006
University of Bergen
Field of study
  • Bioinformatics (Computer Science)
January 1990 - February 1992
University of Bergen
Field of study
  • Pattern recognition (Computer Science)
August 1986 - December 1989
University of Bergen
Field of study
  • Computer science

Publications

Publications (285)
Article
Full-text available
Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better unders...
Article
Full-text available
Background SNP arrays, short- and long-read genome sequencing are genome-wide high-throughput technologies that may be used to assay copy number variants (CNVs) in a personal genome. Each of these technologies comes with its own limitations and biases, many of which are well-known, but not all of them are thoroughly quantified. Results We assemble...
Article
Full-text available
Objective Little is known concerning the stability of the lower airway microbiome. We have compared the microbiota identified by repeated bronchoscopy in healthy subjects and patients with ostructive lung diseaseases (OLD). Methods 21 healthy controls and 41 patients with OLD completed two bronchoscopies. In addition to negative controls (NCS) and...
Article
Full-text available
Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetit...
Article
Full-text available
How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal-and heat-responsive genes, and is collec...
Preprint
Full-text available
This is a duplicate, see https://www.researchgate.net/publication/350106692_The_salmon_louse_genome_copepod_features_and_parasitic_adaptations for full text.
Preprint
Full-text available
Background The salmon louse ( Lepeophtheirus salmonis ) is an obligate ectoparasitic copepod, living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better und...
Chapter
Full-text available
Biomarkers are of great importance in many fields, such as cancer research, toxicology, diagnosis and treatment of diseases, and to better understand biological response mechanisms to internal or external intervention. High-throughput gene expression profiling technologies, such as DNA microarrays and RNA sequencing, provide large gene expression d...
Preprint
Full-text available
Copepods encompass a range of ecological roles from parasites to phytoplankton grazers linking primary producers to higher trophic levels. Despite these important roles, copepod genome assemblies are scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod. We present the 695.4 Mbp L. salmonis genome assem...
Preprint
Full-text available
How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is colle...
Article
Full-text available
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 prone to extensive false positive calls when applied to biobank scale arrays. Moreover, there is a lack of methods exploiting co...
Article
Full-text available
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 bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotyp...
Article
Full-text available
Because of their global consumption and persistence, per- and polyfluoroalkyl substances (PFASs), are ubiquitously distributed in the environment, as well as in wildlife and humans. In the present study, we have employed an ex vivo organ culture technique, based on the floating agarose method, of Atlantic cod ovarian tissue to investigate the effec...
Article
Full-text available
Motivation: Mass spectrometry (MS) based quantitative proteomics experiments typically assay a subset of up to 60% of the ∼20,000 human protein coding genes. Computational methods for imputing the missing values using RNA expression data usually allow only for imputations of proteins measured in at least some of the samples. In silico methods for...
Article
Full-text available
Background: Current technology allows rapid assessment of DNA sequences and methylation levels at a single-site resolution for hundreds of thousands of sites in the human genome, in thousands of individuals simultaneously. This has led to an increase in epigenome-wide association studies (EWAS) of complex traits, particularly those that are poorly...
Article
Lung cancer in East Asia is characterized by a high percentage of never-smokers, early onset and predominant EGFR mutations. To illuminate the molecular phenotype of this demographically distinct disease, we performed a deep comprehensive proteogenomic study on a prospectively collected cohort in Taiwan, representing early stage, predominantly fema...
Article
Full-text available
In the present study, a previously capped waste disposal site at Kollevåg (Norway) was selected to study the effects of contaminant leakage on biomarkers associated with Atlantic cod (Gadus morhua) reproductive endocrinology and development. Immature cod were caged for 6 weeks at 3 locations, selected to achieve a spatial gradient of contamination,...
Preprint
Full-text available
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 bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotype...
Article
Increased exploitation of resources in sensitive marine ecosystems emphasizes the importance of knowledge regarding ecological impacts. However, current bio-monitoring practices are limited in terms of target-organisms and temporal resolution. Hence, developing new technologies is vital for enhanced ecosystem understanding. In this study, we have a...
Article
Full-text available
The etiology of Parkinson's disease is largely unknown. Genome-wide transcriptomic studies in bulk brain tissue have identified several molecular signatures associated with the disease. While these studies have the potential to shed light into the pathogenesis of Parkinson's disease, they are also limited by two major confounders: RNA post-mortem d...
Article
Full-text available
Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition,...
Article
Full-text available
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 data has to be processed through a number of steps resulting in a quantification of expression of each gene/transcript in each of...
Article
Full-text available
Motivation: Technological advances in metatranscriptomics have enabled a deeper understanding of the structure and function of microbial communities. "Total RNA" metatranscriptomics, sequencing of total reverse transcribed RNA, provides a unique opportunity to investigate both the structure and function of active microbial communities from all thr...
Article
Full-text available
Abstract Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue (https://bio.tools) of tools and databases that can be used in these workflows. bio.tools not onl...
Chapter
Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its simplicity and interpretability. A characteristic of methods for DEA is that they treat genes individually, disregarding the correla...
Preprint
Full-text available
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 data has to be processed through a number of steps resulting in a quantification of expression of each gene / transcript in each of...
Conference Paper
Ensemble feature selection has drawn more and more attention in recent years. There are mainly two strategies for ensemble feature selection, namely data perturbation and function perturbation. Data perturbation performs feature selection on data subsets sampled from the original dataset and then selects the features consistently ranked highly acro...
Preprint
Full-text available
Background The etiology of Parkinson’s disease (PD) is largely unknown. Genome-wide transcriptomic studies in bulk brain tissue have identified several molecular signatures associated with the disease. While these studies have the potential to shed light into the pathogenesis of PD, they are also limited by two major confounders: RNA post mortem de...
Article
Full-text available
Permafrost contains one of the least known soil microbiomes, where microbial populations reside in an ice-locked environment. Here, 56 prokaryotic metagenome-assembled genome (MAG) sequences from 13 phyla are reported. These MAGs will provide information on metabolic pathways that could mediate biogeochemical cycles in Svalbard permafrost.
Preprint
Full-text available
Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its simplicity and interpretability. A characteristic of methods for DEA is that they treat genes individually, disregarding the correla...
Preprint
Full-text available
The genetic code is tightly linked to epigenetic instructions as to what genes to express, and when and where to express them. The most studied epigenetic mark is DNA methylation at CpG dinucleotides. Today's technology enables a rapid assessment of DNA sequence and methylation levels at a single-site resolution for hundreds of thousands of sites i...
Preprint
Full-text available
Ensemble learning that can be used to combine the predictions from multiple learners has been widely applied in pattern recognition, and has been reported to be more robust and accurate than the individual learners. This ensemble logic has recently also been more applied in feature selection. There are basically two strategies for ensemble feature...
Article
Full-text available
Background Towards discovering robust cancer biomarkers, it is imperative to unravel the cellular heterogeneity of patient samples and comprehend the interactions between cancer cells and the various cell types in the tumor microenvironment. The first generation of ‘partial’ computational deconvolution methods required prior information either on t...
Article
Full-text available
We have identified nine highly connected and differentially expressed gene subnetworks between aggressive primary tumors and metastatic lesions in endometrial carcinomas. We implemented a novel pipeline combining gene set and network approaches, which here allows integration of protein-protein interactions and gene expression data. The resulting su...
Data
Correlation of normalized enrichment scores (NES) between gene and sample-based permutation methods of GSEA. Plots show correlation of NES between gene and sample-based permutation of GSEA of the identified subnetworks. The correlation plots of four types of subnetworks derived according to their initial gene-gene correlations source and enrichment...
Data
TOM plots. TOM plots of primary tumor (A) and metastatic (B) correlations, respectively. The plots are after integration of the expression correlations and PPI. (PDF)
Data
Dataset for subnetworks identification (Dataset 1) and for biological signal investigation (Dataset 2). The table shows a number of samples used in the Dataset 1, a dataset for subnetwork identification, and Dataset 2, an expanded panel for biological signal investigation of the detected subnetworks. The progression stages from low to high disease...
Data
Scale free topology plot. Plots between power parameters of soft threshold vs scale free topology fit and mean connectivity, respectively. The plots of primary tumor (A) and metastasis (B) correlations integrated with PPI are shown, respectively. For each correlation type, plots between power parameters and scale free topology fit (left), and plots...
Data
A ranked list of differentially expressed genes. Table shows a ranked gene list from ordinary differentially expressed genes (SAM, FDR < 0.01) and the genes overlapped with genes in our detected subnetworks. (XLS)
Data
Disease specific survival in TCGA cohort. Disease specific survival analyzes according to gene signature scores of the (A) PTME3 (Quantile values of Q1-3 vs Q4 for the patient groups of low and high signature scores, respectively) and (B) MEPT3 (Q1 vs Q2-4 for the groups of low and high signature scores, respectively) subnetworks in TCGA endometria...
Data
Scale free topology property of the integrated subnetworks. (DOC)
Article
Full-text available
There is increasing interest in finding new, more efficient methods for routine monitoring of anthropogenic effects on benthic biodiversity and ecosystems. A range of molecular methods have been developed for assessing biodiversity the last decades. Particularly interesting are microarrays targeting phylogenetic marker genes, such as the small subu...
Article
Full-text available
The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confiden...
Poster
Full-text available
Project website: http://bioxsd.org Source code: https://github.com/bioxsd/bioxsd Licence: Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0). Additional Code of Conduct for development and derived work is stated in BioXSD-1.1.xsd. Contact: developers@bioxsd.org, @BioXSD BioXSD has been developed as a tree-structured d...
Article
Polycyclic aromatic hydrocarbons such as benzo[a]pyrene (BaP) that activate the aryl hydrocarbon receptor (Ahr) pathway, and endocrine disruptors acting through the estrogen receptor pathway are among environmental pollutants of major concern. In this work, we exposed Atlantic cod (Gadus morhua) precision-cut liver slices (PCLS) to BaP (10 nM and 1...
Article
Full-text available
Platelet activation contributes to normal haemostasis but also to pathologic conditions like stroke and cardiac infarction. Signalling by cGMP and cAMP inhibit platelet activation and are therefore attractive targets for thrombosis prevention. However, extensive cross-talk between the cGMP and cAMP signalling pathways in multiple tissues complicate...
Article
Full-text available
We here examined whether Nestin, by protein and mRNA levels, could be a predictor of BRCA1 related breast cancer, a basal-like phenotype, and aggressive tumours. Immunohistochemical staining of Nestin was done in independent breast cancer hospital cohorts (Series I-V, total 1257 cases). Also, TCGA proteomic data (n = 103), mRNA microarray data from...
Poster
Full-text available
Project website: http://bioxsd.org Source code: https://github.com/bioxsd/bioxsd Licence: Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0). Additional Code of Conduct for development and derived work is stated in BioXSD-1.1.xsd. Contact: developers@bioxsd.org, @BioXSD BioXSD has been developed as a tree-structured...
Article
Full-text available
The aim was to evaluate susceptibility of oropharyngeal contamination with various bronchoscopic sampling techniques. 67 patients with obstructive lung disease and 58 control subjects underwent bronchoscopy with small-volume lavage (SVL) through the working channel, protected bronchoalveolar lavage (PBAL) and bilateral protected specimen brush (PSB...
Article
Full-text available
Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biod...
Data
Taxonomic classification and category (protists, metazoa or unknown) for representative OTU sequences. (TSV)
Data
Rarefaction analysis of protist OTU richness for pooled samples (grey lines) and individual replicats (black lines). Mean and standard error of expected richness was calculated based on repeated random sub-samples at each read interval from replicates of the samples Fine Sand (A; n = 5), Coarse Sand (B; n = 7) and Clay (C, n = 5), after taxonomic f...
Data
Rarefaction analysis of metazoan OTU richness for pooled samples (grey lines) and individual replicates (black lines). Mean and standard error of expected richness was calculated based on repeated random sub-samples at each read interval from replicates of the samples Fine Sand (A; n = 5), Coarse Sand (B; n = 7) and Clay (C, n = 5), after taxonomic...
Data
Rarefaction analysis of pooled samples illustrating the effect of retaining singletons. Rarefaction curves using solid lines represent the studied dataset where singletons were retained (and correspond to Figs 1 and 2), whereas dashed lines result from rarefaction curves after removing singletons. (TIF)
Data
Overview of sequence depth, richness and taxonomic composition (protists and metazoa) for all replicates and pooled samples. (XLSX)
Article
Full-text available
Background Little is known about the role of glial host cells in brain tumours. However, supporting stromal cells have been shown to foster tumour growth in other cancers. Methods We isolated stromal cells from patient-derived glioblastoma (GBM) xenografts established in GFP-NOD/scid mice. With simultaneous removal of CD11b+ immune and CD31+ endoth...