A5012964587- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Protein Structure and Dynamics
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Community Ecology and Physiology
- Genomics and Chromatin Dynamics
- Enzyme Structure and Function
- Prostate Cancer Treatment and Research
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- Pancreatic function and diabetes
- Scientific Computing and Data Management
- Aquaculture disease management and microbiota
- Machine Learning in Bioinformatics
- Identification and Quantification in Food
- Environmental DNA in Biodiversity Studies
- Diabetes Management and Research
- Genomic variations and chromosomal abnormalities
- Protein Interaction Studies and Fluorescence Analysis
- Aquaculture Nutrition and Growth
- RNA regulation and disease
- Enzyme Production and Characterization
- Single-cell and spatial transcriptomics
- Algorithms and Data Compression
University of Bergen
2016-2025
Haukeland University Hospital
2006-2020
Uni Research (Norway)
2006-2017
Novo Nordisk (Denmark)
1997-2015
European Bioinformatics Institute
1998-2013
University of Manchester
2010-2013
Norwegian Institute of Marine Research
2010-2013
Novo Nordisk (United Kingdom)
2004-2012
Technical University of Denmark
2010
Université Claude Bernard Lyon 1
2010
Abstract The whole-genome duplication 80 million years ago of the common ancestor salmonids (salmonid-specific fourth vertebrate duplication, Ss4R) provides unique opportunities to learn about evolutionary fate a duplicated genome in 70 extant lineages. Here we present high-quality assembly for Atlantic salmon ( Salmo salar ), and show that large genomic reorganizations, coinciding with bursts transposon-mediated repeat expansions, were crucial post-Ss4R rediploidization process. Comparisons...
Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster an unusual immune architecture compared to other sequenced vertebrates. The assembly was obtained exclusively by 454 sequencing shotgun paired-end libraries, automated annotation identified 22,154 genes. major histocompatibility (MHC)...
In recent years, analogs of human insulin have been engineered with the aim improving therapy for people diabetes. To ensure that safety profile hormone is not compromised by molecular modifications, toxico-pharmacological properties should be carefully monitored. this study, we compared and IGF-I receptor binding metabolic mitogenic potencies aspart (B28Asp insulin), lispro (B28Lys,B29Pro glargine (A21Gly,B31Arg,B32Arg detemir (NN304) [B29Lys(epsilon-tetradecanoyl), desB30 insulin],...
High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal prokaryotic or eukaryotic groups of interest. Full primer universality difficult impossible to achieve and using different sets make comparisons problematic. The aim this study was design optimize could be as a standard future Using alignment all sequences from publicly available SILVA database, we generated full...
Basal insulins with improved kinetic properties can potentially be produced using acylation by fatty acids that enable soluble, high-molecular weight complexes to form post-injection. A series of insulins, acylated at B29 via glutamic acid spacers, were examined deduce the structural requirements.Self-association, molecular masses and hexameric conformations studied size exclusion chromatography monitored UV or multi-angle light scattering dynamic scattering, circular dichroism spectroscopy...
Abstract Objective To identify gene expression signatures in minor salivary glands (MSGs) from patients with primary Sjögren's syndrome (SS). Methods A 16K complementary DNA microarray was used to generate profiles MSGs obtained 10 SS and control subjects. The data were analyzed by 2 different strategies, one strict analysis subanalysis that allowed for inclusion of genes no signal more than 3 samples each group. results validated quantitative reverse transcriptase–polymerase chain reaction...
Although 75% of endometrial cancers are treated at an early stage, 15% to 20% these recur. We performed integrated analysis genome-wide expression and copy-number data for primary carcinomas with extensive clinical histopathological detect features predictive recurrent disease. Unsupervised the distinguished 2 major clusters strikingly different phenotypes, including significant differences in disease-free survival. To identify possible mechanisms differences, we a global genomic survey...
The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in salmon acts as reference for other salmonids.
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 this demographically distinct disease, we performed deep comprehensive proteogenomic study on prospectively collected cohort Taiwan, representing stage, predominantly female, non-smoking lung adenocarcinoma. Integrated genomic, proteomic, phosphoproteomic analysis delineated attributes hallmarks tumor progression. Mutational...
Abstract Motivation: Advancing the search, publication and integration of bioinformatics tools resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM an operations (tool or workflow functions), types data identifiers, application domains formats. supports semantic annotation diverse entities as Web services, databases, programmatic libraries, standalone tools, interactive applications,...
Sequencing of taxonomic or phylogenetic markers is becoming a fast and efficient method for studying environmental microbial communities. This has resulted in steadily growing collection marker sequences, most notably the small-subunit (SSU) ribosomal RNA gene, an increased understanding phylogeny, diversity community composition patterns. However, to utilize these large datasets together with new sequencing technologies, reliable flexible system classification critical. We developed CREST...
InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as means of rationalising the complementary efforts PROSITE, PRINTS, Pfam ProDom database projects.Merged annotations from PROSITE form core. Each combined entry includes descriptions literature references, links are made back to relevant parent database(s), allowing users see at glance whether particular family or domain has associated patterns, profiles, fingerprints,...
We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences regular expression-type patterns with goal identifying potential regulatory elements. To achieve this goal, we have developed new sequence pattern discovery algorithm that searches exhaustively priori unknown are over-represented given set sequences. applied two cases, (1) complete >6000 sequences taken putative genes and (2) similar expression profiles. In first case, looked occur more...
Abstract Summary: J-Express is a Java application that allows the user to analyze gene expression (microarray) data in flexible way giving access multidimensional scaling, clustering, and visualization methods an integrated manner. Specifically, includes implementations of hierarchical k-means, principal component analysis, self-organizing maps. At present, it does not include for comparing two or more experiments differentially expressed genes. The completely portable requires only runtime...
Albumin is a multifunctional transport protein that binds wide variety of endogenous substances and drugs. Insulins with affinity for albumin were engineered by acylation the epsilon-amino group LysB29 saturated fatty acids containing 10-16 carbon atoms. The association constants binding acid acylated insulins to human are in order 10(4)-10(5) M-1. apparently involves both non-polar ionic interactions protein. bind at long-chain sites, but lower than free depends relatively small degree on...
Abstract We present a new method for the identification of conserved patterns in set unaligned related protein sequences. It is able to discover quite general form, allowing both ambiguous positions and variable length wildcard regions. allows user define class (e.g., degree ambiguity allowed number gaps), then guaranteed find this scoring highest according significance measure defined. Identified may be refined using one two algorithms. (nonstatistical) flexible patterns. The shown recover...
Methods for extracting useful information from the datasets produced by microarray experiments are at present of much interest. Here we new methods finding gene sets that well suited distinguishing experiment classes, such as healthy versus diseased tissues. Our based on evaluating genes in pairs and how a pair combination distinguishes two classes. We tested ability our pair-based to select generalize differences between classes compared performance relative standard methods. To assess...
In this work, highly infiltrative brain tumors with a stem-like phenotype were established by xenotransplantation of human in immunodeficient nude rats. These coopted the host vasculature and presented as an aggressive disease without signs angiogenesis. The malignant cells expressed neural stem cell markers, showed migratory behavior similar to normal cells, gave rise vivo after regrafting. Serial passages animals gradually transformed into angiogenesis-dependent phenotype. This process was...
This article investigates aspects of pairwise and multiple structure comparison, the problem automatically discover common patterns in a set structures. Descriptions representation structures are described, as well scoring algorithms for comparison discovery. A framework nomenclature is developed classifying different methods, many these reviewed placed into this framework.
Abstract We have characterized several stages of normal human B cell development in adult bone marrow by gene expression profiling hemopoietic stem cells, early (E-B), pro-B, pre-B, and immature using RNA amplification Lymphochip cDNA microarrays (n = 6). Hierarchical clustering 758 differentially expressed genes clearly separated the five populations. used sets to investigate functional assignment genes. Genes involved VDJ recombination as well lineage-associated transcription factors (TCF3...
Abstract Motivation: The commercial launch of 454 pyrosequencing in 2005 was a milestone genome sequencing terms performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 base pairs are thus approaching obtained from traditional Sanger sequencing. Study design projects would benefit being able simulate experiments. Results: We explore raw data investigate its characteristics derive empirical distributions for flow values generated by...
Background Increasing evidence implicates the critical roles of epigenetic regulation in cancer. Very recent reports indicate that global gene silencing cancer is associated with specific modifications. However, relationship between switches and more dynamic patterns activation repression has remained largely unknown. Methodology/Principal Findings Genome-wide profiling trimethylation histone H3 lysine 4 (H3K4me3) 27 (H3K27me3) was performed using chromatin immunoprecipitation coupled whole...