A5088456124- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Cancer Genomics and Diagnostics
- Sarcoma Diagnosis and Treatment
- Cancer-related molecular mechanisms research
- Preterm Birth and Chorioamnionitis
- Neuroinflammation and Neurodegeneration Mechanisms
- Molecular Biology Techniques and Applications
- Bone Metabolism and Diseases
- Epigenetics and DNA Methylation
- Neonatal Respiratory Health Research
- Immune Response and Inflammation
- Bone health and osteoporosis research
- Algorithms and Data Compression
- Neonatal and fetal brain pathology
- Neonatal and Maternal Infections
- Immune Cell Function and Interaction
- Bacterial Infections and Vaccines
- Scientific Computing and Data Management
- Genomic variations and chromosomal abnormalities
- Biomedical Ethics and Regulation
- Congenital Anomalies and Fetal Surgery
- Genetic Associations and Epidemiology
- Retinopathy of Prematurity Studies
University of Gothenburg
2020-2024
University of Oslo
2010-2018
Oslo University Hospital
2010-2015
University of Bergen
2013
Norwegian Computing Center
2013
Norwegian University of Science and Technology
2013
Children's Hospital of Philadelphia
2007-2008
Wilmington University
2005
Abstract High‐grade osteosarcoma is a tumor with complex genomic profile, occurring primarily in adolescents second peak at middle age. The extensive alterations obscure the identification of genes driving tumorigenesis during development. To identify such driver genes, we integrated DNA copy number profiles (Affymetrix SNP 6.0) 32 diagnostic biopsies 84 expression (Illumina Human‐6 v2.0) high‐grade as compared its putative progenitor cells, i.e., mesenchymal stem cells ( n = 12) or...
Background Osteosarcomas are the most common non-haematological primary malignant tumours of bone, and all conventional osteosarcomas high-grade showing complex genomic aberrations. We have integrated genome-wide genetic epigenetic profiles from EuroBoNeT panel 19 human osteosarcoma cell lines based on microarray technologies. Principal Findings The showed patterns DNA copy number changes, where gains were significantly associated with gene-rich regions losses gene-poor regions. By...
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack established methodology with required flexibility and power. We propose first principled approach statistical analysis sequence-level information. provide growing collection generic biological investigations that query pairwise relations between tracks, represented as mathematical objects, along genome. Genomic HyperBrowser implements is available at http://hyperbrowser.uio.no .
The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, are faced with challenge how best analyze interpret their genome-scale datasets. A powerful way representing data is feature-specific coordinates relative reference genome assemblies, i.e. tracks. Genomic HyperBrowser...
Abstract Sensitivity to environmental stressors largely depend on the genetic complement of organism. Recent sequencing and assembly teleost fish genomes enable us trace evolution defense genes in largest most diverse group vertebrates. Through genomic searches in-depth analysis gene loci 76 genomes, we show here that xenosensor pregnane X receptor (Pxr, Nr1i2) is absent more than half these species. Notably, out 27 genome assemblies belong Gadiformes order, pxr was only retained Merluccidae...
Staphylococcus epidermidis (S. epidermidis) is the most common nosocomial pathogen in preterm infants and associated with increased risk of cognitive delay, however, underlying mechanisms are unknown. We employed morphological, transcriptomic physiological methods to extensively characterize microglia immature hippocampus following S. infection. 3D morphological analysis revealed activation after epidermidis. Differential expression combined network identified NOD-receptor signaling...
Preterm infants exposed to chorioamnionitis and with a fetal inflammatory response are at risk for severe neonatal morbidities adverse outcome. Alarmins S100A8, S100A9, S100A12 expressed by myeloid cells have been associated activation monocyte modulation. Aim: To study S100A alarmin expression in cord blood monocytes from term healthy preterm relate results clinical findings, biomarkers protein levels, as well pathways identified differentially regulated genes. Cord CD14+ were isolated...
Abstract Background Cytokines and growth factors (GF) have been implicated in the development of retinopathy prematurity (ROP) bronchopulmonary dysplasia (BPD). We hypothesize that even small coordinated changes inflammatory proteins or GFs may reveal underlying regulating mechanisms do not induce obvious concentration individual proteins. therefore applied correlation network analysis serum to determine early characteristics these conditions. Methods Concentrations 17 cytokines five were...
Several high-density oligonucleotide microarray platforms are available for genome-wide single nucleotide polymorphism (SNP) detection and microarray-based comparative genomic hybridisation (array CGH), which may be used to detect copy number aberrations in human tumours. As part of the EuroBoNeT network excellence research on bone tumours (eurobonet.eu), we have evaluated four different commercial high-resolution order identify most appropriate technology mapping DNA such tumours.DNA from...
Abstract Background Transcription factors in disease-relevant pathways represent potential drug targets, by impacting a distinct set of that may be modulated through gene regulation. The influence transcription is typically studied on per disease basis, and no current resources provide global overview the relations between disease. Furthermore, existing pipelines for related large-scale analysis are tailored particular sources input data, there need generic methodology integrating...
Clustering is a popular technique for explorative analysis of data, as it can reveal subgroupings and similarities between data in an unsupervised manner. While clustering routinely applied to gene expression there lack appropriate general methodology sequence-level genomic epigenomic e.g. ChIP-based data. We here introduce sets coordinates relative genome assembly, i.e. tracks. By defining feature extraction approaches similarity measures, we allow biologically meaningful be performed...
We used the Genetic Analysis Workshop 15 Problem 1 data set to search for expression phenotype quantitative trait loci in a highly selected group of genes with supposedly correlated role development enteric nervous system. Our strategy was reduce level multiple testing by analyzing at genome-wide limited number considered be most promising system candidates on basis mouse data, and then extend analysis larger traits only small candidate linked regions. Such study design allowed us identify...
Abstract High-grade osteosarcoma is a tumor with complex genomic profile, occurring primarily in adolescents. The extensive alterations obscure the identification of genes driving tumorigenesis progenitor cells. In order to identify such driver genes, we integrated DNA copy number profiles (Affymetrix SNP 6.0) 32 diagnostic biopsies 84 expression (Illumina Human-6 v2.0) as compared its putative cells, i.e. mesenchymal stem cells (n=12) or osteoblasts (n=3). addition, performed paired...
Hematopoietic stem and progenitor cells (HSPC) from umbilical cord blood (UCB) are used for transplantation to treat disorders. Methods estimate the HSPC count in blood, thereby identify high-value units, time-consuming costly. Recent studies indicate that UCB plasma protein composition relates count. We compared proteome of with high vs low cell (>115 × 106 < 51 CD34+ l−1) by using a combination global untargeted MS quantitative proteomics targeted proximity extension assay (PEA)...
Abstract Staphylococcus epidermidis ( S. ) is the most common nosocomial pathogen in preterm infants and associated with increased risk of cognitive delay, however, underlying mechanisms are unknown. We employed morphological, transcriptomic physiological methods to extensively characterize microglia immature hippocampus following infection. 3D morphological analysis revealed activation after . Differential expression combined network identified NOD-receptor signalling trans-endothelial...