A5084054353- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Computational Drug Discovery Methods
- Gene Regulatory Network Analysis
- Genomics and Chromatin Dynamics
- Semantic Web and Ontologies
- Infant Nutrition and Health
- Helicobacter pylori-related gastroenterology studies
- Glycosylation and Glycoproteins Research
- Pancreatic function and diabetes
- Neuroendocrine Tumor Research Advances
- Machine Learning in Bioinformatics
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Rough Sets and Fuzzy Logic
- Advanced Biosensing Techniques and Applications
- Digestive system and related health
- NF-κB Signaling Pathways
- Escherichia coli research studies
- Immune Response and Inflammation
- Cell Image Analysis Techniques
- RNA and protein synthesis mechanisms
- Neuropeptides and Animal Physiology
- Cancer Treatment and Pharmacology
Norwegian University of Science and Technology
2014-2024
Uppsala University
2003
Karolinska University Hospital
1995
Miles College
1994
Cancer Registry of Norway
1994
St Olav's University Hospital
1993
University of Oslo
1986-1987
National Institute of Occupational Health
1985
Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding functions of genes and gene products. Here, we report advances consortium over past two years. new GO-CAM annotation framework was notably improved, formalized model with a computational schema to check validate rapidly increasing repository 2838 GO-CAMs. In addition, describe impacts several collaborations refine GO 10% increase in number annotations,...
Gene regulation plays a critical role in the cellular processes that underlie human health and disease. The regulatory relationship between transcription factors (TFs), key regulators of gene expression, their target genes, so called TF regulons, can be coupled with computational algorithms to estimate activity TFs. However, interpret these findings accurately, regulons high reliability coverage are needed. In this study, we present evaluate collection created using CollecTRI meta-resource...
Abstract Motivation: The Gene Ontology (GO) is a widely used terminology for gene product characterization in, example, interpretation of biology underlying microarray experiments. current GO defines term relationships within each the independent subontologies: molecular function, biological process and cellular component. However, it evident that there also exist between terms different subontologies. Our aim was to connect three subontologies enable cover more knowledge, consistent use...
Discovery of efficient anti-cancer drug combinations is a major challenge, since experimental testing all possible clearly impossible. Recent efforts to computationally predict combination responses retain this search space, as model definitions typically rely on extensive perturbation data. We developed dynamical representing cell fate decision network in the AGS gastric cancer line, relying background knowledge extracted from literature and databases. defined set logical equations...
Inhibitory activity of enterotoxin from Escherichia coli and Vibrio cholerae was associated with the ganglioside fraction human milk. Both milk fat skim contained gangliosides that inhibited toxins. The most purified three glycolipid components, which two migrated close to GM1 on thin-layer chromatography plates. A component a slightly different mobility appeared be inhibitory activity. Milk fraction, derived 2 ml milk, 1 4 micrograms lipid-bound sialic acid completely 0.1 cholera toxin in...
Abstract Summary: Gene regulatory network assembly and analysis requires high-quality knowledge sources that cover functional aspects of the various components gene machinery. A multiplicity resources exists with information about mammalian transcription factors (TFs); yet, only few these provide sufficiently accurate classifications roles individual TFs, or standardized evidence would justify on which are based. We compiled list all putative TFs from nine different resources, ignored such...
ABSTRACT Gene regulation plays a critical role in the cellular processes that underlie human health and disease. The regulatory relationship between transcription factors (TFs), key regulators of gene expression, their target genes, so called TF regulons, can be coupled with computational algorithms to estimate activity TFs. However, interpret these findings accurately, regulons high reliability coverage are needed. In this study, we present evaluate collection created using CollecTRI...
The aim of the present study was to generate hypotheses on involvement uncharacterized genes in biological processes. To this end, supervised learning used analyze microarray-derived time-series gene expression data. Our method objectively evaluated known using cross-validation and provided high-precision Gene Ontology process classifications for 211 213 data set used. In addition, new roles were hypothesized genes. uses knowledge expressed by generates a rule model associating with minimal...
Microarray technology enables large-scale inference of the participation genes in biological process from similar expression profiles. Our aim is to induce classificatory models data and knowledge that can automatically associate with novel hypotheses process.We report a systematic supervised learning approach predicting time series gene knowledge. Biological expressed using ontology this associated discriminatory expression-based features form minimal decision rules. The resulting rule...
Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands genes. This created a need tools facilitating interpretation biological data in "batch" mode. However, such often leave the investigator with large volumes apparently unorganized information. To meet this challenge, gene-set, or cluster testing become popular analytical tool. Many gene-set and software packages are now...
Transcription factors control which information in a genome becomes transcribed to produce RNAs that function the biological systems of cells and organisms. Reliable comprehensive about transcription is invaluable for large-scale network-based studies. However, existing factor knowledge bases are still lacking well-documented functional information.
The gastrointestinal peptide hormones cholecystokinin and gastrin exert their biological functions via receptors CCK1R CCK2R respectively. Gastrin, a central regulator of gastric acid secretion, is involved in growth differentiation colonic mucosa, there evidence that it pro-carcinogenic. Cholecystokinin implicated digestion, appetite control body weight regulation, may play role several digestive disorders.We performed detailed analysis the literature reporting experimental on signaling...
Abstract TNF signaling mechanisms involved in activation of transcription factor NF-κB were studied the human keratinocyte cell line HaCaT. We show that TNF-induced was inhibited by well-known selective inhibitors cytosolic phospholipase A2 (cPLA2): trifluoromethyl ketone analogue arachidonic acid (AACOCF3) and methyl arachidonyl fluorophosphate. The eicosapentaenoic (EPACOCF3) also suppressed vitro cPLA2 enzyme activity with a similar potency as AACOCF3. (AACOCH3) eicosapentanoyl...
The functional role of human tumor necrosis factor receptor (TNFR) p75 was studied by the use TNFR p75-specific agonistic antibodies. Human SW480T adenocarcinoma cells, stably transfected with a reporter construct containing beta-galactosidase under control cytomegalovirus immediate early enhancer, were stimulated anti-TNFR polyclonal antiserum or monoclonal antibodies followed measurement activity and analysis electrophoretic mobility shift assays. It found that cross-linking led to strong...
While there is a high interest in drug combinations cancer therapy, openly accessible datasets for combination responses are sparse. Here we present dataset comprising 171 pairwise of 19 individual drugs targeting signal transduction mechanisms across eight cell lines, where the effect each and reported as viability assessed by metabolic activity. Drugs chosen their capacity to specifically interfere with well-known mechanisms. Signalling processes targeted include PI3K/AKT, NFkB, JAK/STAT,...
Combining multiple layers of information underlying biological complexity into a structured framework represent challenge in systems biology. A key task is the formalization such models describing how entities interact to mediate response external and internal signals. Several databases with signalling information, focus on capturing, organizing displaying interactions by representing them as binary, causal relationships between entities. The curation efforts that build these individual...
Abstract Drug combinations have been proposed to combat drug resistance, but putative treatments are challenged by low bench-to-bed translational efficiency. To explore the effect of cell culture format and readout methods on identification synergistic in vitro, we studied response 21 clinically relevant standard planar (2D) layouts physiologically more spheroid (3D) cultures HCT-116, HT-29 SW-620 cells. By assessing changes viability, confluency size, were able identify readout-...
Transcription plays a central role in defining the identity and functionalities of cells, as well their responses to changes cellular environment. The Gene Ontology (GO) provides rigorously defined set concepts that describe functions gene products. A GO annotation is statement about function particular product, represented an association between product biological concept term defines. Critically, each based on traceable scientific evidence. Here, we different terms are associated with...
Background Sequence similarity to characterized proteins provides testable functional hypotheses for less than 50% of the identified by genome sequencing projects. With structural genomics it is believed that similarities may give many remaining proteins. Methodology/Principal Findings We provide a systematic analysis structure-function relationship in using novel concept local descriptors protein structure. A descriptor small substructure which includes both short- and long-range...