Affiliation: University of Bergen
Location: Bergen, Norway
- The Taverna Interaction Service: enabling manual interaction in workflowsAnders Lanzen
Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, 5008 Bergen, Norway
Bioinformatics 24:1118-20. 2008..The Taverna Interaction Service extends the functionality of Taverna by defining human interaction within a workflow and acting as a mediation layer between the automated workflow engine and one or more users...
- New insight into stratification of anaerobic methanotrophs in cold seep sedimentsIrene Roalkvam
Department of Biology, Centre for Geobiology, University of Bergen, Norway
FEMS Microbiol Ecol 78:233-43. 2011..In intermediate horizons, typical microbial groups associated with methane seeps were recovered. The data are discussed with respect to co-occurring microbial assemblages and interspecies interactions...
- Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNAAnders Lanzen
Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
FEMS Microbiol Ecol 77:577-89. 2011..Further, predicted diversity from RNA samples was consistently lower than that from DNA. In summary, this study illustrates how different methods can provide complementary ecological insights...
- Characterisation of the coccolithovirus inteinMichael J Allen
Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
Mar Genomics 4:1-7. 2011..The biochemical mechanism of its protein splicing activity is hypothesised, and the prevalence of the intein among natural coccolithovirus isolates is tested...
- Removing noise from pyrosequenced ampliconsChristopher Quince
Department of Civil Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LT, UK
BMC Bioinformatics 12:38. 2011..We use data sets where samples of known diversity have been amplified and sequenced to quantify the effect of each of the sources of error on OTU inflation and to validate these algorithms...
- Effects of short-term starvation on ghrelin, GH-IGF system, and IGF-binding proteins in Atlantic salmonE M Hevrøy
National Institute of Nutrition and Seafood Research NIFES, Nordnes, Bergen, Norway
Fish Physiol Biochem 37:217-32. 2011..In conclusion, we have shown that circulating ghrelin and ghrelin-1 mRNA is related to changes in energy metabolism in Atlantic salmon...
- Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsimSusanne Balzer
Institute of Marine Research, University of Bergen, Bergen, Norway
Bioinformatics 26:i420-5. 2010..Study design of sequencing projects would benefit from being able to simulate experiments...
- Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic contextRita Bartossek
Department of Biology, Centre for Geobiology, University of Bergen, PO Box 7803, 5020 Bergen, Norway
Environ Microbiol 12:1075-88. 2010..Transcription of the potential archaeal nirK in soil was demonstrated at different water contents, but no significant increase in transcript copy number was observed with increased denitrifying activity...
- Identification of immune related genes in Atlantic halibut (Hippoglossus hippoglossus L.) following in vivo antigenic and in vitro mitogenic stimulationSonal Patel
Institute of Marine Research IMR, Bergen, Norway
Fish Shellfish Immunol 27:729-38. 2009....
- Accurate determination of microbial diversity from 454 pyrosequencing dataChristopher Quince
Department of Civil Engineering, Rankine Building, University of Glasgow, Glasgow, UK
Nat Methods 6:639-41. 2009..We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated...
- Gene expression profiling in Atlantic cod (Gadus morhua L.) from two contaminated sites using a custom-made cDNA microarrayKai K Lie
National Institute of Nutrition and Seafood Research, Nordnesboder 2, N 5005 Bergen, Norway
Environ Toxicol Chem 28:1711-21. 2009..As expected, farmed fish displayed less variation in gene expression compared to the wild fish. Pearson correlation divided the farmed cod and natural cod into two principal clusters...
- Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptomeTim Urich
Centre of Geobiology, Department of Biology, University of Bergen, Bergen, Norway
PLoS ONE 3:e2527. 2008..Experimental approaches studying these systems usually focus on either the soil community's taxonomic structure or its functional characteristics. Many methods target DNA as marker molecule and use PCR for amplification...
- The genome sequence of Atlantic cod reveals a unique immune systemBastiaan Star
Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066, Blindern, N 0316 Oslo, Norway
Nature 477:207-10. 2011..These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates...