Motivation Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. Results To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. Availability and implementation STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.

/pdf/star-ultrafast-universal-rna-seq-aligner-r1vlt61g3c.pdf

STAR: ultrafast universal RNA-seq aligner

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

/pdf/an-integrated-encyclopedia-of-dna-elements-in-the-human-52ukbi8ats.pdf

An integrated encyclopedia of DNA elements in the human genome

Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.

Tissue-based map of the human proteome

An integrated encyclopedia of DNA elements in the human genome.

The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.

NCBI GEO: archive for functional genomics data sets—update

Numerical Integration and Interpolation in Marine Pollutant Transport Modelling

Vertical mixing and horizontal drift of oil spills: simulations with the open source oil spill model OpenOil

Formation water in oil and gas fields contain elevated concentrations of several radionuclides compared with seawater. It is therefore of interest to track the fate of these radionuclides when they are released into the ocean along with the produced water stream. In this work we have simulated the fate of radionuclides in produced water discharge from all relevant installations on the Norwegian continental shelf for periods up to 20 years. We investigated separately the fate of the radionuclide Ra-226 in solid and in dissolved phase. Our findings show that when Ra-226 spreads as a solid it has the highest potential for reaching the sediments in the areas around the Oseberg and Ekofisk fields. The estimated contribution above background at these sites over a 30 year period was estimated to be from 2 Bq/kg to 10 Bq/kg, depending on the degree of burial, bioturbation and sediment mixing. Our simulations of dissolved Ra-226 showed transport along the Norwegian coast up past Svalbard. We found that the maximal contribution of dissolved Ra-226 to radioactivity in sediments over a 30 year period lies in the range 0.6 2 Bq/kg at several locations along the Norwegian coast.

Jørgen Skancke

Papers

Numerical Integration and Interpolation in Marine Pollutant Transport Modelling

Vertical mixing and horizontal drift of oil spills: simulations with the open source oil spill model OpenOil

Long-term fate of Ra-226 originating from offshore produced water discharges

Attachment of APAM to mineral particles in seawater

Analyser av flammepunkt og helsefarlige forbindelser for oljeemulsjoner i kystnær beredskap