Author
Jørgen Skancke
Other affiliations: Norwegian University of Science and Technology
Bio: Jørgen Skancke is an academic researcher from SINTEF. The author has contributed to research in topics: Gene & Human genome. The author has an hindex of 7, co-authored 21 publications receiving 6756 citations. Previous affiliations of Jørgen Skancke include Norwegian University of Science and Technology.
Papers
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Cold Spring Harbor Laboratory1, University of California, Irvine2, California Institute of Technology3, Florida State University College of Arts and Sciences4, Yale University5, Wellcome Trust Sanger Institute6, Norwegian University of Science and Technology7, Affymetrix8, University of North Carolina at Chapel Hill9, University of Lausanne10, University of Geneva11, Genome Institute of Singapore12, Stanford University13, Pompeu Fabra University14
TL;DR: Evidence that three-quarters of the human genome is capable of being transcribed is reported, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs that prompt a redefinition of the concept of a gene.
Abstract: Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
4,450 citations
01 Sep 2012
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
2,767 citations
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TL;DR: In this article, the authors investigated the 3D development of a marine oil spill on the ocean surface and in the water column using numerical model simulations, including wave entrainment of oil, two alternative formulations for the droplet size and turbulent mixing.
Abstract: . Vertical and horizontal transport mechanisms for marine oil spills
are investigated using numerical model simulations. To realistically resolve
the 3-D development of a spill on the ocean surface and in the water column,
recently published parameterizations for the vertical mixing of oil spills
are implemented in the open-source trajectory framework OpenDrift
( https://doi.org/10.5281/zenodo.1300358 , last access: 7 April 2018). The parameterizations include the
wave entrainment of oil, two alternative formulations for the droplet size
spectra, and turbulent mixing. The performance of the integrated oil spill
model is evaluated by comparing model simulations with airborne observations
of an oil slick. The results show that an accurate description of a chain of
physical processes, in particular vertical mixing and oil weathering, is
needed to represent the horizontal spreading of the oil spill. Using
ensembles of simulations of hypothetic oil spills, the general drift behavior
of an oil spill during the first 10 days after initial spillage is evaluated
in relation to how vertical processes control the horizontal transport.
Transport of oil between the surface slick and the water column is identified
as a crucial component affecting the horizontal transport of oil spills. The
vertical processes are shown to control differences in the drift of various
types of oil and in various weather conditions.
58 citations
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TL;DR: The OSCAR oil spill model is updated to use sea-ice velocity and coverage fields from coupled ice-ocean models to improve simulation of oil fate and transport in ice-covered waters.
34 citations
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TL;DR: The Oceanography 29, no. 3 (2016): 96-107, doi:10.5670/oceanog.2016.74.74 as discussed by the authors The Oceanography Society, 2016.
Abstract: Author Posting. © The Oceanography Society, 2016. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 29, no. 3 (2016): 96–107, doi:10.5670/oceanog.2016.74.
26 citations
Cited by
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TL;DR: 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 outperforms other aligners by a factor of >50 in mapping speed.
Abstract: 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/.
30,684 citations
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TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Abstract: 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.
13,548 citations
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TL;DR: In this paper, 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.
Abstract: 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.
9,745 citations
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TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Abstract: 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.
8,106 citations
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TL;DR: The Gene Expression Omnibus is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community and supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable.
Abstract: 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.
6,683 citations