| 1. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
- Enoksson, Fredrik, 1977-
(författare)
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Adaptable metadata creation for the Web of Data
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- One approach to manage collections is to create data about the things in it. This descriptive data is called metadata, and this term is in this thesis used as a collective noun, i.e no plural form exists. A library is a typical example of an organization that uses metadata, to manage a collection of books. The metadata about a book describes certain attributes of it, for example who the author is. Metadata also provides possibilities for a person to judge if a book is interesting without having to deal with the book itself. The metadata of the things in a collection is a representation of the collection that is easier to deal with than the collection itself. Nowadays metadata is often managed in computer-based systems that enable search possibilities and sorting of search results according to different principles. Metadata can be created both by computers and humans. This thesis will deal with certain aspects of the human activity of creating metadata and includes an explorative study of this activity. The increased amount of public information that is produced is also required to be easily accessible and therefore the situation when metadata is a part of the Semantic Web has been considered an important part of this thesis. This situation is also referred to as the Web of Data or Linked Data.With the Web of Data, metadata records living in isolation from each other can now be linked together over the web. This will probably change what kind of metadata that is being created, but also how it is being created. This thesis describes the construction and use of a framework called Annotation Profiles, a set of artifacts developed to enable an adaptable metadata creation environment with respect to what metadata that can be created. The main artifact is the Annotation Profile Model (APM), a model that holds enough information for a software application to generate a customized metadata editor from it. An instance of this model is called an annotation profile, that can be seen as a configuration for metadata editors. Changes to what metadata can be edited in a metadata editor can be done without modifying the code of the application. Two code libraries that implement the APM have been developed and have been evaluated both internally within the research group where they were developed, but also externally via interviews with software developers that have used one of the code-libraries. Another artifact presented is a protocol for how RDF metadata can be remotely updated when metadata is edited through a metadata editor. It is also described how the APM opens up possibilities for end user development and this is one of the avenues of pursuit in future research related to the APM.
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| 3. |
- Huvila, Isto, Professor, 1976-, et al.
(författare)
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Documenting Information Processes and Practices : Paradata, Provenance Metadata, Life-Cycles and Pipelines
- 2021
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Ingår i: Proceedings of the Association for Information Science and Technology. - : Wiley. - 2373-9231. ; 58:1, s. 604-609
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Tidskriftsartikel (refereegranskat)abstract
- Processes and practices–and in general, informational doings and their diverse constellations–are pertinent elements of the information landscape. This panel presents research on documentation and description of processes and practices in the information field addressing: 1) how different conceptualisations of processes and practices influence how they emerge as describable entities; 2) what different approaches to document and describe processes and practices exist and have been proposed in information science and technology research; 3) what aspects of processes and practices different documentation approaches capture, make visible and invisible; and 4) what novel insights from the current state-of-the-art research can be drawn to support practitioners in different areas of the information field, including knowledge organisation, information management, information literacy instruction, and development of information systems and services.
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| 4. |
- Kim, Kwangwoo, et al.
(författare)
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High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci
- 2015
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 74:3
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Tidskriftsartikel (refereegranskat)abstract
- Objective A highly polygenic aetiology and high degree of allele-sharing between ancestries have been well elucidated in genetic studies of rheumatoid arthritis. Recently, the high-density genotyping array Immunochip for immune disease loci identified 14 new rheumatoid arthritis risk loci among individuals of European ancestry. Here, we aimed to identify new rheumatoid arthritis risk loci using Korean-specific Immunochip data. Methods We analysed Korean rheumatoid arthritis case-control samples using the Immunochip and genome-wide association studies (GWAS) array to search for new risk alleles of rheumatoid arthritis with anticitrullinated peptide antibodies. To increase power, we performed a meta-analysis of Korean data with previously published European Immunochip and GWAS data for a total sample size of 9299 Korean and 45 790 European case-control samples. Results We identified eight new rheumatoid arthritis susceptibility loci (TNFSF4, LBH, EOMES, ETS1-FLI1, COG6, RAD51B, UBASH3A and SYNGR1) that passed a genome-wide significance threshold (p<5x10(-8)), with evidence for three independent risk alleles at 1q25/TNFSF4. The risk alleles from the seven new loci except for the TNFSF4 locus (monomorphic in Koreans), together with risk alleles from previously established RA risk loci, exhibited a high correlation of effect sizes between ancestries. Further, we refined the number of single nucleotide polymorphisms (SNPs) that represent potentially causal variants through a trans-ethnic comparison of densely genotyped SNPs. Conclusions This study demonstrates the advantage of dense-mapping and trans-ancestral analysis for identification of potentially causal SNPs. In addition, our findings support the importance of T cells in the pathogenesis and the fact of frequent overlap of risk loci among diverse autoimmune diseases.
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| 5. |
- Okada, Yukinori, et al.
(författare)
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Genetics of rheumatoid arthritis contributes to biology and drug discovery
- 2014
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 506:7488, s. 376-381
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA)(1). Here we performed a genome-wide association study meta-analysis in a total of >100,000 subjects of European and Asian ancestries (29,880 RA cases and 73,758 controls), by evaluating similar to 10 million single-nucleotide polymorphisms. We discovered 42 novel RA risk loci at a genome-wide level of significance, bringing the total to 101 (refs 2-4). We devised an in silico pipeline using established bioinformatics methods based on functional annotation(5), cis-acting expression quantitative trait loci(6) and pathway analyses(7-9)-as well as novel methods based on genetic overlap with human primary immunodeficiency, haematological cancer somatic mutations and knockout mouse phenotypes-to identify 98 biological candidate genes at these 101 risk loci. We demonstrate that these genes are the targets of approved therapies for RA, and further suggest that drugs approved for other indications may be repurposed for the treatment of RA. Together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to RA pathogenesis, and provides empirical evidence that the genetics of RA can provide important information for drug discovery.
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