| 1. |
- Ramdas, S., et al.
(författare)
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A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids
- 2022
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 109:8, s. 1366-1387
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
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| 4. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 5. |
- Pattaro, Cristian, et al.
(författare)
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Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.
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| 6. |
- Gutt, J., et al.
(författare)
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Shifts in Antarctic megabenthic structure after ice-shelf disintegration in the Larsen area east of the Antarctic Peninsula
- 2013
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Ingår i: Polar Biology. - : Springer Science and Business Media LLC. - 0722-4060 .- 1432-2056. ; 36:6, s. 895-906
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to contribute to a general understanding of the response of the Antarctic macrobenthos to environmental variability and climate-induced changes. The change in population size of selected macrobenthic organisms was investigated in the Larsen A area east of the Antarctic Peninsula in 2007 and 2011 using ROV-based imaging methods. The results were complemented by data from the Larsen B collected in 2007 to allow a conceptual reconstruction of the environment-driven changes before the period of investigation. Both Larsen areas are characterised by ice-shelf disintegration in 1995 and 2002, respectively, as well as high inter-annual variability in sea-ice cover and oceanographic conditions. In 2007 one ascidian species, Molgula pedunculata, was abundant north and south of the stripe of remaining ice shelf between Larsen A and B. Population densities decreased drastically in the Larsen A between 2007 and 2011, coincident with the decrease in Corella eumyota, another ascidian. Among the ophiuroids, the population of deposit feeders increased, while suspension feeders halved their abundance. Current measurements indicated a northward flow between the Larsen B and Larsen A, suggesting that a major physical forcing on benthic population development comes from the South. The results demonstrate that Antarctic macrobenthic populations can exhibit dramatic population dynamics. Analyses of sea-ice dynamics, salinity, temperature and surprisingly ice-shelf disintegration history, however, did not provide any clear evidence for environmental drivers underlying the apparent changes.
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| 7. |
- Kurilshikov, Alexander, et al.
(författare)
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Large-scale association analyses identify host factors influencing human gut microbiome composition
- 2021
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 53:2, s. 156-165
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Tidskriftsartikel (refereegranskat)abstract
- To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 x 10(-8)) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 x 10(-20)), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 x 10(-10) < P < 5 x 10(-8)) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.
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| 8. |
- Rainovski, G, et al.
(författare)
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Shape coexistence at high spin in the N = Z+2 nucleus Se-70
- 2002
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Ingår i: Journal of Physics G: Nuclear and Particle Physics. - : IOP Publishing. - 0954-3899. ; 28:10, s. 2617-2625
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Tidskriftsartikel (refereegranskat)abstract
- The nucleus Se-70 was studied using the Ca-40(Ca-40, 2alpha2p) reaction at a beam energy of 185 MeV. Gamma rays were measured with the EUROBALL III spectrometer. The known positive-parity bands have been extended and one new band of positive parity and two of negative parity have been identified. These bands are interpreted in terms of the cranked Nilsson-Strutinsky approach. Calculations suggest that the two negative-parity bands, which have the same signature, are both based on a configuration with two protons and three neutrons lifted from the fp shell to the g(9/2) orbital, but at different nuclear shapes. This represents a shape coexistence at high spin.
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| 9. |
- Valiente-Dobon, JJ, et al.
(författare)
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Evidence for nontermination of rotational bands in Kr-74
- 2005
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Ingår i: Physical Review Letters. - 1079-7114. ; 95:23
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Tidskriftsartikel (refereegranskat)abstract
- Three rotational bands in Kr-74 were studied up to (in one case one transition short of) the maximum spin I-max of their respective single-particle configurations. Their lifetimes have been determined using the Doppler-shift attenuation method. The deduced transition quadrupole moments reveal a modest decrease, but far from a complete loss of collectivity at the maximum spin I-max. This feature, together with the results of mean field calculations, indicates that the observed bands do not terminate at I=I-max.
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