| 1. |
- Romagnoni, A, et al.
(författare)
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
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Tidskriftsartikel (refereegranskat)abstract
- Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
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| 6. |
- Lalkovski, S., et al.
(författare)
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Core-coupled states and split proton-neutron quasiparticle multiplets in Ag122-126
- 2013
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 87:3, s. 034308-
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Tidskriftsartikel (refereegranskat)abstract
- Neutron-rich silver isotopes were populated in the fragmentation of a Xe-136 beam and the relativistic fission of U-238. The fragments were mass analyzed with the GSI Fragment Separator and subsequently implanted into a passive stopper. Isomeric transitions were detected by 105 high-purity germanium detectors. Eight isomeric states were observed in Ag122-126 nuclei. The level schemes of Ag-122,Ag-123,Ag-125 were revised and extended with isomeric transitions being observed for the first time. The excited states in the odd-mass silver isotopes are interpreted as core-coupled states. The isomeric states in the even-mass silver isotopes are discussed in the framework of the proton-neutron split multiplets. The results of shell-model calculations, performed for the most neutron-rich silver nuclei are compared to the experimental data.
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| 7. |
- Söderström, Pär-Anders, et al.
(författare)
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Spectroscopy of neutron-rich Dy-168,Dy-170 : Yrast band evolution close to the NpNn valence maximum
- 2010
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 81:3, s. 034310-
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Tidskriftsartikel (refereegranskat)abstract
- The yrast sequence of the neutron-rich dysprosium isotope Dy-168 has been studied using multinucleon transfer reactions following collisions between a 460-MeV Se-82 beam and an Er-170 target. The reaction products were identified using the PRISMA magnetic spectrometer and the gamma rays detected using the CLARA HPGe-detector array. The 2(+) and 4(+) members of the previously measured ground-state rotational band of Dy-168 have been confirmed and the yrast band extended up to 10(+). A tentative candidate for the 4(+) -> 2(+) transition in Dy-170 was also identified. The data on these nuclei and on the lighter even-even dysprosium isotopes are interpreted in terms of total Routhian surface calculations and the evolution of collectivity in the vicinity of the proton-neutron valence product maximum is discussed.
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| 8. |
- Wadsworth, R., et al.
(författare)
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THE NORTHWEST FRONTIER : SPECTROSCOPY OF N similar to Z NUCLEI BELOW MASS 100
- 2009
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Ingår i: Acta Physica Polonica B. - 0587-4254 .- 1509-5770. ; 40:3, s. 611-620
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Tidskriftsartikel (refereegranskat)abstract
- The spectroscopy and structure of excited states of N similar to Z nuclei in the mass 70-100 region has been investigated using two techniques. In the A similar to 70-80 region fusion evaporation reactions coupled with the recoil-beta-tagging method have been employed at Jyvaskyla to study low-lying states in odd-odd N = Z nuclei. Results from these and other data for known odd-odd nuclei above mass 60 will be discussed. In the heavier mass 90 region a fragmentation experiment has been performed using the RIS-ING/FRS setup at GSI. This experiment was primarily aimed at searching for spin gap isomers in nuclei around A similar to 96. The objectives of the latter experiment will be discussed.
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| 9. |
- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 10. |
- Morales, A. I., et al.
(författare)
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beta -Delayed gamma -Ray Spectroscopy of Heavy Neutron Rich Nuclei "South" of Lead
- 2009
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Ingår i: Acta Physica Polonica B. - 0587-4254. ; 40:3, s. 867-870
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Konferensbidrag (refereegranskat)abstract
- Relativistic projectile fragmentation of a Pb-208 primary beam has been used to produce neutron-rich nuclei with proton-holes relative to the Z = 82 shell closure, i.e., "south" of Pb. beta-delayed gamma-ray spectroscopy allows to investigate the structural properties of such nuclei with A similar to 195 -> 205. The current work presents transitions de-exciting excited states in Au-204, which are the first spectroscopic information on this N = 125 isotone.
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