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- 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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| 3. |
- Momozawa, Y, et al.
(författare)
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IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes
- 2018
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9:1, s. 2427-
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Tidskriftsartikel (refereegranskat)abstract
- GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach.
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| 9. |
- Sanchez-Barriga, J., et al.
(författare)
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Effects of spin-dependent quasiparticle renormalization in Fe, Co, and Ni photoemission spectra : An experimental and theoretical study
- 2012
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 85:20, s. 205109-
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated the spin-dependent quasiparticle lifetimes and the strength of electron correlation effects in the ferromagnetic 3d transition metals Fe, Co, and Ni by means of spin- and angle-resolved photoemission spectroscopy. The experimental data are accompanied by state-of-the-art many-body calculations within the dynamical mean-field theory and the three-body scattering approximation, including fully relativistic calculations of the photoemission process within the one-step model. Our quantitative analysis reveals that inclusion of local many-body Coulomb interactions are of ultimate importance for a realistic description of correlation effects in ferromagnetic 3d transition metals. However, we found that more sophisticated many-body calculations with larger modifications in the case of Fe and Co are still needed to improve the quantitative agreement between experiment and theory. In general, it turned out that not only the dispersion behavior of energetic structures should be affected by nonlocal correlations but also the line widths of most of the photoemission peaks are underestimated by the current theoretical approaches. The increasing values of the on-site Coulomb interaction parameter U and the band narrowing of majority spin states obtained when moving from Fe to Ni indicate that the effect of nonlocal correlations becomes weaker with increasing atomic number, whereas correlation effects tend to be stronger.
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| 10. |
- Sanchez-Barriga, J., et al.
(författare)
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Quantitative determination of spin-dependent quasiparticle lifetimes and electronic correlations in hcp cobalt
- 2010
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 82:10, s. 104414-
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Tidskriftsartikel (refereegranskat)abstract
- We report on a quantitative investigation of the spin-dependent quasiparticle lifetimes and electron correlation effects in ferromagnetic hcp Co (0001) by means of spin-and angle-resolved photoemission spectroscopies. The experimental spectra are compared in detail to state-of-the-art many-body calculations within the dynamical mean-field theory and the three-body scattering approximation, including a full calculation of the one-step photoemission process. From this comparison we conclude that although strong local many-body Coulomb interactions are of major importance for the qualitative description of correlation effects in Co, more sophisticated many-body calculations are needed in order to improve the quantitative agreement between theory and experiment, in particular, concerning the linewidths. The quality of the overall agreement obtained for Co indicates that the effect of nonlocal correlations becomes weaker with increasing atomic number.
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