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Article
Mass cytometry uncovers a distinct peripheral immune profile and upregulated CD38 expression in patients with hidradenitis suppurativa
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Article
Open AccessIntegrative scATAC-seq and scRNA-seq analyses map thymic iNKT cell development and identify Cbfβ for its commitment
Unlike conventional αβT cells, invariant natural killer T (iNKT) cells complete their terminal differentiation to functional iNKT1/2/17 cells in the thymus. However, underlying molecular programs that guide iNKT ...
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Article
Open AccessAuthor Correction: Genome-wide association study identifies Sjögren’s risk loci with functional implications in immune and glandular cells
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Article
Open AccessAuthor Correction: Genome-wide association study identifies Sjögren’s risk loci with functional implications in immune and glandular cells
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Article
Open AccessSingle-cell analysis reveals differences among iNKT cells colonizing peripheral organs and identifies Klf2 as a key gene for iNKT emigration
Invariant natural killer T cell (iNKT) subsets are differentially distributed in various immune organs. However, it remains unclear whether iNKT cells exhibit phenotypical and functional differences in different ...
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Article
Open AccessGenome-wide association study identifies Sjögren’s risk loci with functional implications in immune and glandular cells
Sjögren’s disease is a complex autoimmune disease with twelve established susceptibility loci. This genome-wide association study (GWAS) identifies ten novel genome-wide significant (GWS) regions in Sjögren’s ...
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Article
Open AccessHistone deacetylase 3 controls lung alveolar macrophage development and homeostasis
Alveolar macrophages (AMs) derived from embryonic precursors seed the lung before birth and self-maintain locally throughout adulthood, but are regenerated by bone marrow (BM) under stress conditions. However,...
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Article
Open AccessNRG1 variant effects in patients with Hirschsprung disease
Hirschsprung disease (HSCR) is a heterogeneous genetic disorder characterized by absence of ganglion cells along the intestines resulting in functional bowel obstruction. Mutations in neuregulin 1 (NRG1) gene hav...
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Protocol
Estimating Allele Frequencies
Methods of estimating allele frequencies from data on unrelated and related individuals are described in this chapter. For samples of unrelated individuals with simple codominant markers, the natural estimator...
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Article
Open AccessDetrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data
Adapter trimming and removal of duplicate reads are common practices in next-generation sequencing pipelines. Sequencing reads ambiguously mapped to repetitive and low complexity regions can also be problemati...
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Article
Machine-learning classifiers for imbalanced tornado data
Learning from imbalanced data, where the number of observations in one class is significantly larger than the ones in the other class, has gained considerable attention in the machine learning community. Assum...
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Article
Open AccessPerformance of HLA allele prediction methods in African Americans for class II genes HLA-DRB1, −DQB1, and –DPB1
The expense of human leukocyte antigen (HLA) allele genoty** has motivated the development of imputation methods that use dense single nucleotide polymorphism (SNP) genotype data and the region’s haplotype stru...
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Article
Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome
Kathy Sivils and colleagues report results of a large-scale association study of Sjögren's syndrome, a common autoimmune disease. They confirm strong associations with the HLA region and establish genome-wide ...
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Protocol
Estimating Allele Frequencies
Methods of estimating allele frequencies from data on unrelated and related individuals are described in this chapter. For samples of unrelated individuals with simple codominant markers, the natural estimator...
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Article
Kernel logistic regression using truncated Newton method
Kernel logistic regression (KLR) is a powerful nonlinear classifier. The combination of KLR and the truncated-regularized iteratively re-weighted least-squares (TR-IRLS) algorithm, has led to a powerful classi...
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Article
Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus
Patrick Gaffney and colleagues perform a fine-map** study of the TNFAIP3 region in systemic lupus erythematosus using individuals from diverse ancestral populations. They identify a putative causal variant in a...
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Chapter
Genetic Epidemiology of Obesity and Cancer
To understand the genetic epidemiology of obesity and cancer means to consider the genetics of not only these two complex diseases but also the many risk factors associated with them and the molecular mechanis...
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Chapter
Missing Data Imputation Through Machine Learning Algorithms
How to address missing data is an issue most researchers face. Computerized algorithms have been developed to ingest rectangular data sets, where the rows represent observations and the columns represent varia...
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Chapter and Conference Paper
Active Learning with Support Vector Machines for Tornado Prediction
In this paper, active learning with support vector machines (SVMs) is applied to the problem of tornado prediction. This method is used to predict which storm-scale circulations yield tornadoes based on the ra...
