Related papers: Meta-analysis for Discovering Which Genes are Diff…
General Effect Modelling (GEM) is an umbrella over different methods that utilise effects in the analyses of data with multiple design variables and multivariate responses. To demonstrate the methodology, we here use GEM in gene expression…
Microarray is a technology to quantitatively monitor the expression of large number of genes in parallel. It has become one of the main tools for global gene expression analysis in molecular biology research in recent years. The large…
We present a technique to characterize differentially expressed genes in terms of their position in a high-dimensional co-expression network. The set-up of Gaussian graphical models is used to construct representations of the co-expression…
We present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic integration of network inference and network topological analysis…
A significant association between a polymorphism in the D repeat of the gene encoding asporin and osteoarthritis, the most frequent of articular diseases, has been recently reported. The goal of the present study was to investigate the…
Subtyping neuropsychiatric disorders like schizophrenia is essential for improving the diagnosis and treatment of complex diseases. Subtyping schizophrenia is challenging because it is polygenic and genetically heterogeneous, rendering the…
Adenosine receptors are G-protein-coupled receptors involved in a wide range of physiological and pathological phenomena in most mammalian systems. All four receptors are widely expressed in the central nervous system, where they modulate…
Traditional voxel-level multiple testing procedures in neuroimaging, mostly $p$-value based, often ignore the spatial correlations among neighboring voxels and thus suffer from substantial loss of power. We extend the…
Stain variability is a pervasive source of distribution shift and potential shortcut learning in renal pathology AI. We ask whether lupus nephritis glomerular lesion classifiers exploit stain as a shortcut, and how to mitigate such bias…
Introduction: Tuberculous meningitis (TBM) is a serious brain infection caused by Mycobacterium tuberculosis, characterized by inflammation of the meninges covering the brain and spinal cord. Diagnosis often requires invasive lumbar…
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…
Medical imaging datasets are inherently high dimensional with large variability and low sample sizes that limit the effectiveness of deep learning algorithms. Recently, generative adversarial networks (GANs) with the ability to synthesize…
Graph neural networks (GNNs) provide powerful insights for brain neuroimaging technology from the view of graphical networks. However, most existing GNN-based models assume that the neuroimaging-produced brain connectome network is a…
Segmenting glomerular intraglomerular tissue and lesions traditionally depends on detailed morphological evaluations by expert nephropathologists, a labor-intensive process susceptible to interobserver variability. Our group previously…
In routine colorectal cancer management, histologic samples stained with hematoxylin and eosin are commonly used. Nonetheless, their potential for defining objective biomarkers for patient stratification and treatment selection is still…
A major issue in the association of genes to neuroimaging phenotypes is the high dimension of both genetic data and neuroimaging data. In this article, we tackle the latter problem with an eye toward developing solutions that are relevant…
Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…
To establish the relationship between locomotory behavior and dynamics of neural circuits in the nematode C. elegans we combined molecular and theoretical approaches. In particular, we quantitatively analyzed the motion of C. elegans with…
Multi Expression Programming (MEP) is a Genetic Programming variant that uses a linear representation of chromosomes. MEP individuals are strings of genes encoding complex computer programs. When MEP individuals encode expressions, their…
The Allen Brain Atlas (ABA) of the adult mouse consists of digitized expression profiles of thousands of genes in the mouse brain, co-registered to a common three-dimensional template (the Allen Reference Atlas). This brain-wide,…