Related papers: Meta-analysis for Discovering Which Genes are Diff…
Neurodegenerative diseases are characterized as the progressive loss of neural cells, e.g. neurons, glial cells. Ageing, monogenic variations, viral infections, and many other factors are determined and speculated as causes for them. While…
Epilepsy is a chronic neurological condition characterized by recurrent seizures, with global prevalence estimated at 50 million people worldwide. While progress in high-throughput sequencing has allowed for broad-based transcriptomic…
The novel data analytical platform General Effect Modelling (GEM), is an umbrella platform covering different data analytical methods that handle data with multiple design variables (or pseudo design variables) and multivariate responses.…
Two cliques of genes identified computationally for their high co-expression in the mouse brain according to the Allen Brain Atlas, and for their enrichment in genes related to autism spectrum disorder, have recently been shown to be highly…
Disease heterogeneity has been a critical challenge for precision diagnosis and treatment, especially in neurologic and neuropsychiatric diseases. Many diseases can display multiple distinct brain phenotypes across individuals, potentially…
Background: Patients carrying MEF2C haploinsufficiency develop a recognizable neurodevelopmental syndrome featuring intellectual disability, treatment-resistant seizures, and autism spectrum behaviors. While MEF2C's critical roles in…
Much of the genome is expressed in the vertebrate brain, with individual genes exhibiting different spatially-varying patterns of expression. These variations are not independent, with pairs of genes exhibiting complex patterns of…
Quantitative criteria are proposed to identify genes (and sets of genes) whose expression marks a specific brain region (or a set of brain regions). Gene-expression energies, obtained for thousands of mouse genes by numerization of in-situ…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…
Gene expression represents a fundamental interface between genes and environment in the development and ongoing plasticity of the human organism. Individual differences in gene expression are likely to underpin much of human diversity,…
Heterogeneity of brain diseases is a challenge for precision diagnosis/prognosis. We describe and validate Smile-GAN (SeMI-supervised cLustEring-Generative Adversarial Network), a novel semi-supervised deep-clustering method, which dissects…
Familial hemiplegic migraine (FHM) is a rare subtype of migraine with aura. A mutation causing FHM type 3 (FHM3) has been identified in SCN1A encoding the Nav1.1 Na$^+$ channel. This genetic defect affects the inactivation gate. While the…
Inflammation of brain tissue is a complex response of the immune system to the presence of toxic compounds or to cell injury, leading to a cascade of pathological processes that include glial cell activation. Noninvasive magnetic resonance…
We use the Allen Gene Expression Atlas (AGEA) and the OMA ortholog dataset to investigate the evolution of mouse-brain neuroanatomy from the standpoint of the molecular evolution of brain-specific genes. For each such gene, using the…
Affymetrix GeneChip technology is used to detect gene expression levels in samples of cells under different conditions. In this project, we analyzed the gene expression profiling data for mouse induced pluripotent stem cell (iPSCs)…
By use of complex network dynamics and graph-based machine learning, we identified critical determinants of lineage-specific plasticity across the single-cell transcriptomics of pediatric high-grade glioma (pHGGs) subtypes: IDHWT…
Pediatric high grade gliomas are lethal evolutionary disorders with stalled developmental trajectories and disrupted differentiation hierarchies. We integrate transcriptional and algorithmic network complexity based perturbation analysis to…
Fetal neuroinflammation and prenatal stress (PS) may contribute to lifelong neurological disabilities. Astrocytes and microglia, among the brain's non-neuronal glia cell populations, play a pivotal role in neurodevelopment, predisposition…
The three-dimensional data-driven Allen Gene Expression Atlas of the adult mouse brain consists of numerized in-situ hybridization data for thousands of genes, co-registered to the Allen Reference Atlas. We propose quantitative criteria to…
Glioblastoma is a highly aggressive form of brain cancer characterized by rapid progression and poor prognosis. Despite advances in treatment, the underlying genetic mechanisms driving this aggressiveness remain poorly understood. In this…