相关论文: Brain Gene Expression Analysis: a MATLAB toolbox f…
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,…
We review quantitative methods and software developed to analyze genome-scale, brain-wide spatially-mapped gene-expression data. We expose new methods based on the underlying high-dimensional geometry of voxel space and gene space, and on…
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…
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…
The Allen Atlas of the adult mouse brain is used to estimate the region-specificity of 64 cell types whose transcriptional profile in the mouse brain has been measured in microarray experiments. We systematically analyze the preliminary…
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…
The Allen Atlas of the adult mouse brain is a brain-wide, genome-wide data set that has been made available online, triggering a renaissance in neuroanatomy. In particular, it has been used to define brain regions in a computational,…
We propose a quantitative method to estimate the statistical properties of sets of genes for which expression data are available and co-registered to a reference atlas of the brain. It is based on graph-theoretic properties of co-expression…
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of…
The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack…
Characterizing the transcriptome architecture of the human brain is fundamental in gaining an understanding of brain function and disease. A number of recent studies have investigated patterns of brain gene expression obtained from an…
The voxelized Allen Atlas of the adult mouse brain (at a resolution of 200 microns) has been used in [arXiv:1303.0013] to estimate the region-specificity of 64 cell types whose transcriptional profile in the mouse brain has been measured in…
We present the first automated pipeline to create an atlas of in situ hybridization gene expression in the adult marmoset brain in the same stereotaxic space. The pipeline consists of segmentation of gene expression from microscopy images…
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…
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…
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…
Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms…
Understanding how emotional expression in language relates to brain function is a challenge in computational neuroscience and affective computing. Traditional neuroimaging is costly and lab-bound, but abundant digital text offers new…
Estimating brain age (BA) from T1-weighted magnetic resonance images (MRIs) provides a powerful framework for quantifying anatomical brain aging. Whereas global BA (GBA) summarizes overall brain health, local BA (LBA) provides cortically…
Alzheimer's disease (AD) is a serious neurodegenerative disease consisting of four stages where the illness gets progressively worse. It is of great significance to detect the gene regulatory mechanism as AD progresses and, thus, to help us…