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SNOMAD is a collection of algorithms for the normalization and standardization of gene expression datasets derived from diverse biological and technological sources. In addition to conventional transformations and visualization tools, SNOMAD includes two non-linear transformations which correct for bias and variance which are non-uniformly distributed(More)
  • Kenji Matsushita, Craig N. Morrell, Beatrice Cambien, Shui-Xiang Yang, Munekazu Yamakuchi, Clare Bao +8 others
  • 2003
Nitric oxide (NO) inhibits vascular inflammation, but the molecular basis for its anti-inflammatory properties is unknown. We show that NO inhibits exocytosis of Weibel-Palade bodies, endothelial granules that mediate vascular inflammation and thrombosis, by regulating the activity of N-ethylmaleimide-sensitive factor (NSF). NO inhibits NSF disassembly of(More)
Mosaic somatic alterations are present in all multi-cellular organisms, but the physiological effects of low-level mosaicism are largely unknown. Most mosaic alterations remain undetectable with current analytical approaches, although the presence of such alterations is increasingly implicated as causative for disease. Here, we present the(More)
Many of the images in this powerpoint presentation are from Bioinformatics and Functional Genomics These images and materials may not be used without permission from the publisher. We welcome instructors to use these powerpoints for educational purposes, but please acknowledge the source. BLAST Practical use Algorithm Strategies Fi di di t tl l t d t i(More)
It is an assumption of large, population-based datasets that samples are annotated accurately whether they correspond to known relationships or unrelated individuals. These annotations are key for a broad range of genetics applications. While many methods are available to assess relatedness that involve estimates of identity-by-descent (IBD) and/or(More)
BACKGROUND Down syndrome, caused by trisomic chromosome 21, is the leading genetic cause of mental retardation. Recent studies demonstrated that dosage-dependent increases in chromosome 21 gene expression occur in trisomy 21. However, it is unclear whether the entire transcriptome is disrupted, or whether there is a more restricted increase in the(More)
Although more than 2,400 genes have been shown to contain variants that cause Mendelian disease, there are still several thousand such diseases yet to be molecularly defined. The ability of new whole-genome sequencing technologies to rapidly indentify most of the genetic variants in any given genome opens an exciting opportunity to identify these disease(More)
Here we present a methodology for the normalization of element signal intensities to a mean intensity calculated locally across the surface of a DNA microarray. These methods allow the detection and/or correction of spatially systematic artifacts in microarray data. These include artifacts that can be introduced during the robotic printing, hybridization,(More)
We describe the discovery of a novel, 20 kDa, secreted human protein named mesencephalic astrocyte-derived neurotrophic factor, or MANF. The homologous, native molecule was initially derived from a rat mesencephalic type-1 astrocyte cell line and recombinant MANF subcloned from a cDNA encoding human arginine-rich protein. MANF selectively protects nigral(More)