Browsing by Subject "Oligonucleotide Array Sequence Analysis"
Now showing items 1-20 of 38
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A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2.
(PLoS One, 2013)There is great potential for host-based gene expression analysis to impact the early diagnosis of infectious diseases. In particular, the influenza pandemic of 2009 highlighted the challenges and limitations of traditional ... -
A nucleosome-guided map of transcription factor binding sites in yeast.
(PLoS Comput Biol, 2007-11)Finding functional DNA binding sites of transcription factors (TFs) throughout the genome is a crucial step in understanding transcriptional regulation. Unfortunately, these binding sites are typically short and degenerate, ... -
A Transcriptional Signature Identifies LKB1 Functional Status as a Novel Determinant of MEK Sensitivity in Lung Adenocarcinoma.
(Cancer research, 2017-01)LKB1 is a commonly mutated tumor suppressor in non-small cell lung cancer that exerts complex effects on signal transduction and transcriptional regulation. To better understand the downstream impact of loss of functional ... -
Advances to Bayesian network inference for generating causal networks from observational biological data.
(Bioinformatics, 2004-12-12)MOTIVATION: Network inference algorithms are powerful computational tools for identifying putative causal interactions among variables from observational data. Bayesian network inference algorithms hold particular promise ... -
Automatic annotation of spatial expression patterns via sparse Bayesian factor models.
(PLoS Comput Biol, 2011-07)Advances in reporters for gene expression have made it possible to document and quantify expression patterns in 2D-4D. In contrast to microarrays, which provide data for many genes but averaged and/or at low resolution, ... -
Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies.
(BMC Bioinformatics, 2010-11-09)BACKGROUND: Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such techniques ... -
Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.
(Nucleic Acids Res, 2010-05)Determination of copy number variants (CNVs) inferred in genome wide single nucleotide polymorphism arrays has shown increasing utility in genetic variant disease associations. Several CNV detection methods are available, ... -
Comparison of pattern detection methods in microarray time series of the segmentation clock.
(PLoS One, 2008-08-06)While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data ... -
Diagnosis of partial body radiation exposure in mice using peripheral blood gene expression profiles.
(PLoS One, 2010-07-12)In the event of a terrorist-mediated attack in the United States using radiological or improvised nuclear weapons, it is expected that hundreds of thousands of people could be exposed to life-threatening levels of ionizing ... -
Differential Apaf-1 levels allow cytochrome c to induce apoptosis in brain tumors but not in normal neural tissues.
(Proc Natl Acad Sci U S A, 2007-12-26)Brain tumors are typically resistant to conventional chemotherapeutics, most of which initiate apoptosis upstream of mitochondrial cytochrome c release. In this study, we demonstrate that directly activating apoptosis downstream ... -
Evidence-ranked motif identification.
(Genome Biol, 2010)cERMIT is a computationally efficient motif discovery tool based on analyzing genome-wide quantitative regulatory evidence. Instead of pre-selecting promising candidate sequences, it utilizes information across all sequence ... -
Expression in aneuploid Drosophila S2 cells.
(PLoS Biol, 2010-02-23)Extensive departures from balanced gene dose in aneuploids are highly deleterious. However, we know very little about the relationship between gene copy number and expression in aneuploid cells. We determined copy number ... -
Expression signatures of TP53 mutations in serous ovarian cancers.
(BMC Cancer, 2010-05-26)BACKGROUND: Mutations in the TP53 gene are extremely common and occur very early in the progression of serous ovarian cancers. Gene expression patterns that relate to mutational status may provide insight into the etiology ... -
Ferrochelatase is a conserved downstream target of the blue light-sensing White collar complex in fungi.
(Microbiology, 2010-08)Light is a universal signal perceived by organisms, including fungi, in which light regulates common and unique biological processes depending on the species. Previous research has established that conserved proteins, originally ... -
Gene expression signatures that predict radiation exposure in mice and humans.
(PLoS Med, 2007-04)BACKGROUND: The capacity to assess environmental inputs to biological phenotypes is limited by methods that can accurately and quantitatively measure these contributions. One such example can be seen in the context of exposure ... -
Gene expression-based classifiers identify Staphylococcus aureus infection in mice and humans.
(PLoS One, 2013)Staphylococcus aureus causes a spectrum of human infection. Diagnostic delays and uncertainty lead to treatment delays and inappropriate antibiotic use. A growing literature suggests the host's inflammatory response to the ... -
Gene selection using iterative feature elimination random forests for survival outcomes.
(IEEE/ACM Trans Comput Biol Bioinform, 2012-09)Although many feature selection methods for classification have been developed, there is a need to identify genes in high-dimensional data with censored survival outcomes. Traditional methods for gene selection in classification ... -
Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis.
(Plant Physiol, 2011-11)SHORT-ROOT (SHR) is a key regulator of root growth and development in Arabidopsis (Arabidopsis thaliana). Made in the stele, the SHR protein moves into an adjacent cell layer, where it specifies endodermal cell fate; it ... -
Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals.
(PLoS Pathog, 2010-02-26)There is great interindividual variability in HIV-1 viral setpoint after seroconversion, some of which is known to be due to genetic differences among infected individuals. Here, our focus is on determining, genome-wide, ... -
High-resolution microarray analysis unravels complex Xq28 aberrations in patients and carriers affected by X-linked blue cone monochromacy.
(Clin Genet, 2016-01)The human X chromosome contains ∼ 1600 genes, about 15% of which have been associated with a specific genetic condition, mainly affecting males. Blue cone monochromacy (BCM) is an X-linked condition caused by a loss-of-function ...
