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Article
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk ...
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Article
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics...
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Article
Production of interspecies somatic/pluripotent heterokaryons using polyethylene glycol (PEG) and selection by imaging flow cytometry for the study of nuclear reprogramming
Fusion of somatic cells to embryonic stem cells induces reprogramming of the somatic nucleus and can be used to study the effect of trans-acting factors from the pluripotent cell over the differentiated nucleu...
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Article
Open AccessChanges in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces
Clostridium perfringens is a Gram-positive anaerobic pathogen that causes multiple diseases in humans and animals. C. perfringens lack flagella but have type IV pili (TFP) and can glide on agar surfaces. When C. ...
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Article
Open AccessGenome-wide transcriptome analyses of develo** seeds from low and normal phytic acid soybean lines
Low phytic acid (lpa) crops are potentially eco-friendly alternative to conventional normal phytic acid (PA) crops, improving mineral bioavailability in monogastric animals as well as decreasing phosphate polluti...
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Article
Characterization of the hypothalamic transcriptome in response to food deprivation reveals global changes in long noncoding RNA, and cell cycle response genes
The hypothalamus integrates energy balance information from the periphery using different neuronal subtypes within each of the hypothalamic areas. However, the effects of prandial state on global mRNA, microRN...
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Article
Open AccessThe genome of woodland strawberry (Fragaria vesca)
The International Strawberry Sequencing Consortium reports the draft genome of the woodland strawberry (Fragaria vesca). The genome of this diploid species should serve as a reference genome for the Fragaria genu...
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Article
Open AccessDifferentially expressed alternatively spliced genes in Malignant Pleural Mesothelioma identified using massively parallel transcriptome sequencing
Analyses of Expressed Sequence Tags (ESTs) databases suggest that most human genes have multiple alternative splice variants. The alternative splicing of pre-mRNA is tightly regulated during development and in...
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Article
Open AccessTranscriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing
Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising t...
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Article
Open AccessErratum to: Gene expression and isoform variation analysis using Affymetrix exon arrays
Correction to Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J: Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics 2008, 9: 529.
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Article
Open AccessGene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays
Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are bec...
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Article
Open AccessThe balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not repr...
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Article
Open AccessIdentification of new genes in Sinorhizobium melilotiusing the Genome Sequencer FLX system
Sinorhizobium meliloti is an agriculturally important model symbiont. There is an ongoing need to update and improve its genome annotation. In this study, we used a high-throughput pyrosequencing approach to sequ...
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Article
Replacing cRNA targets with cDNA reduces microarray cross-hybridization
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Article
Using RNA sample titrations to assess microarray platform performance and normalization techniques
We have assessed the utility of RNA titration samples for evaluating microarray platform performance and the impact of different normalization methods on the results obtained. As part of the MicroArray Quality...
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Article
Evaluation of DNA microarray results with quantitative gene expression platforms
We have evaluated the performance characteristics of three quantitative gene expression technologies and correlated their expression measurements to those of five commercial microarray platforms, based on the ...
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Article
Better therapeutics through microarrays
DNA microarrays are an integral part of the process for therapeutic discovery, optimization and clinical validation. At an early stage, investigators use arrays to prioritize a few genes as potential therapeut...
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Chapter
Nmda-Activated Conductances Provide Short-Term Memory for Dendritic Spine Logic Computations
Numerical models of dendritic trees indicate that the nonlinear interaction of postsynaptic potentials in active spines can generate simple logic operations such as AND, OR and NAND gates. However, because the...
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Article
Quantum chaos
What are the special properties of strongly perturbed quantum systems when the corresponding classical mechanical systems exhibit chaotic behaviour? This is the central question of quantum chaos. Theoretical a...
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Chapter and Conference Paper
Chaotic ionization of highly excited hydrogen atoms
Recent experimental measurements of the microwave ionization of highly excited hydrogen atoms with principal quantum numbers ranging from n = 30 to 90 are well described by a classical treatment of the nonlinear ...
