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153
RESEARCH ARTICLE Comparative high-throughput transcriptome sequencing and development of SiESTa, the
"... Background: The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently deve ..."
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developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing
A Method Enabling High-Throughput Sequencing of Human Cytomegalovirus Complete Genomes from Clinical Isolates
"... Human cytomegalovirus (HCMV) is a ubiquitous virus that can cause serious sequelae in immunocompromised patients and in the developing fetus. The coding capacity of the 235 kbp genome is still incompletely understood, and there is a pressing need to characterize genomic contents in clinical isolates ..."
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isolates. In this study, a procedure for the high-throughput generation of full genome consensus sequences from clinical HCMV isolates is presented. This method relies on low number passaging of clinical isolates on human fibroblasts, followed by digestion of cellular DNA and purification of viral DNA
Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data. PLoS ONE 9(6): e98855
, 2014
"... Linkage maps enable the study of important biological questions. The construction of high-density linkage maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. However, the marker number explosio ..."
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Cited by 4 (2 self)
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explosion and genotyping errors from NGS data challenge the computational efficiency and linkage map quality of linkage study methods. Here we report the HighMap method for constructing high-density linkage maps from NGS data. HighMap employs an iterative ordering and error correction strategy based on a k
GeneScreen: a program for high-throughput mutation detection in DNA sequence electropherograms
"... Background While massively parallel DNA sequencing methods continue to evolve rapidly, the benchmark technique for detection and verification of rare (particularly disease-causing) sequence variants remains four-colour dye-terminator sequencing by capillary electrophoresis. The high throughput and l ..."
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-nucleotide polymorphism detection, the identification, verification and annotation of very rare sequence variants remains a rather labour-intensive process for which few software aids exist. Aim To provide a freely available, intuitive software application for highly efficient mutation screening of large sequence batches
A cell-free fluorometric high-throughput screen for inhibitors of Rtt109-catalyzed histone acetylation. PLoS One 2013
"... The lysine acetyltransferase (KAT) Rtt109 forms a complex with Vps75 and catalyzes the acetylation of histone H3 lysine 56 (H3K56ac) in the Asf1-H3-H4 complex. Rtt109 and H3K56ac are vital for replication-coupled nucleosome assembly and genotoxic resistance in yeast and pathogenic fungal species suc ..."
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such as Candida albicans. Remarkably, sequence homologs of Rtt109 are absent in humans. Therefore, inhibitors of Rtt109 are hypothesized as potential and minimally toxic antifungal agents. Herein, we report the development and optimization of a cell-free fluorometric high-throughput screen (HTS) for small
DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches
"... The genetic analysis of faecal material represents a relatively non-invasive way to study animal diet and has been widely adopted in ecological research. Due to the heterogeneous nature of faecal material the primary obstacle, common to all genetic approaches, is a means to dissect the constituent D ..."
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DNA sequences. Traditionally, bacterial cloning of PCR amplified products was employed; less common has been the use of species-specific quantitative PCR (qPCR) assays. Currently, with the advent of High-Throughput Sequencing (HTS) technologies and indexed primers it has become possible to conduct
data
"... Background: Differential RNA sequencing (dRNA-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (TSS) in particular. Hitherto, dRNA-seq data were analyzed by visualizing the sequenc ..."
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Background: Differential RNA sequencing (dRNA-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (TSS) in particular. Hitherto, dRNA-seq data were analyzed by visualizing
Research Article IROme, a NewHigh-Throughput Molecular Tool for the Diagnosis of Inherited Retinal Dystrophies
, 2012
"... Copyright © 2013 Daniel F. Schorderet et al. is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. e molecular diagnosis of retinal dystrophi ..."
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-linked genes and three candidate genes (942 exons). Pyrosequencing was performed on a Roche 454GS Junior benchtop high-throughput sequencing platform. In total, 23 patients affected by retinitis pigmentosa were analyzed. Per patient, 39.6Mb were generated, and 1111 sequence variants were detected on average
Magnet: Robust and Efficient Collection through Control and Data Plane Integration
"... Despite being a core networking primitive, collection protocols today often suffer from poor reliability (e.g., 70%) in practice, and heavily used protocols have never been evaluated in terms of communication efficiency. Using detailed experimental studies, we describe three challenges that cause ex ..."
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Despite being a core networking primitive, collection protocols today often suffer from poor reliability (e.g., 70%) in practice, and heavily used protocols have never been evaluated in terms of communication efficiency. Using detailed experimental studies, we describe three challenges that cause
doi:10.1093/comjnl/bxp026 A Digest and Pattern Matching-Based Intrusion Detection Engine
, 2008
"... Intrusion detection/prevention systems (IDSs/IPSs) heavily rely on signature databases and pattern matching (PM) techniques to identify network attacks. The engines of such systems often employ traditional PM algorithms to search for telltale patterns in network flows. The observations that real-wor ..."
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digests or fingerprints for attack signatures during its programming phase. In its querying phase, the framework quickly identifies attack-free connections by transforming input traffic into its fingerprint space and matching its digest against those of attack signatures. If the legitimacy of a stream
Results 1 - 10
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153
