12 Result(s)
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Article
Nicholas F. Lahens
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Challenges and best practices in omics benchmarking
Technological advances enabling massively parallel measurement of biological features — such as microarrays, high-throughput sequencing and mass spectrometry — have ushered in the omics era, now in its third d...
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Open AccessDiurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank
Many chronic disease symptomatologies involve desynchronized sleep-wake cycles, indicative of disrupted biorhythms. This can be interrogated using body temperature rhythms, which have circadian as well as slee...
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Open AccessRNA splicing analysis using heterogeneous and large RNA-seq datasets
The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such d...
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Open AccessCAMPAREE: a robust and configurable RNA expression simulator
The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms. Simulated datasets are an invaluable tool to accura...
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Open AccessMOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis
The effects of confounding factors on gene expression analysis have been extensively studied following the introduction of high-throughput microarrays and subsequently RNA sequencing. In contrast, there is a l...
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Open AccessComparative evaluation of full-length isoform quantification from RNA-Seq
Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA...
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Open AccessA circadian clock regulates efflux by the blood-brain barrier in mice and human cells
The blood-brain barrier (BBB) is critical for neural function. We report here circadian regulation of the BBB in mammals. Efflux of xenobiotics by the BBB oscillates in mice, with highest levels during the act...
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Open AccessComparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input
Library preparation is a key step in sequencing. For RNA sequencing there are advantages to both strand specificity and working with minute starting material, yet until recently there was no kit available enab...
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Open AccessA Pilot Characterization of the Human Chronobiome
Physiological function, disease expression and drug effects vary by time-of-day. Clock disruption in mice results in cardio-metabolic, immunological and neurological dysfunction; circadian misalignment using f...
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Open AccessA comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression
Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analy...
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Open AccessThe Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression
Benjamin Voight and colleagues report the annotated genome of the golden orb-weaver spider. They describe 28 spider silk genes (spidroins), characterize their expression in distinct silk gland types and identi...
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Open AccessIVT-seq reveals extreme bias in RNA sequencing
RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction meth...
