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QuASAR: quantitative allele-specific analysis of reads
TLDR
We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. Expand
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QuASAR‐MPRA: accurate allele‐specific analysis for massively parallel reporter assays
TLDR
We use QuASAR (quantitative allele‐specific analysis of reads) to analyze allele-specific signals in barcoded read counts data from MPRA. Expand
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Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity
The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast waterExpand
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Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding?
Large experimental efforts are characterizing the regulatory genome, yet we are still missing a systematic definition of functional and silent genetic variants in non-coding regions. Here, weExpand
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A high-throughput RNA-seq approach to profile transcriptional responses
TLDR
We have established a new two-step high-throughput RNA-seq approach: the first step consists of gene expression screening of a large number of conditions, while the second step focuses on deep sequencing of the most relevant conditions. Expand
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QuASAR-MPRA: Accurate allele-specific analysis for massively parallel reporter assays
Motivation The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variantsExpand
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A high-throughput RNA-seq approach to profile transcriptional responses
In recent years, different technologies have been used to measure genome-wide gene expression levels across many types of tissues and in response to in vitro treatments. However, a full understandingExpand
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Which genetic variants in DNase I sensitive regions are functional?
Ongoing large experimental characterization is crucial to determine all regulatory sequences, yet we do not know which genetic variants in those regions are non-silent. Here, we present a novelExpand
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