14 Result(s)
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Open AccessEnhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targe...
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Open AccessGel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling
Sequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale map** of DNA methylation have been employed, throughput has been a key limitation ...
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Open AccessEfficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We ap...
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RNA-Seq methods for imperfect samples: development, evaluation and applications
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RNA-Seq methods for imperfect samples: development, evaluation and applications
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Open AccessHybrid selection for sequencing pathogen genomes from clinical samples
We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as ...
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Open AccessAnalyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequen...
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Development and evaluation of RNA-seq methods
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Analyzing and minimizing bias in Illumina sequencing libraries
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Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes
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Open AccessStrand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
Recent studies in budding yeast have shown that antisense transcription occurs at many loci. However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been sugg...
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Open AccessTargeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by hybridization to oligo...
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Open AccessALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jum**) reads from five microbial genomes of varied GC composi...
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Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophilagenome
It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be de...
