19 Result(s)
within
Andreas Gnirke
Life Sciences
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Article
Capturing sequence diversity in metagenomes with comprehensive and scalable probe design
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nuc...
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Article
Author Correction: Global delay in nascent strand DNA methylation
Following online publication of this article, the Gene Expression Omnibus records corresponding to accession codes GSM2406773, MN-d6, and GSM2406772, MN-d14, listed in the data availability statement were dele...
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Open AccessTargeted bisulfite sequencing of the dynamic DNA methylome
The ability to measure DNA methylation precisely and efficiently continues to drive our understanding of this modification in development and disease. Whole genome bisulfite sequencing has the advantage of the...
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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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Article
Correction: Corrigendum: Comparative analysis of RNA sequencing methods for degraded or low-input samples
Nat. Methods 10, 623–629 (2013); published online 19 May 2013; corrected after 2 December 2013 In the version of this article initially published, in the Online Methods “RNase H libraries” section, the sentenc...
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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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Article
Evaluation of bacterial ribosomal RNA (rRNA) depletion methods for sequencing microbial community transcriptomes
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Article
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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Article
Correction: Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
Nat. Biotechnol. 28, 503–510 (2010); published online 02 May 2010; corrected after print 9 July 2010 In the version of this article initially published, the fourth sentence in the Online Methods section “RNA e...
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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...
