25 Result(s)
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Article
Andreas Gnirke
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Article
Open AccessCorrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
Cancer evolution is fueled by epigenetic as well as genetic diversity. In chronic lymphocytic leukemia (CLL), intra-tumoral DNA methylation (DNAme) heterogeneity empowers evolution. Here, to comprehensively st...
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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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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 AccessGenome-wide tracking of dCas9-methyltransferase footprints
In normal mammalian development cytosine methylation is essential and is directed to specific regions of the genome. Despite notable advances through map** its genome-wide distribution, studying the direct c...
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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 AccessTranscription factor binding dynamics during human ES cell differentiation
Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome-wid...
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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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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 AccessThe African coelacanth genome provides insights into tetrapod evolution
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar...
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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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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...
