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RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
TLDR
It is found that the Illumina sequencing data are highly replicable, with relatively little technical variation, and thus, for many purposes, it may suffice to sequence each mRNA sample only once (i.e., using one lane). Expand
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
TLDR
A method is presented for transcriptome-wide m(6)A localization, which combines m( 6)A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) and reveals insights into the epigenetic regulation of the mammalian transcriptome. Expand
An integrated map of structural variation in 2,504 human genomes
TLDR
An integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which are constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations are described. Expand
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
TLDR
An R package that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and Hydroxymethylation sequencing experiments is described, which includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNAmethylation. Expand
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
TLDR
It is demonstrated that increasing the number of replicate samples significantly improves detection power over increased sequencing depth, and array-based methods adapted to RNA-seq data perform comparably to methods designed forRNA-seq. Expand
Extensive sequencing of seven human genomes to characterize benchmark reference materials
TLDR
A large, diverse set of sequencing data for seven human genomes is described; five are current or candidate NIST Reference Materials and two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry are described. Expand
Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome
TLDR
m6A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) is developed and used to demonstrate that antibodies to m6A can induce specific mutational signatures at m 6A residues after ultraviolet light–induced antibody-RNA cross- linking and reverse transcription. Expand
Assembly and diploid architecture of an individual human genome via single-molecule technologies
TLDR
This work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality. Expand
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium
TLDR
The complete SEQC data sets, comprising >100 billion reads, provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings, and measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. Expand
Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells
TLDR
It is shown that viral infection triggers a massive increase in m6A in both host and viral mRNAs, which identifies a new mechanism for the control of HIV-1 replication and its interaction with the host immune system. Expand
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