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Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila
TLDR
Examination of piwi-interacting RNAs associated with each Drosophila Piwi protein finds that Piwi and Aubergine bind RNAs that are predominantly antisense to transposons, whereas Ago3 complexes contain predominantly sense piRNAs. Expand
Transcriptional regulatory code of a eukaryotic genome
TLDR
An initial map of yeast's transcriptional regulatory code is constructed by identifying the sequence elements that are bound by regulators under various conditions and that are conserved among Saccharomyces species. Expand
Integrative analysis of 111 reference human epigenomes
TLDR
It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Expand
GENCODE: the reference human genome annotation for The ENCODE Project.
TLDR
This work has examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites, and over one-third of GENCODE protein-Coding genes aresupported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. Expand
The Genotype-Tissue Expression (GTEx) project
TLDR
The Genotype-Tissue Expression (GTEx) project is described, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues. Expand
ChromHMM: automating chromatin-state discovery and characterization
TLDR
ChromHMM is developed, an automated computational system for learning chromatin states, characterizing their biological functions and correlations with large-scale functional datasets, and visualizing the resulting genome-wide maps of chromatin state annotations. Expand
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
TLDR
HaploReg is presented, a tool for exploring annotations of the non-coding genome among the results of published GWAS or novel sets of variants, and will be useful to researchers developing mechanistic hypotheses of the impact of non-Coding variants on clinical phenotypes and normal variation. Expand
Sequencing and comparison of yeast species to identify genes and regulatory elements
TLDR
A comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species, which inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. Expand
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
TLDR
It is demonstrated that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFκB, Sox2, Oct4 (also known as Pou5f1) and Nanog, defining a unique collection of functional linc RNAs that are highly conserved and implicated in diverse biological processes. Expand
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
TLDR
The landscape of gene expression across tissues is described, thousands of tissue-specific and shared regulatory expression quantitative trait loci (eQTL) variants are cataloged, complex network relationships are described, and signals from genome-wide association studies explained by eQTLs are identified. Expand
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