Eric Rynes
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View article: Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations
Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations Open
Functional genomics data, such as chromatin state maps, provide critical insights into biological processes, but are hard to navigate and interpret. We present Epilogos to address this challenge by offering a simple information-theoretic f…
View article: The ENCODE Uniform Analysis Pipelines
The ENCODE Uniform Analysis Pipelines Open
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across…
View article: Differences in nanoscale organization of regulatory active and inactive human chromatin
Differences in nanoscale organization of regulatory active and inactive human chromatin Open
Methodological advances in conformation capture techniques have fundamentally changed our understanding of chromatin architecture. However, the nanoscale organization of chromatin and its cell-to-cell variance are less studied. Analyzing g…
View article: The accessible chromatin landscape of the human genome
The accessible chromatin landscape of the human genome Open
DNaseI hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers, and locus control regions. Here we present…
View article: Global reference mapping of human transcription factor footprints
Global reference mapping of human transcription factor footprints Open
Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits 1 , but it remains challeng…
View article: Atlas and developmental dynamics of mouse DNase I hypersensitive sites
Atlas and developmental dynamics of mouse DNase I hypersensitive sites Open
Early mammalian development is orchestrated by genome-encoded regulatory elements populated by a changing complement of regulatory factors, creating a dynamic chromatin landscape. To define the spatiotemporal organization of regulatory DNA…
View article: Global reference mapping and dynamics of human transcription factor footprints
Global reference mapping and dynamics of human transcription factor footprints Open
Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits 1 , yet it remains challeng…
View article: Index and biological spectrum of accessible DNA elements in the human genome
Index and biological spectrum of accessible DNA elements in the human genome Open
DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA and harbor disease- and phenotypic trait-associated genetic variation. We established high-precision maps of DNase I hypersensitive sites from 733 human biosamples e…
View article: Index and biological spectrum of accessible DNA elements in the human genome
Index and biological spectrum of accessible DNA elements in the human genome Open
Data associated with the manuscript titled "Index and biological spectrum of accessible DNA elements in the human genome" https://doi.org/10.1101/822510 Code repositories for these data are available here: https://github.com/Altius/Index h…
View article: Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma
Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma Open
Integrated transcriptomic and epigenomic analysis of matched tumor and normal tissues from even a small number of primary patient samples revealed remarkably convergent shared regulatory landscapes. Several transcription factors appear to …
View article: Cryptic Promoter Activation Drives <i>POU5F1</i> (<i>OCT4</i>) Expression in Renal Cell Carcinoma
Cryptic Promoter Activation Drives <i>POU5F1</i> (<i>OCT4</i>) Expression in Renal Cell Carcinoma Open
Transcriptional dysregulation drives cancer formation but the underlying mechanisms are still poorly understood. As a model system, we used renal cell carcinoma (RCC), the most common malignant kidney tumor which canonically activates the …