Systematic localization of common disease-associated variation in regulatory DNA
…, D Bates, RS Hansen, S Neph, PJ Sabo, S Heimfeld… - Science, 2012 - science.org
… of pathogenic cell types for Crohn’s disease, multiple sclerosis, and … Although Crohn’s
pathology has classically been associated … any prior knowledge about Crohn’s disease pathology. …
pathology has classically been associated … any prior knowledge about Crohn’s disease pathology. …
[HTML][HTML] Integrative analysis of 111 reference human epigenomes
The reference human genome sequence set the stage for studies of genetic variation and
its association with human disease, but epigenomic studies lack a similar reference. To …
its association with human disease, but epigenomic studies lack a similar reference. To …
[HTML][HTML] The accessible chromatin landscape of the human genome
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned
the discovery of all classes of cis-regulatory elements including enhancers, promoters, …
the discovery of all classes of cis-regulatory elements including enhancers, promoters, …
[HTML][HTML] A comparative encyclopedia of DNA elements in the mouse genome
…, T Kutyavin, E Haugen, D Dunn, AP Reynolds, S Neph… - Nature, 2014 - nature.com
The laboratory mouse shares the majority of its protein-coding genes with humans, making
it the premier model organism in biomedical research, yet the two mammals differ in …
it the premier model organism in biomedical research, yet the two mammals differ in …
[HTML][HTML] An expansive human regulatory lexicon encoded in transcription factor footprints
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage
by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting …
by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting …
BEDOPS: high-performance genomic feature operations
S Neph, MS Kuehn, AP Reynolds, E Haugen… - …, 2012 - academic.oup.com
The large and growing number of genome-wide datasets highlights the need for high-performance
feature analysis and data comparison methods, in addition to efficient data storage …
feature analysis and data comparison methods, in addition to efficient data storage …
[HTML][HTML] The human mitochondrial transcriptome
The human mitochondrial genome comprises a distinct genetic system transcribed as precursor
polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, …
polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, …
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
The orchestrated binding of transcriptional activators and repressors to specific DNA sequences
in the context of chromatin defines the regulatory program of eukaryotic genomes. We …
in the context of chromatin defines the regulatory program of eukaryotic genomes. We …
[HTML][HTML] Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification
…, X Peng, A Reynolds, R Sandstrom, S Neph… - Cell, 2012 - cell.com
… The observed differences in chromatin accessibility were associated with directionally
consistent changes in the nearest gene’s expression (Figure 1D). In contrast to the nearly identical …
consistent changes in the nearest gene’s expression (Figure 1D). In contrast to the nearly identical …
[HTML][HTML] Circuitry and dynamics of human transcription factor regulatory networks
The combinatorial cross-regulation of hundreds of sequence-specific transcription factors (TFs)
defines a regulatory network that underlies cellular identity and function. Here we use …
defines a regulatory network that underlies cellular identity and function. Here we use …