-
Article
Open AccessAuthor Correction: An NF-κB-microRNA regulatory network tunes macrophage inflammatory responses
Li-Fan Lu and Alexander Y. Rudensky, who supplied miR-146a floxed mice used in this study, were inadvertently omitted from the author list in the originally published version of this Article. This has now been...
-
Article
Open AccessAn NF-κB-microRNA regulatory network tunes macrophage inflammatory responses
The innate inflammatory response must be tightly regulated to ensure effective immune protection. NF-κB is a key mediator of the inflammatory response, and its dysregulation has been associated with immune-rel...
-
Article
Open AccessTranscriptomic analysis of the role of RasGEF1B circular RNA in the TLR4/LPS pathway
Circular RNAs (circRNAs) have recently emerged as a large class of novel non-coding RNA species. However, the detailed functional significance of the vast majority of them remains to be elucidated. Most functi...
-
Protocol
Identification of Candidate Functional Elements in the Genome from ChIP-seq Data
ChIP-seq datasets provide a wealth of information for the identification of candidate regulatory elements in the genome. For this potential to be fully realized, methods for evaluating data quality and for dis...
-
Protocol
ChIP-seq for the Identification of Functional Elements in the Human Genome
Functional elements in the genome express their function through physical association with particular proteins: transcription factors, components of the transcription machinery, specific histone modifications,...
-
Article
Open AccessConservation and divergence of the histone code in nucleomorphs
Nucleomorphs, the remnant nuclei of photosynthetic algae that have become endosymbionts to other eukaryotes, represent a unique example of convergent reductive genome evolution in eukaryotes, having evolved in...
-
Article
Open AccessA deeper confusion
The Deeper Genome: Why there is more to the human genome than meets the eye, edited by John Parrington, (Oxford, United Kingdom: Oxford University Press), 2015. pp. xx + 272. ISBN:978-0-1...
-
Article
Open AccessA ratiometric-based measure of gene co-expression
Gene co-expression analysis has previously been based on measures that include correlation coefficients and mutual information, as well as newcomers such as MIC. These measures depend primarily on the degree o...
-
Article
Open AccessA comparative encyclopedia of DNA elements in the mouse genome
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 significant ways. To gain greater in...
-
Article
Open AccessFully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies
Chromatin immunoprecipitation coupled with DNA sequencing (ChIP-seq) is the major contemporary method for map** in vivo protein-DNA interactions in the genome. It identifies sites of transcription factor, co...
-
Article
Open AccessLandscape of transcription in human cells
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and th...
-
Article
An encyclopedia of mouse DNA elements (Mouse ENCODE)
To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed fo...
