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Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
TLDR
A suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data are described that include methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale.
GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
TLDR
The experiments define the most rigorous framework for genome-wide identification of RGN off-target effects to date and provide a method for evaluating the safety of these nucleases before clinical use.
Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in Rheumatoid Arthritis
TLDR
DNA methylation is a potential mediator of genetic risk for rheumatoid arthritis and is corrected for cellular heterogeneity by estimating and adjusting for cell-type proportions in blood-derived DNA samples and used mediation analysis to filter out associations likely to be a consequence of disease.
Engineered CRISPR-Cas9 nucleases with altered PAM specificities
TLDR
It is shown that the commonly used Streptococcus pyogenes Cas9 (SpCas9) can be modified to recognize alternative PAM sequences using structural information, bacterial selection-based directed evolution, and combinatorial design, and the feasibility of engineering a wide range of Cas9s with altered and improved PAM specificities is established.
Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing
TLDR
D dimeric RNA-guided FokI nucleases (RFNs) are described that can recognize extended sequences and edit endogenous genes with high efficiencies in human cells and are likely to be useful in applications that require highly precise genome editing.
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
TLDR
Substantial hypermethylation and hypomethylation of cytosine-phosphate-guanine island shores in nine human iPS cell lines as compared to their parental fibroblasts are found, suggesting two mechanisms for epigenetic reprogramming in iPS cells and cancer.
Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review
TLDR
A systematic review of articles published between 1990 and 2011 reporting at least one of 13 pathogens in children <5 years of age hospitalized with diarrhea found rotavirus caused more than half of all diarrheal deaths in children under 5 years in the world.
Diarrhea incidence in low- and middle-income countries in 1990 and 2010: a systematic review
TLDR
The results indicate that diarrhea incidence rates may be declining slightly, the total burden on the health of each child due to multiple episodes per year is tremendous and additional funds are needed to improve both prevention and treatment practices in low- and middle-income countries.
Reversible switching between epigenetic states in honeybee behavioral subcastes
TLDR
Reverting foragers back to nurses reestablished methylation levels for a majority of genes and provides the first evidence in any organism of reversible epigenetic changes associated with behavior.
EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma.
TLDR
Divergent chromatin-remodeling patterns repress tumor suppressors and mesenchymal lineage regulators while activating oncogenes and potential therapeutic targets, such as the kinase VRK1.
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