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A Novel Genetic Score Approach Using Instruments to Investigate Interactions between Pathways and Environment: Application to Air Pollution
(Public Library of Science, 2014)
Air pollution has been associated with increased systemic inflammation markers. We developed a new pathway analysis approach to investigate whether gene variants within relevant pathways (oxidative stress, endothelial ...
Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs
(Public Library of Science, 2014)
The CRISPR/Cas9 system has been implemented in a variety of model organisms to mediate site-directed mutagenesis. A wide range of mutation rates has been reported, but at a limited number of genomic target sites. To uncover ...
Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells
(Public Library of Science, 2014)
Genome-wide association studies (GWAS) and subsequent dense-genotyping of associated loci identified over a hundred single-nucleotide polymorphism (SNP) variants associated with the risk of rheumatoid arthritis (RA), type ...
Genetic Diversity in the Interference Selection Limit
(Public Library of Science, 2014)
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical ...
An Insulin-to-Insulin Regulatory Network Orchestrates Phenotypic Specificity in Development and Physiology
(Public Library of Science, 2014)
Insulin-like peptides (ILPs) play highly conserved roles in development and physiology. Most animal genomes encode multiple ILPs. Here we identify mechanisms for how the forty Caenorhabditis elegans ILPs coordinate diverse ...
Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance
(Public Library of Science, 2016)
The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to ...
Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi
(Public Library of Science, 2016)
Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the ...
Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution
(Public Library of Science, 2016)
The vast majority of mutations in the exome of cancer cells are passengers, which do not affect the reproductive rate of the cell. Passengers can provide important information about the evolutionary history of an individual ...
Angiotensin II Induced Cardiac Dysfunction on a Chip
(Public Library of Science, 2016)
In vitro disease models offer the ability to study specific systemic features in isolation to better understand underlying mechanisms that lead to dysfunction. Here, we present a cardiac dysfunction model using angiotensin ...
Missense Mutations Allow a Sequence-Blind Mutant of SpoIIIE to Successfully Translocate Chromosomes during Sporulation
(Public Library of Science, 2016)
SpoIIIE directionally pumps DNA across membranes during Bacillus subtilis sporulation and vegetative growth. The sequence-reading domain (γ domain) is required for directional DNA transport, and its deletion severely impairs ...