Benchmarking DNA methylation assays in a reef-building coral. Published: October, 2020 Abstract:
Interrogation of chromatin modifications, such as DNA methylation, has the potential to improve forecasting and conservation of marine ecosystems. The standard method for assaying DNA methylation (whole genome bisulphite sequencing), however, is c... Read more »
SMaSH: Sample matching using SNPs in humans. Published: December, 2019 Abstract:
BACKGROUND: Inadvertent sample swaps are a real threat to data quality in any medium to large scale omics studies. While matches between samples from the same individual can in principle be identified from a few well characterized single nucleotid... Read more »
Role of gene body methylation in acclimatization and adaptation in a basalmetazoan. Published: December, 2018 Abstract:
Gene body methylation (GBM) has been hypothesized to modulate responses to environmental change, including transgenerational plasticity, but the evidence thus far has been lacking. Here we show that coral fragments reciprocally transplanted betwee... Read more »
Evolutionary Consequences of DNA Methylation in a Basal Metazoan. Published: September, 2016 Abstract:
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylat... Read more »
Genic DNA methylation drives codon bias in stony corals Published: May, 2016 Abstract:
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein coding sequences is particularly puzzling, because methylat... Read more »
∆ DNMT3B4-del Contributes to Aberrant DNA Methylation Patterns in Lung Tumorigenesis Published: October, 2015 Abstract:
Aberrant DNA methylation is a hallmark of cancer but mechanisms contributing to the abnormality remain elusive. We have previously shown that ∆DNMT3B is the predominantly expressed form of DNMT3B. In this study, we found that most of the lung canc... Read more »
Development of a unique epigenetic signature during in vivo Th17 differentiation. Published: January, 2015 Abstract:
Activated naive CD4(+) T cells are highly plastic cells that can differentiate into various T helper (Th) cell fates characterized by the expression of effector cytokines like IFN-γ (Th1), IL-4 (Th2) or IL-17A (Th17). Although previous studies hav... Read more »
Mining for viral fragments in methylation enriched sequencing data Published: January, 2015 Abstract:
Most next generation sequencing experiments generate more data than is required for the experimental set up. For example, methyl-CpG binding domain (MBD) affinity purification based sequencing is often used for DNA-methylation profiling, but up to... Read more »
Strategies for validation and testing of DNA methylation biomarkers. Published: December, 2014 Abstract:
DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and thera... Read more »
Alterations of the lung methylome in allergic airway hyper-responsiveness. Published: April, 2014 Abstract:
Asthma is a chronic airway disorder characterized by recurrent attacks of breathlessness and wheezing, affecting 300 million people around the world (available at: www.who.int). To date, genetic factors associated with asthma susceptibility have b... Read more »
Differential programming of B cells in AID deficient mice. Published: July, 2013 Abstract:
The Aicda locus encodes the activation induced cytidine deaminase (AID) and is highly expressed in germinal center (GC) B cells to initiate somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes. Besides thes... Read more »
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Published: May, 2011 Abstract:
Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression and maintaining cellular identity. Recently, TET1 was found to hydroxylate the methyl group of mC, converting it to 5-hydroxym... Read more »
Combining genomic and proteomic approaches for epigenetics research. Abstract:
Epigenetics is the study of changes in gene expression or cellular phenotype that do not change the DNA sequence. In this review, current methods, both genomic and proteomic, associated with epigenetics research are discussed. Among them, chromati... Read more »
