Fine-mapping causal variants is challenging due to linkage disequilibrium and the lack 11 of interpretation of noncoding mutations. Existing fine-mapping methods do not scale 12 well on inferring multiple causal variants per locus and causal variants across multiple 13 related diseases. Moreover, many complex traits are not only genetically related but 14 also potentially share causal mechanism...

Growing mouse pluripotent stem cells in defined media with signaling inhibitors establishes a naive ground state different from that of cells grown in serum. Recently in Cell, Marks et al. (2012) reported differences in the transcriptional and epigenomic landscapes of naive and serum-exposed mouse stem cells that improve our understanding of the pluripotent ground state.

Prostate cancer (PC) is the second most frequently diagnosed cancer and the second leading cause of cancer deaths in man. The treatment of localized PC includes surgery or radiation therapy. In case of relapse after a definitive treatment or in patients with locally advanced or metastatic disease, the standard treatment includes the androgen-deprivation therapy (ADT). By reducing the levels of ...

Age is a well-established risk factor for chronic diseases. However, the cellular and molecular changes associated with aging processes that are related to chronic disease initiation and progression are not well-understood. Thus, there is an increased need to identify new markers of cellular and molecular changes that occur during aging processes. In this study, we use genome-wide DNA methylati...

Meagan J. McManus,2 Michael P. Murphy,3 and James L. Franklin1 1Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, Athens, Georgia 30602, 2Center of Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Colket Translational Research Building, Philadelphia, Pennsylvania 19104, and 3Medical Research Council Mitochondrial Biol...

Understanding the intratumoral heterogeneity of hepatocellular carcinoma is instructive for developing personalized therapy and identifying molecular biomarkers. Here we applied whole-exome sequencing to 69 samples from 11 patients to resolve the genetic architecture of subclonal diversification. Spatial genomic diversity was found in all 11 hepatocellular carcinoma cases, with 29% of driver mu...

The discovery of innate lymphoid cells (ILCs) with selective production of cytokines typically attributed to subsets of T helper cells forces immunologists to reassess the mechanisms by which selective effector functions arise. The parallelism between ILCs and T cells extends beyond these two cell types and comprises other innate-like T lymphocytes. Beyond the recognition of specialized effecto...

Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organisation of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various pl...

Arabidopsis thaliana (Arabidopsis) is ideally suited for studies of natural phenotypic variation. This species has also provided an unparalleled experimental system to explore the mechanistic link between genetic and epigenetic variation, especially with regard to cytosine methylation. Using high-throughput sequencing methods, genotype to epigenotype to phenotype observations can now be extende...

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIPseq) is widely used in biological research. ChIP-seq experiments yield many ambiguous tags that can be mapped with equal probability to multiple genomic sites. Such ambiguous tags are typically eliminated from consideration resulting in a potential loss of important biological information. We have developed a Gibbs sampli...