Connection Between Epigenome, Selective Mutability, Evolution, and Human Disease
Li, Harris et al., PLoS Genetics
Researchers at the Baylor College of Medicine and elsewhere propose a "connection between the epigenome, selective mutability, evolution, and human disease" based on the findings of their study on associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination mediated by low-copy repeats. "Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability," the Baylor-led team writes.
GPU-Powered Amber 11
Amber 11, the most recent release of the popular molecular dynamics software application, is now optimized to run on Nvidia GPUs. Depending on the type of simulations you're running, the Nvidia cards can accelerate tasks by up 100-fold over a traditional CPU-based implementation.
This latest version of AMBER is specifically designed to take advantage of Nvidia Tesla 20-series GPUs. According to Ross Walker, a professor at the San Diego Supercomputer Center, at the University of California, San Diego, and a principle Amber contributor, during the initial release of Amber 11, over a dozen users reported back speedups of 30-times on a range of bio-molecular simulations.
"With GPUs, we can now do most of our work at the desktop and that changes everything. Any research department looking to invest in computing resources to run AMBER should start by equipping every researcher with GPU-enabled workstations," Walker says.
For more info, you can visit Nvidia's Tesla Bio Workbench, which is now finally being referred to as a website and not an actual product.
Here's a video featuring Walker discussing Amber on GPUs from SC09: