Using computational models, researchers are gaining traction toward understanding what makes a stem cell a stem cell; how gene expression drives stem cell differentiation; why studying stem cell heterogeneity is important; and, ultimately, how stem cells control their fate.
To the casual observer, stem cells offer the almost magical promise of—Voila!—turning into exactly the kind of cell needed to repair an injured spinal cord or replace a damaged organ. And...
Apr, 01, 2010
Decades of steady progress in pharmacogenetics have unearthed hundreds of associations between genes and drug response. But the field has to solve some theoretical and practical issues before it can deliver on the promise of personalized drug therapy.
As algorithms go, it’s deceptively simple. Just add together eight weighted pieces of patient information—age, height, weight, race, data about two genes, and a pair of clinical...
Jul, 01, 2009
Kim Branson of Vertex Pharmaceuticals uses OpenMM as the GPU accelerator for Yank, a program for quickly estimating molecular binding affinities that he’s building with collaborators from Pande’s lab.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Kim Branson, PhD, a research scientist in the modeling and simulation group at Vertex...
Oct, 01, 2009
Using Rosetta@Home, a program that runs on the personal computers of 150,000 volunteers worldwide, David Baker’s team predicted the structure of a 112-amino-acid protein from scratch.
When nature folds an amino acid sequence into a protein, it usually knows that just one conformation is the right one. But when a computer tries to do the same thing, it often predicts multiple...
Jan, 01, 2008
Having developed detailed and sophisticated models of both E. Coli and human metabolism, researchers can begin to build toward a whole cell model that will be useful for the study of human health and disease.
If biologists really understood the functioning of the genome, they could in principle recreate it in silico. Instead of a choreographed swirl of molecules inside a living cell, electrons...
Oct, 01, 2008
The complexity and variability of aging itself, along with the fragmented nature of researchers’ current understanding of aging, call for tools that can help scientists dig through mounds of data to find often subtle connections.
Jeanne Louise Calment of Arles, France rode a bicycle until she was 100 years old. When she gave up smoking at age 117, her doctor suspected it was out of pride. (She couldn’t see well enough...
Apr, 01, 2008
Current methods of tracking the flu all come with a bit of a time lag—which is unfortunate when trying to monitor for potential pandemics like today’s swine flu crisis. There is a faster...
Jul, 01, 2009
Cultured brain cells draw pictures
MEART’s creators link the basic components of the brain (isolated neurons) to a mechanical body (robotic arms) through the mediation of a digital processing engine across the Internet. The goal...
Oct, 01, 2010
Upcoming biocomputing conferences
The 6th Annual International Conference on Computational Systems Bioinformatics (CSB2007) coordinated by the Life Sciences Society.
WHAT: This conference is designed for any scientist interested in...
Jul, 01, 2007
Classifying variability of gene expression
Genetically identical cells or organisms grown in identical environments will differ phenotypically, because—even with a common script—gene expression is inherently variable, or noisy....
Apr, 01, 2006