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
Supercomputers open up new horizons, offering the possibility of discovering new ways to understand life’s complexity
Their very names sound like dinosaurs. Teracomputers. Petacomputers. These are, in fact, the dinosaurs of the digital world—monstrous, hungry and powerful. But unlike the extinct...
Oct, 01, 2006
Public databases impact not only how research is done but what kind of research is done in the first place.
The setting: a scientific conference in January 2008. The speaker, Bruce Ponder, MD, PhD, an oncology professor at Cambridge University, is describing a previously unknown link between a particular...
Oct, 01, 2008
Metagenomes give a picture of the genes driving metabolic processes important to bacterial growth and survival in different environments.
We know they are there, but most microbial denizens of deep oceans, sea floor vents, even our own intestines, remain a mystery. Because most microbes won’t grow in the lab, researchers have few...
Jul, 01, 2008
A combination of genomics data and molecular dynamics modeling is sufficient to predict protein complex structure
The zone where two proteins interact presents a possible target for drug design. But identifying possible drugs requires a detailed understanding of the interface between the proteins. Computer...
Apr, 01, 2010
A pair of challenges increasingly threaten the success of bioinformatics research: convincing biologists to share their data and convincing computational colleagues to share their code. Many of us...
Jul, 01, 2006
Predicting protein localization
Joe works in a factory; Jane works in a hospital; protein X works in the Golgi apparatus. Just as one might guess a worker’s job by knowing where he or she is employed, biologists can guess a...
Apr, 01, 2006
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
Hi-C technique looks at chromosomes at unprecedented level of resolution
Try taking a human hair as long as Manhattan and cramming it—unsnarled—inside a marble. This is the challenge faced by a 2-meter-long strand of DNA as it folds into its compact array of...
Jan, 01, 2010
The fittest organisms survive and produce offspring, according to the Darwinian theory of natural selection. And the changes that make an organism fit happen at the molecular level: when genes mutate...
Oct, 01, 2007