Archive by category | Bioinformatics

Some resources and tools related to noncoding RNAs

In ‘Meet some code-breakers of noncoding RNAs,’ the technology feature in the February issue of Nature Methods, we speak with a few scientists about the path ahead in methods for characterize the noncoding RNAs.  Read more

Computable sugars: some computational resources in glycoscience

Glycoscience is sweet science

As glycoscience advances, labs will increasingly want to ask questions about glycosylation sites on a protein or the structure of a sugar, says Raja Mazumder, a bioinformatician at George Washington University. They might ask for example: are there glycosyltransferases that are expressed in liver but not in the heart, or, which ones are overexpressed by a factor of three in more than two cancers. Such questions require infrastructure building, he says, because right now there is no mechanism to allow such queries. But he and others are building such capabilities. Mazumder along with William York at the University of Georgia are starting to build a glycoscience informatics portal.  Read more

Light sheet imaging in Nature Methods

It was only a few months before Nature Methods was launched in October 2004 that Jan Huisken and Ernst Stelzer had published a paper in Science in which they used light sheet microscopy – what they called selective plane illumination microscopy or SPIM – to image fluorescence within transgenic embryos. Simplistically put, this century-old technique achieves optical sectioning by illuminating a sample through its width with a thin sheet of light. In the last decade, Nature Methods has published a steady stream of papers reporting developments in light-sheet imaging. Here are the highlights.  Read more