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
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
Over the years, Nature Methods has published many methods to generate and analyze complex sequence data for microbial studies. We cover highlights from our papers below. Read more
Nature Methods has published popular analysis tools to make sense of the ever-increasing amount of high throughput (HTP) sequencing data. Some tools in this field have a short half life, due to pressure to always improve and innovate, others have staying power. Let’s look back over some of the highlights in our pages. Read more
Software plays an important role in scientific research, and published studies increasingly rely on custom software code developed by authors. This calls for better transparency in research articles and improved access to the software and code itself. Read more
A large proportion of original research published in Nature Methods relies to varying degress on custom algorithms and software developed by the authors. Here we provide guidance on our relevant material sharing and reporting policies. Read more
The scientist profiled in the February issue of Nature Methods (the Author File) is Janet Thornton, the director of the European Bioinformatics Institute. Read more
Nature Methods has long been an advocate of the value of community experiments (or competitions/challenges) to assess and compare the performance of algorithms and software tools. In 2008 we discussed the value of these competitions and advocated that they also be used to assess the performance of less widely used algorithms such as those used for single particle tracking. Such an experiment for assessing single particle tracking was run in 2012, although the results are still awaiting publication. Read more