CRISPR standards
Share your thoughts on the editorial in our June issue. Read more
Share your thoughts on the editorial in our June issue. Read more
As is our tradition every year we have chosen a method, or in this case a set of methods, that have experienced rapid growth in the last years. This year’s choice of epitranscriptome analysis does not comprise a single technique but is based on advances in detecting, enriching and profiling base modifications on all RNA species. Read more
To understand disease one needs to understand the genetic variations that underlie it. Many tools exist that predict the deleteriousness of variants in the human genome; PolyPhen2, SIFT or CADD (combined annotation dependent depletion), to name only a few examples. On page 109 of our March issue Yuval Itan et al. present the mutation significance cutoff (MSC) to replace a global threshold for calling variants deleterious, often used for CADD scores, with a gene-level threshold. For MSC, as for any other variant prediction tool, it was important to validate the quality of the predictions with variants known to be deleterious. Established mutation databases are often used as ground truth to test the quality of prediction tools. MSC, for example, was validated against variants found in two large databases, HGMD and ClinVar. 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
The release of the 38th build of the human reference genome gets a well-deserved rock-star greeting by the scientific community. Read more
Stephen Quake responds to a blog post by Lior Pachter that analyzes data from his recent analysis of single-cell RNA sequencing methods published in Nature Methods. Read more
No more (trade) secrets … Read more
Nature Methods and Nature Biotechnology will host a live discussion on why histone modifications matter in health and disease. Read more
It is hard to overstate the importance of the human reference genome. In our editorial we want to acknowledge the value of this resource and at the same time ask what it would take to improve it further towards a reference that better reflects human diversity. Read more
For geneticists working on model organisms, the job is all about linking genotype and phenotype. But nowadays, these researchers are facing a historical reversal in terms of experimental limitations. As more microarrays and other genomic tools become available—and hopefully increasingly affordable—the genotyping part of the problem, which traditionally has been most time-consuming, is not that complicated anymore. The real bottleneck is now phenotyping. Read more