Method of the Year 2016

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

Glycoscience: a tea party no longer

Later this year or early next Richard Cummings plans to launch The Human Glycome Project. It will happen during a workshop that he is currently organizing and which is open to scientists from near and far. The workshop is slated to be held at the Radcliffe Institute for Advanced Study at Harvard University. Also in the works is a Harvard-based center for glycoscience that reaches out to potential collaborators at all Boston-area universities and academic medical centers.  Read more

Understanding and documenting variation in human genomes

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

Genomics at top-speed: Q&A with Stephen Kingsmore

Stephen Kingsmore

Biomedical researcher Stephen Kingsmore is on the move. He has just taken on his new post running the new Rady Pediatric Genomics and Systems Medicine Institute, which is part of Rady Children’s Hospital in San Diego. He is leaving Children’s Mercy Hospital (CMH) in Kansas City where he founded the Center for Pediatric Genomic Medicine.  Read more

The ethics of self-organizing tissue

It becomes increasingly clear that stem cells are able to form remarkably complex structures in vitro, if they are handled right. In this month’s issue, two pieces raise the question of whether recent developments in methods for patterning embryonic stem cells in vitro raise potential ethical, regulatory or public perception concerns, or if they may do so in the future.  Read more

DIY Biolabs – and why they matter

When proponents of Do-it-yourself Biology  explain their motivation for getting involved in the movement  they often resort to colorful imagery. Take for example Patrick D’haeseleer who helps organize the Counter Culture Labs in the San Francisco Bay Area. He asks, “When the first village tamed fire, the neighboring village was freaking out. Should only the village elders be allowed to make fire or should we teach everybody?”  “Any new technology has risk, but it behooves us to have all citizens know how these technologies work and what the risks are. “ he continues, “ the technology needs to be democratized because it will dominate the 21th century.”  … Read more