Articles in 2011

Targeting portions of the transcriptome for deep sequencing reveals very rare transcripts.

A new fluorination approach enables the synthesis of diverse PET probes.

A method uses single-molecule, real-time DNA sequencing to detect the modified base 5-hydroxymethylcytosine, an epigenetic mark recently suspected of having essential roles in genome regulation.

A brief description of tools for targeted cleavage and tailored modification of genomes is presented.

Microbial rhodopsins convert light into ion flux; in neurons, this can be used to control activity. New work shows that the opposite is also true: rhodopsins can be used to visualize neural activity.

Enhancement of pattern discovery through graphical representation of data.

A combination of chromosome conformation capture carbon copy (5C), modeling and automated imaging renders an empirical three-dimensional model of a bacterial genome.

Measuring single-molecule forces with light.

Synthetic clusters of membrane-bound droplets may provide a useful means for simulating tissues or transporting therapeutic payloads.

Adaptive technologies are helping researchers combine and organize experimental results.

Zinc-finger nuclease dimers are more difficult to engineer than single DNA-binding domains, but the development of new methods could help.

Precise ways to modify the genome arose from unexpected places. Monya Baker reports.

Engineered nucleases have advanced the field of gene therapy with the promise of targeted genome modification as a treatment for human diseases. Here we discuss why engineered nucleases are an exciting research tool for gene editing and consider their applications to a range of biological questions.

This Review covers recent technological developments to label and manipulate genes in selected populations of cells in Drosophila melanogaster. The Review is intended as a user guide to help with the selection of the best expression systems and clonal analysis techniques for developmental studies in the fly.

Authors present workflows for the analysis of metabolism phenotypes in mice and recommend analysis of covariance to asses body composition effects.

HHblits is a protein sequence search tool that works by iterative pairwise comparison of profile hidden Markov models. It outperforms existing tools in terms of speed, sensitivity and alignment quality.