Articles in 2011

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.

The Splitread algorithm uses a split-read strategy to detect structural variants and small insertions and deletions (indels) in whole-exome and whole-genome sequence datasets at high sensitivity. It maps the breakpoints at single-base-pair resolution, even in low-complexity regions, and can detect novel processed pseudogenes.

In this Analysis, the authors directly experimentally compare microbial opsins used for the control of neural activity. They extract essential principles and key parameters that can help end users with the design and interpretation of optogenetic experiments and guide tool developers in the characterization of future tools.

An efficient haplotype-estimation algorithm that features linear complexity allows the rapid and accurate phasing of diploid genomes from trios, duos and unrelated samples.

The controlled overexpression or knockdown of gene expression in primary organoid cultures of mouse endodermal epithelia is described. This should enable ex vivo studies of mammalian gene function.

Bayesian analysis of fluorophore blinking and bleaching in image data collected from simple xenon arc lamp illumination and high-speed wide-field imaging of standard fluorescent proteins allows localization microscopy in living cells with a 50 nm spatial and a 4 s temporal resolution.

In this paper, the authors report GFP reconstitution across synaptic partners (GRASP) adapted for synapse visualization in the mammalian brain.

Site-directed seamless modification of bacterial artificial chromosomes is enhanced more than tenfold in efficiency by improving the counterselection step. A set of plasmids and oligonucleotide design software also make this E. coli recombineering approach markedly faster and easier.

A self-imaging Petri dish monitors cell cultures as they grow in the incubator.

Researchers pave the way to high-throughput studies of intact protein isoforms.

Long noncoding RNA interactions with chromatin can be mapped genome-wide using biotinylated tiling oligos.

Fusing light-activated proteins for precise optogenetic control

Chromatin immunoprecipitation and yeast one-hybrid systems are complementary approaches to identify protein-DNA interactions. Improvements to these methods now make them more versatile and high-throughput, and should lead to the generation of rich datasets for the study of gene regulation.