Brief Communications in 2013

With an optimized protocol and unique molecular identifiers (UMIs) to tag individual transcripts, the mRNA complement of a single cell can be quantified on an absolute scale with almost no amplification bias.

A data-independent acquisition (DIA) mass spectrometry approach, ultradefinition (UD)MS^E, offers high reproducibility and improved proteome coverage over alternative DIA and data-dependent acquisition workflows.

Protein-lipid interactions can be systematically analyzed using a quantitative, multiplexed liposome microarray–based assay (LiMA).

For allele-specific expression and RNA editing studies, targeted RNA sequencing using microfluidic multiplexed PCR (mmPCR-seq) gives robust high-throughput measurements of allelic ratios across the dynamic range of gene expression, even for low-quantity or low-quality RNA.

A line-scanning method is applied to obtain onset times of fMRI responses in rats. The authors show that onset time of the fMRI response can be used to infer information about which cortical layers receive the connectivity input from other brain areas.

High-resolution isoelectric focusing (HiRIEF) of peptides followed by mass spectrometry analysis, combined with accurate peptide pI prediction, allows a reduction of protein database search space, enabling deep proteome coverage and the discovery of protein-coding loci in human and mouse.

A method and software tool, ResMap, for quantifying the local resolution across 3D electron cryo-microscopy density maps is reported.

Discrepancies between model prediction and experimental measurements enable molecular-level discovery with a whole-cell model of Mycoplasma genitalium.

A method and software for profiling microbial communities from shotgun sequence data uses universal single-copy marker sequences for accurate species-level assignment. The method can classify species lacking a reference genome sequence, making it possible to analyze the large fraction of unknown microbes in the human gut.

Amphipols, bicelles and nanodiscs are used to study intact membrane protein complexes by mass spectrometry, with better preservation of oligomeric complexes than traditional detergent micelles.

A simple method for preparing entirely monovalent quantum dots is described. These reagents can be targeted to protein and lipid tags and used as imaging probes in live cells.

A database of known drug-gene interactions, with information derived from many public sources, allows the identification of genes that are currently targeted by a drug and the membership of genes in a category, such as kinase genes, that have a high potential for drug development.

This paper introduces and benchmarks a statistic, the hierarchical interaction score, a statistic for measuring functional interactions between genes from large-scale data, and provides accessible methods for calculating this score.

pLogo visualizes sequence motifs according to their statistical significance rather than their frequency.

An approach combining the sampling methodology and energy function of Rosetta with the X-ray refinement methodology of Phenix enables improved low-resolution crystallographic refinement.

By fusing genomic data, the eXtasy tool effectively prioritizes rare human exomic sequence variants as causal disease variants.

The metagenomeSeq tool robustly detects the differential abundance of microbes in marker-based microbial surveys by tackling the problems of data sparsity and undersampling common to these data sets.

Smart-seq2 improves yield and length in single cell-derived cDNA libraries and uses off-the-shelf reagents.

By targeting calcium indicators to primary cilia, micrometer-long protrusions from the cellular plasma membrane, the authors measure Ca²⁺ signaling in these sensory organelles.

A system to control gene expression based on a destabilized form of Cre recombinase is reported. Drug-induced stabilization of Cre triggers recombination of 'floxed' alleles in the genome and is here used to genetically modify the activity of neural circuits in the mouse brain.