Volume 10 Issue 12, December 2013

Software can be like music, but an evaluation of software tools can involve some hard-to-play chords.

The ability to detect experimental effects is undermined in studies that lack power.

GFP targeted to satellite repeats via transcription activator–like effectors (TALEs) allows the imaging of nuclear dynamics early in mouse development.

Researchers define conditions in which human stem cells can be maintained in the ground state of pluripotency.

Long-read sequencing uncovers transcript features missed by short-read methods.

A genetically encoded sensor of ATP:ADP ratio reveals the energy status of living mammalian cells.

An imaging strategy based on telecommunications technology dramatically accelerates fluorescence microscopy.

Chromatin interaction dynamics are quantified using a modified ChIP method that measures cross-linking kinetics.

Laser-guided assembly of protein microscaffolds lets researchers construct multispecies cellular communities.

Bacteria's ability to withstand broad genomic editing offers a potential route toward more robust and useful genetically modified organisms.

Imaging with better than 200-nanometer resolution brings new subcellular-scale details into focus. Practitioners share how they weigh trade-offs in speed, resolution and phototoxicity.

RNA-seq is a recent and immensely popular technology for cataloging and comparing gene expression. Two papers from the international RGASP consortium report on large-scale competitions to identify the best algorithms for RNA-seq analysis, with surprising variability in the results.

This Perspective describes statistical measures commonly used to quantify whether nodes in biological networks have similar interaction profiles and discusses which indices are best suited for specific tasks.

The RGASP consortium compared 25 RNA-seq analysis programs in their ability to identify exons, reconstruct transcripts and quantify expression levels. Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge.

Authors compare RNA-seq aligners on mouse and human data sets using benchmarks such as alignment yield, splice junction accuracy and suitability for transcript reconstruction. The work highlights the strength of each program and discusses outstanding needs in RNA-seq analysis.

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.

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.

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.

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 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.

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

ATAC-seq queries the location of open chromatin, the binding of DNA-associated proteins and chromatin compaction at nucleotide resolution.

The Spinach2 RNA aptamer provides substantially improved imaging over its predecessor Spinach, enabling live-cell imaging of many tagged RNA species including toxic trinucleotide repeat–containing RNAs.

This paper describes a platform for high-throughput image-based profiling of human pluripotent stem cells (hPSCs). It is used to quantify differentiation bias and endogenous signaling levels in hPSC lines.

Genetically encoded sensors based on GFP enable the visualization of subcellular thermal changes noninvasively in intact cells.

Changes to protein interactomes as a result of mutations to the bait protein or addition of a pharmacological inhibitor are robustly monitored with affinity purification coupled with data-independent acquisition–based mass spectrometry and an automated data analysis pipeline. Also in this issue, Collins et al. describe a similar method.

Dynamic changes to the 14-3-3 protein interactome are robustly followed over time using affinity-purification data-independent analysis–based mass spectrometry. Also in this issue, Lambert et al. describe a similar method.