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A statistical method and software yields accurate predictions of sequencing library complexity on the basis of initial shallow sequencing surveys, allowing robust estimates of how deep to sequence for adequate coverage.
iceFISH labels nascent RNA along a single chromosome, revealing chromosome territories and potential regulatory mechanisms working at the chromosome scale.
TAL effector (TALE)–based transcription factors robustly induce transcription when targeted to DNase I hypersensitive sites in a gene promoter in human cells, even more so when several TALE transcription factors work in synergy at the same promoter. Tunable expression of endogenous genes will be of great interest in basic research and in synthetic biology.
The combination of several TALE-TFs that bind the same gene promoter at different positions induces high and tunable activation, even in heterochromatic genes, and offers the promise of engineering complex synthetic gene expression systems.
A technique based on the fusion of zebrafish blastulae, which leads to conjoined organisms that share a common blood stream, or parabiosis, is described. This procedure permits the in vivo visualization of hematopoietic cell migration and homing to niches and peripheral tissues in zebrafish parabiotes of different genetic backgrounds.
A modular optogenetic method for higher-order protein oligomerization uses a single cryptochrome 2-based fusion for rapid, reversible and tunable oligomerization in response to blue light. Inducible aggregation can be used to specifically activate different signaling pathways.
This microRNA target–prediction program, based on biophysical parameters of mRNA and microRNA, outperforms current programs when it comes to finding noncanonical sites.
Highly accurate and sensitive predictions of RNA editing sites can be obtained using RNA sequencing data from multiple individuals or species, without relying on matched genomic DNA sequence. Reanalyzing existing RNA sequencing data in this way greatly expands the catalog of human protein recoding events.
A systematic evaluation of parameters that affect short amplicons sequenced on Illumina platforms provides guidelines for how to eliminate erroneous reads and improve data interpretation.
Improved mass spectrometry–based detection of low-abundance proteins in complex proteomes is made possible with a method to selectively digest and deplete high-abundance proteins.
A method is reported for optical trap calibration on lipid droplets in cell extract. It should permit quantitative studies of motor proteins in a more natural context than on beads.
The eXpress software uses an online algorithm to accurately assign ambiguously mapping sequence reads for real-time read abundance estimation, thereby dramatically enhancing the efficiency of any analysis that uses large-scale sequencing.
Open-source software that allows biologists to create a variety of behavior classifiers for automatically annotating video of behaving animals is presented. The program, called JAABA, uses state-of-the-art machine-learning methods and is applicable to tracking data from different organisms, including mice and adult and larval Drosophila.