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SeqControl uses 15 quality metrics of high-throughput sequencing experiments to predict how much sequencing is needed to reach a desired depth of coverage.
The specificity of exogenous sequence insertion into the genome of human cells following designer nuclease–mediated cleavage is substantially affected by the nature of the donor template, the paper reports.
An adaptive optics method using multiplexed light measurement and modulation in multiple pupil segments improves structural and functional in vivo imaging over large volumes in strongly scattering mouse brain with only a single aberration correction.
A 'protein quake' is directly monitored on the picosecond timescale using the method of time-resolved wide-angle X-ray scattering at an X-ray free-electron laser.
Single guide RNAs driven by a T7 promoter target Cas9 to two endogenous loci, leading to fast and efficient genome editing in the malaria parasite P. falciparum.
Integration of genome visualization with Bioconductor-based analysis tools allows rapid and interactive analysis of genomes, transcriptomes and epigenomes.
High-resolution, three-dimensional protein structures can be solved using MicroED, an electron diffraction method that uses three-dimensional microcrystals. An improved MicroED data collection approach described here increases data quality and resolution and extends its broad applicability.
To find causative mutations in rare disorders, the Phen-Gen software combines disease symptoms and sequencing data with prior knowledge about the gene.
The compositional heterogeneity of proteoliposome reconstitution can skew the results of ensemble-average measurements of transmembrane protein structure and function. These compositional heterogeneities can be exploited, however, with a single-proteoliposome, high-content screening method.
An open-source library of analytical tools for mapping large-scale patterns of brain activity using cluster computing finds structure in two-photon imaging data from mouse and whole-brain light-sheet functional imaging data from behaving larval zebrafish. Vladimirov et al., also in this issue, describes the light-sheet functional imaging system used here.
This paper describes immunocompromised rag2 mutant zebrafish, which allow efficient and robust cell transplantations in adult zebrafish, thereby facilitating stem cell, cancer and regeneration research.
This paper describes automated methods for the accurate segmentation and tracking of tens of thousands of nuclei in time-lapse imaging data of developing embryos.
A series of technical and analytical improvements to light sheet microscopy is described, permitting dynamic imaging of the beating zebrafish heart at cellular resolution.
Application of the founder principle from population genetics to variant selection after recombineering allows the isolation of rare unselected recombinants.
The combination of selective 2'-hydroxyl acylation of RNA with high-throughput sequencing of the transcribed cDNA allows identification of chemically modified sites as mutations in the sequence that then yield highly accurate secondary-structure models of the RNA.
Ligand nanocalipers made using DNA nanotechnology are used to display ephrin-A5 at well-defined spatial intervals to study how nanoscale ligand spacing affects EphA2 receptor activation in breast cancer cells.
A synthetic library of nucleosomes, each with a DNA-barcode characteristic for a defined post-translational modification (PTM), is used to probe PTM-based recruitment and modulation of histone mark readers and writers.