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The prix fixe strategy and software uses cofunction networks to identify causal genes among candidate genes in disease-associated loci from genome-wide association studies.
Here, the authors present an approach for the simultaneous optogenetic manipulation and recording of neural activity at cellular resolution using two-photon microscopy and apply their strategy in the mouse barrel cortex.
QTI-seq (quantitative translation initiation sequencing) maps the position of the start codon and thus allows the determination of initiation efficiency in response to various stimuli, such as starvation, in cell culture and in vivo.
Software to model, pack and integrate biological structures at the scale of macromolecular complexes and cellular organelles is described. It is applied in several contexts, including hypothesis generation and testing.
An improved genetically encoded red calcium sensor enables the monitoring of neuronal activity in cell culture and in vivo. R-CaMP2 has fast kinetics and a high affinity to calcium and can follow action potentials up to 40 Hz.
This paper presents FpClass, a prediction method for physical protein-protein interactions. The method is benchmarked against experimental data and is used to predict, among others, partners of interactome 'orphans'.
This paper presents an efficient method for generating nanobodies with high affinity and high specificity. In addition, a collection of nanobodies specific for GFP or mCherry that resulted from this work is described.
Cell-based reporters for dopamine and norepinephrine allow real-time measurements of these neurotransmitters in vivo with high specificity. They can address the temporal and spatial dynamics of volume neurotransmission in behaving animals.
Designer ribozymes show protein-responsive translational control and can be combined with transcriptional control elements to program complex gene circuits.
This paper reports an autofluorescent signal in cancer stem cells within epithelial tumors and describes its use as a marker to isolate and study these cells.
This paper reports a combination of two small molecules for very efficient mouse cell reprogramming to induced pluripotency, achieving close to 100% reprogramming within a few days for some cell types.
Quantum dots sequentially loaded into cells are used to generate barcodes that can identify thousands of individual cells within a population and that can be used to track cells over many hours.
A model that incorporates the quantitative relationship between microRNA and the expression of its target gene achieves predictable and robust genetic circuits.
LiFE is an algorithm that evaluates human connectome models derived from magnetic resonance imaging (MRI) and tractography methods. The algorithm achieves this goal by assessing the contribution of all the fiber tracts in a connectome to predict the measured MRI signal.
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.