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University Imaging Centers - Where the University sees the future

Journal Articles

In vitro intestine model for gut microbiome

Nature Methods - 27 June 2019 - 12:00am

Nature Methods, Published online: 27 June 2019; doi:10.1038/s41592-019-0489-5

In vitro intestine model for gut microbiome
Categories: Journal Articles

Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells

Nature Methods - 27 June 2019 - 12:00am

Nature Methods, Published online: 27 June 2019; doi:10.1038/s41592-019-0455-2

A microfluidic approach allows spatiotemporal control of morphogen distribution in human pluripotent stem cell cultures. This approach recapitulates early developmental processes such as localized signaling and symmetry-breaking events.
Categories: Journal Articles

LADL: light-activated dynamic looping for endogenous gene expression control

Nature Methods - 24 June 2019 - 12:00am

Nature Methods, Published online: 24 June 2019; doi:10.1038/s41592-019-0436-5

A fusion of CIBN to dCas9 and a Cry2 bridge enables blue-light-inducible long-range chromatin loops.
Categories: Journal Articles

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

Nature Methods - 24 June 2019 - 12:00am

Nature Methods, Published online: 24 June 2019; doi:10.1038/s41592-019-0437-4

The protein-level assembler can assemble protein catalogs from raw metagenomic sequencing data, enabling large-scale metagenomics studies.
Categories: Journal Articles

Thermophoretic trap for single amyloid fibril and protein aggregation studies

Nature Methods - 24 June 2019 - 12:00am

Nature Methods, Published online: 24 June 2019; doi:10.1038/s41592-019-0451-6

A thermophoretic trapping approach enables users to observe the behavior of single amyloid fibrils in solution for hours without any immobilization.
Categories: Journal Articles

EcoFABs: advancing microbiome science through standardized fabricated ecosystems

Nature Methods - 21 June 2019 - 12:00am

Nature Methods, Published online: 21 June 2019; doi:10.1038/s41592-019-0465-0

Microbiomes play critical roles in ecosystems and human health, yet in most cases scientists lack standardized and reproducible model microbial communities. The development of fabricated microbial ecosystems, which we term EcoFABs, will provide such model systems for microbiome studies.
Categories: Journal Articles

Gene Information eXtension (GIX): effortless retrieval of gene product information on any website

Nature Methods - 19 June 2019 - 12:00am

Nature Methods, Published online: 19 June 2019; doi:10.1038/s41592-019-0477-9

Gene Information eXtension (GIX): effortless retrieval of gene product information on any website
Categories: Journal Articles

Engineers embrace microbiome messiness

Nature Methods - 19 June 2019 - 12:00am

Nature Methods, Published online: 19 June 2019; doi:10.1038/s41592-019-0460-5

The gut, plant roots, ocean sediments: microbiome engineers travel to explore and model microbially complex systems.
Categories: Journal Articles

Moving beyond <i>P</i> values: data analysis with estimation graphics

Nature Methods - 19 June 2019 - 12:00am

Nature Methods, Published online: 19 June 2019; doi:10.1038/s41592-019-0470-3

Moving beyond P values: data analysis with estimation graphics
Categories: Journal Articles

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

Nature Methods - 17 June 2019 - 12:00am

Nature Methods, Published online: 17 June 2019; doi:10.1038/s41592-019-0433-8

Tagging live single cells and nuclei with lipid- or cholesterol-modified oligonucleotides enables massive scRNA-seq sample multiplexing, identifies doublets and recovers cells with low RNA content.
Categories: Journal Articles

Direct wavefront sensing enables functional imaging of infragranular axons and spines

Nature Methods - 17 June 2019 - 12:00am

Nature Methods, Published online: 17 June 2019; doi:10.1038/s41592-019-0434-7

Two-photon microscopy in combination with adaptive optics enables diffraction-limited morphological and functional imaging up to around 800 μm below the pia. This is achieved with the help of fluorescent microvessels serving as guidestars.
Categories: Journal Articles

High-performance calcium sensors for imaging activity in neuronal populations and microcompartments

Nature Methods - 17 June 2019 - 12:00am

Nature Methods, Published online: 17 June 2019; doi:10.1038/s41592-019-0435-6

The ‘jGCaMP7’ sensors are four genetically encoded calcium indicators with better sensitivity than state-of-the-art GCaMP6 and specifically improved for applications such as neuropil or wide-field imaging. The sensors are validated in vivo in both flies and mice.
Categories: Journal Articles

Author Correction: Tabular data

Nature Methods - 12 June 2019 - 12:00am

Nature Methods, Published online: 12 June 2019; doi:10.1038/s41592-019-0474-z

Author Correction: Tabular data
Categories: Journal Articles

FEAST: fast expectation-maximization for microbial source tracking

Nature Methods - 10 June 2019 - 12:00am

Nature Methods, Published online: 10 June 2019; doi:10.1038/s41592-019-0431-x

FEAST provides a computationally efficient tool to estimate the contribution of microbial sources to a target microbial community, as demonstrated for a variety of complex environmental samples.
Categories: Journal Articles

Scattering microscopy takes single-particle tracking to the next level

Nature Methods - 30 May 2019 - 12:00am

Nature Methods, Published online: 30 May 2019; doi:10.1038/s41592-019-0438-3

Interferometric scattering microscopy enables extended monitoring of gold-nanoparticle-labeled membrane proteins with impressive spatiotemporal resolution.
Categories: Journal Articles

Quantile regression

Nature Methods - 30 May 2019 - 12:00am

Nature Methods, Published online: 30 May 2019; doi:10.1038/s41592-019-0406-y

Quantile regression robustly estimates the typical and extreme values of a response.
Categories: Journal Articles

Predicting RNA–protein binding affinity

Nature Methods - 30 May 2019 - 12:00am

Nature Methods, Published online: 30 May 2019; doi:10.1038/s41592-019-0445-4

Predicting RNA–protein binding affinity
Categories: Journal Articles

Tuning GPCR-based sensors

Nature Methods - 30 May 2019 - 12:00am

Nature Methods, Published online: 30 May 2019; doi:10.1038/s41592-019-0440-9

The elimination of all cross-talk in a signaling pathway turns a yeast cell into a model cell that can sense and report on metabolites.
Categories: Journal Articles

Forming coacervates inside liposomes

Nature Methods - 30 May 2019 - 12:00am

Nature Methods, Published online: 30 May 2019; doi:10.1038/s41592-019-0448-1

Forming coacervates inside liposomes
Categories: Journal Articles

Comparing trajectory inference methods

Nature Methods - 30 May 2019 - 12:00am

Nature Methods, Published online: 30 May 2019; doi:10.1038/s41592-019-0443-6

Comparing trajectory inference methods
Categories: Journal Articles

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