University of Minnesota
University Imaging Center
http://uic.umn.edu/
612.624.7938
University Imaging Centers - Where the University sees the future

Journal Articles

Resolution upgrades for light-sheet microscopy

Nature Methods - 19 August 2019 - 12:00am

Nature Methods, Published online: 19 August 2019; doi:10.1038/s41592-019-0542-4

Single objective light-sheet fluorescence microscopes combine the convenience of conventional sample mounting with sensitive subcellular and super-resolution imaging of cells and tissues.
Categories: Journal Articles

Oblique-plane single-molecule localization microscopy for tissues and small intact animals

Nature Methods - 19 August 2019 - 12:00am

Nature Methods, Published online: 19 August 2019; doi:10.1038/s41592-019-0510-z

Single-molecule oblique-plane microscopy (obSTORM) enables deep volumetric super-resolution imaging in a light-sheet microscopy platform that is convenient for standard tissues and small intact animals.
Categories: Journal Articles

A dream of single-cell proteomics

Nature Methods - 12 August 2019 - 12:00am

Nature Methods, Published online: 12 August 2019; doi:10.1038/s41592-019-0540-6

As single-cell proteomics emerges, perhaps labs can avoid the need to infer protein levels from mRNA abundances.
Categories: Journal Articles

BindSpace decodes transcription factor binding signals by large-scale sequence embedding

Nature Methods - 12 August 2019 - 12:00am

Nature Methods, Published online: 12 August 2019; doi:10.1038/s41592-019-0511-y

By embedding DNA sequences that are known to bind transcription factors in vitro together with labels for the TFs in a high-dimensional space, the machine learning approach BindSpace distinguishes between the binding preferences of even closely related TFs.
Categories: Journal Articles

Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts

Nature Methods - 12 August 2019 - 12:00am

Nature Methods, Published online: 12 August 2019; doi:10.1038/s41592-019-0508-6

A single transcript encoding Cas12a and an array of CRISPR RNAs enables multiplexed genome engineering, from multiple knockouts to transcriptional activation or repression to orthogonal transcriptional control and editing in the same sample.
Categories: Journal Articles

Publisher Correction: Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis

Nature Methods - 12 August 2019 - 12:00am

Nature Methods, Published online: 12 August 2019; doi:10.1038/s41592-019-0546-0

Publisher Correction: Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis
Categories: Journal Articles

Stephan Preibisch

Nature Methods - 9 August 2019 - 12:00am

Nature Methods, Published online: 09 August 2019; doi:10.1038/s41592-019-0549-x

Staying mobile and building a Toy-Story-related way to stitch terabyte-sized images in microscopy.
Categories: Journal Articles

Progress and challenges in analyzing rodent energy expenditure

Nature Methods - 7 August 2019 - 12:00am

Nature Methods, Published online: 07 August 2019; doi:10.1038/s41592-019-0513-9

Whole-body energy expenditure is the summed metabolic activities of tissues and, to remove the influence of body size, ratios of energy expenditure to body mass are often applied but can generate spurious differences. In 2011, a group of experts proposed adoption of ANCOVA for the analysis of metabolic rate but, seven years later, analyses based on ratios remain the most frequent. We discuss some of the barriers to adopting better analytical procedures.
Categories: Journal Articles

Author Correction: Kilohertz frame-rate two-photon tomography

Nature Methods - 6 August 2019 - 12:00am

Nature Methods, Published online: 06 August 2019; doi:10.1038/s41592-019-0545-1

Author Correction: Kilohertz frame-rate two-photon tomography
Categories: Journal Articles

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control

Nature Methods - 5 August 2019 - 12:00am

Nature Methods, Published online: 05 August 2019; doi:10.1038/s41592-019-0503-y

FLAM-seq implements a cDNA library preparation followed by single-molecule sequencing, for determining full-length mRNA molecules, including poly(A) tails.
Categories: Journal Articles

High throughput discovery of functional protein modifications by Hotspot Thermal Profiling

Nature Methods - 5 August 2019 - 12:00am

Nature Methods, Published online: 05 August 2019; doi:10.1038/s41592-019-0499-3

A massively parallel biophysical approach, Hotspot Thermal Profiling, analyzes the effects of phosphorylation on protein stability across the proteome in live cells.
Categories: Journal Articles

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples

Nature Methods - 5 August 2019 - 12:00am

Nature Methods, Published online: 05 August 2019; doi:10.1038/s41592-019-0501-0

BigStitcher enables fast and accurate alignment and reconstruction of terabyte-sized imaging datasets of cleared and expanded samples.
Categories: Journal Articles

Glyco-DIA: a method for quantitative <i>O</i>-glycoproteomics with in silico-boosted glycopeptide libraries

Nature Methods - 5 August 2019 - 12:00am

Nature Methods, Published online: 05 August 2019; doi:10.1038/s41592-019-0504-x

O-glycopeptides and O-glycan structures can be identified and quantified on a proteome-wide scale with Glyco-DIA, a data-independent-acquisition mass spectrometry-based method.
Categories: Journal Articles

Joint profiling of DNA methylation and chromatin architecture in single cells

Nature Methods - 5 August 2019 - 12:00am

Nature Methods, Published online: 05 August 2019; doi:10.1038/s41592-019-0502-z

Methyl-HiC combines the elucidation of chromatin architecture with the reading of DNA methylomes in pools and single cells. Regions that are distant on the linear-genome but close in three-dimensional space show coordinated DNA methylation.
Categories: Journal Articles

hPSCs on a diet

Nature Methods - 30 July 2019 - 12:00am

Nature Methods, Published online: 30 July 2019; doi:10.1038/s41592-019-0518-4

hPSCs on a diet
Categories: Journal Articles

Promoting transparency and reproducibility in enhanced molecular simulations

Nature Methods - 30 July 2019 - 12:00am

Nature Methods, Published online: 30 July 2019; doi:10.1038/s41592-019-0506-8

The PLUMED consortium unifies developers and contributors to PLUMED, an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations. Here, we outline our efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations.
Categories: Journal Articles

Atomic-level in-cell protein NMR

Nature Methods - 30 July 2019 - 12:00am

Nature Methods, Published online: 30 July 2019; doi:10.1038/s41592-019-0525-5

A newly developed method allows structure elucidation of proteins inside intact mammalian cells, using solid-state NMR spectroscopy.
Categories: Journal Articles

Optogenetics turns up the heat

Nature Methods - 30 July 2019 - 12:00am

Nature Methods, Published online: 30 July 2019; doi:10.1038/s41592-019-0528-2

Illuminating the brain for optogenetic experiments can have undesirable effects on neural activity.
Categories: Journal Articles

Markov models—Markov chains

Nature Methods - 30 July 2019 - 12:00am

Nature Methods, Published online: 30 July 2019; doi:10.1038/s41592-019-0476-x

You can look back there to explain things, but the explanation disappears. You’ll never find it there. Things are not explained by the past. They’re explained by what happens now. –Alan Watts
Categories: Journal Articles

Reversible covalent inhibitor target search

Nature Methods - 30 July 2019 - 12:00am

Nature Methods, Published online: 30 July 2019; doi:10.1038/s41592-019-0516-6

Reversible covalent inhibitor target search
Categories: Journal Articles

Pages

Subscribe to University Imaging Centers aggregator - Journal Articles