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University Imaging Center
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University Imaging Centers - Where the University sees the future

Journal Articles

Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning

Nature Methods - 18 March 2019 - 12:00am

Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning

Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning, Published online: 18 March 2019; doi:10.1038/s41592-019-0353-7

scScope uses a recurrent network to remove batch effects and iteratively impute zero values in scRNA-seq data.
Categories: Journal Articles

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

Nature Methods - 18 March 2019 - 12:00am

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information, Published online: 18 March 2019; doi:10.1038/s41592-019-0344-8

SIRIUS 4 is a fast and highly accurate tool for molecular structure interpretation from mass-spectrometry-based metabolomics data.
Categories: Journal Articles

3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax

Nature Methods - 18 March 2019 - 12:00am

3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax

3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax, Published online: 18 March 2019; doi:10.1038/s41592-019-0359-1

3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax
Categories: Journal Articles

Peering into cells at high resolution just got easier

Nature Methods - 18 March 2019 - 12:00am

Peering into cells at high resolution just got easier

Peering into cells at high resolution just got easier, Published online: 18 March 2019; doi:10.1038/s41592-019-0373-3

Light-sheet fluorescence microscopes are making it possible to follow subcellular dynamics with unprecedented detail, but they are complex to build and maintain. A new method that can generate arbitrary light sheets provides much-needed simplicity and additional versatility.
Categories: Journal Articles

FPbase: a community-editable fluorescent protein database

Nature Methods - 18 March 2019 - 12:00am

FPbase: a community-editable fluorescent protein database

FPbase: a community-editable fluorescent protein database, Published online: 18 March 2019; doi:10.1038/s41592-019-0352-8

FPbase: a community-editable fluorescent protein database
Categories: Journal Articles

Cell composition analysis of bulk genomics using single-cell data

Nature Methods - 18 March 2019 - 12:00am

Cell composition analysis of bulk genomics using single-cell data

Cell composition analysis of bulk genomics using single-cell data, Published online: 18 March 2019; doi:10.1038/s41592-019-0355-5

Cell Population Mapping (CPM) leverages single-cell RNA-seq data as a rich reference to predict the composition of cell types and cell states from bulk RNA-seq data.
Categories: Journal Articles

Haribabu Arthanari

Nature Methods - 18 March 2019 - 12:00am

Haribabu Arthanari

Haribabu Arthanari, Published online: 18 March 2019; doi:10.1038/s41592-019-0362-6

A spin-jock’s path to biomolecular dynamics with NMR, and why solitude matters.
Categories: Journal Articles

A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria

Nature Methods - 11 March 2019 - 12:00am

A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria

A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria, Published online: 11 March 2019; doi:10.1038/s41592-019-0333-y

The solid media portable cell killing assay uses metabolism-sensitive staining to illuminate the killing of antibiotic-tolerant bacteria under resource-depleted conditions, thereby enabling multiplex, genome-scale analyses for the identification of target strains.
Categories: Journal Articles

An active texture-based digital atlas enables automated mapping of structures and markers across brains

Nature Methods - 11 March 2019 - 12:00am

An active texture-based digital atlas enables automated mapping of structures and markers across brains

An active texture-based digital atlas enables automated mapping of structures and markers across brains, Published online: 11 March 2019; doi:10.1038/s41592-019-0328-8

An active atlas for automatic alignment of brains to a reference atlas is presented. The method uses the fine-scale pattern of tissue. The atlas is refined by each new brain and can inform on the structural variability between different brains.
Categories: Journal Articles

Aromatic <sup>19</sup>F-<sup>13</sup>C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics

Nature Methods - 11 March 2019 - 12:00am

Aromatic 19F-13C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics

Aromatic <sup>19</sup>F-<sup>13</sup>C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics, Published online: 11 March 2019; doi:10.1038/s41592-019-0334-x

The development of 19F-13C TROSY provides a new avenue for the collection of high-sensitivity, background-free information about the structure and dynamics of challenging biomolecular systems by NMR spectroscopy.
Categories: Journal Articles

Author Correction: Methods to study RNA–protein interactions

Nature Methods - 8 March 2019 - 12:00am

Author Correction: Methods to study RNA–protein interactions

Author Correction: Methods to study RNA–protein interactions, Published online: 08 March 2019; doi:10.1038/s41592-019-0366-2

Author Correction: Methods to study RNA–protein interactions
Categories: Journal Articles

Author Correction: Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR

Nature Methods - 28 February 2019 - 12:00am

Author Correction: Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR

Author Correction: Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR, Published online: 28 February 2019; doi:10.1038/s41592-019-0363-5

Author Correction: Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR
Categories: Journal Articles

A trap for intermediate enzyme complexes

Nature Methods - 27 February 2019 - 12:00am

A trap for intermediate enzyme complexes

A trap for intermediate enzyme complexes, Published online: 27 February 2019; doi:10.1038/s41592-019-0339-5

A trap for intermediate enzyme complexes
Categories: Journal Articles

Quantum imaging in biological samples

Nature Methods - 27 February 2019 - 12:00am

Quantum imaging in biological samples

Quantum imaging in biological samples, Published online: 27 February 2019; doi:10.1038/s41592-019-0346-6

The combination of image scanning microscopy and quantum imaging improves resolution up to fourfold compared with the classical diffraction barrier.
Categories: Journal Articles

RNA-binding proteome redux

Nature Methods - 27 February 2019 - 12:00am

RNA-binding proteome redux

RNA-binding proteome redux, Published online: 27 February 2019; doi:10.1038/s41592-019-0349-3

Scientists exploit the basic physicochemical properties of protein–RNA complexes to paint a dynamic portrait of the RNA-binding proteome.
Categories: Journal Articles

Multifunctional miniature microscopy

Nature Methods - 27 February 2019 - 12:00am

Multifunctional miniature microscopy

Multifunctional miniature microscopy, Published online: 27 February 2019; doi:10.1038/s41592-019-0340-z

Multifunctional miniature microscopy
Categories: Journal Articles

How to follow metabolic clues to find cancer’s Achilles heel

Nature Methods - 27 February 2019 - 12:00am

How to follow metabolic clues to find cancer’s Achilles heel

How to follow metabolic clues to find cancer’s Achilles heel, Published online: 27 February 2019; doi:10.1038/s41592-019-0331-0

Labs combine techniques to study why cancer cells are so metabolically flexible.
Categories: Journal Articles

Solid-state nanopores read DNA

Nature Methods - 27 February 2019 - 12:00am

Solid-state nanopores read DNA

Solid-state nanopores read DNA, Published online: 27 February 2019; doi:10.1038/s41592-019-0337-7

Solid-state nanopores read DNA
Categories: Journal Articles

Giving software its due

Nature Methods - 27 February 2019 - 12:00am

Giving software its due

Giving software its due, Published online: 27 February 2019; doi:10.1038/s41592-019-0350-x

Software and algorithm development is crucial for scientific progress; we discuss how to improve the impact and recognition of these tools.
Categories: Journal Articles

Universal light-sheet generation with field synthesis

Nature Methods - 25 February 2019 - 12:00am

Universal light-sheet generation with field synthesis

Universal light-sheet generation with field synthesis, Published online: 25 February 2019; doi:10.1038/s41592-019-0327-9

The field synthesis method for generating any scanned light sheet is based on a new mathematical theorem in Fourier analysis and has important practical implications for simpler, multicolor lattice light-sheet microscopy.
Categories: Journal Articles

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