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University Imaging Centers - Where the University sees the future

Journal Articles

Highly parallel direct RNA sequencing on an array of nanopores

Nature Methods - 15 January 2018 - 12:00am

Highly parallel direct RNA sequencing on an array of nanopores

Highly parallel direct RNA sequencing on an array of nanopores, Published online: 15 January 2018; doi:10.1038/nmeth.4577

Direct sequencing of RNA molecules in real time using nanopores allows for the detection of splice variants and hold promises for profiling RNA modifications.
Categories: Journal Articles

Detecting hierarchical genome folding with network modularity

Nature Methods - 15 January 2018 - 12:00am

Detecting hierarchical genome folding with network modularity

Detecting hierarchical genome folding with network modularity, Published online: 15 January 2018; doi:10.1038/nmeth.4560

3DNetMod identifies nested topologically associating domains (TADs) and subTADs from Hi-C data.
Categories: Journal Articles

Supermultiplexed optical imaging and barcoding with engineered polyynes

Nature Methods - 15 January 2018 - 12:00am

Supermultiplexed optical imaging and barcoding with engineered polyynes

Supermultiplexed optical imaging and barcoding with engineered polyynes, Published online: 15 January 2018; doi:10.1038/nmeth.4578

A class of probes enables highly multiplexed imaging and barcoding applications with Raman microscopy.
Categories: Journal Articles

GIGGLE: a search engine for large-scale integrated genome analysis

Nature Methods - 8 January 2018 - 12:00am

GIGGLE: a search engine for large-scale integrated genome analysis

GIGGLE: a search engine for large-scale integrated genome analysis, Published online: 08 January 2018; doi:10.1038/nmeth.4556

GIGGLE is a genome interval search engine that enables extremely fast queries of genome features from thousands of genome annotation sets.
Categories: Journal Articles

The new XFELs

Nature Methods - 3 January 2018 - 12:00am

The new XFELs

The new XFELs, Published online: 03 January 2018; doi:10.1038/nmeth.4548

New X-ray free-electron (XFEL) facilities will broaden access to this technology, facilitate methods development, and push boundaries in structural biology.
Categories: Journal Articles

A profusion of confusion in NGS methods naming

Nature Methods - 3 January 2018 - 12:00am

A profusion of confusion in NGS methods naming

A profusion of confusion in NGS methods naming, Published online: 03 January 2018; doi:10.1038/nmeth.4558

A profusion of confusion in NGS methods naming
Categories: Journal Articles

Proteomics: Nascent proteome labeling <i>in vivo</i>

Nature Methods - 3 January 2018 - 12:00am

Proteomics: Nascent proteome labeling in vivo

Proteomics: Nascent proteome labeling <i>in vivo</i>, Published online: 03 January 2018; doi:10.1038/nmeth.4562

Proteomics: Nascent proteome labeling in vivo
Categories: Journal Articles

Mass spectrometry: False discovery rate estimation for metabolomics

Nature Methods - 3 January 2018 - 12:00am

Mass spectrometry: False discovery rate estimation for metabolomics

Mass spectrometry: False discovery rate estimation for metabolomics, Published online: 03 January 2018; doi:10.1038/nmeth.4564

Mass spectrometry: False discovery rate estimation for metabolomics
Categories: Journal Articles

Genomics: Annotating full-length long noncoding RNAs

Nature Methods - 3 January 2018 - 12:00am

Genomics: Annotating full-length long noncoding RNAs

Genomics: Annotating full-length long noncoding RNAs, Published online: 03 January 2018; doi:10.1038/nmeth.4566

Genomics: Annotating full-length long noncoding RNAs
Categories: Journal Articles

Imaging: Reflecting on light sheets

Nature Methods - 3 January 2018 - 12:00am

Imaging: Reflecting on light sheets

Imaging: Reflecting on light sheets, Published online: 03 January 2018; doi:10.1038/nmeth.4570

Reflective coverslips can improve spatiotemporal resolution and collection efficiency in diSPIM light-sheet fluorescence microscopy.
Categories: Journal Articles

Bioinformatics: Fast curve fitting on a graphics processing unit

Nature Methods - 3 January 2018 - 12:00am

Bioinformatics: Fast curve fitting on a graphics processing unit

Bioinformatics: Fast curve fitting on a graphics processing unit, Published online: 03 January 2018; doi:10.1038/nmeth.4568

Bioinformatics: Fast curve fitting on a graphics processing unit
Categories: Journal Articles

Interactome INSIDER: a structural interactome browser for genomic studies

Nature Methods - 1 January 2018 - 12:00am

Interactome INSIDER: a structural interactome browser for genomic studies

Interactome INSIDER: a structural interactome browser for genomic studies, Published online: 01 January 2018; doi:10.1038/nmeth.4540

Based on machine learning-predicted interaction interfaces, this resource enables interpretation of genomic variants and disease mutations in light of the protein-protein interactome.
Categories: Journal Articles

Biotinylation by antibody recognition—a method for proximity labeling

Nature Methods - 18 December 2017 - 12:00am

Biotinylation by antibody recognition—a method for proximity labeling

Biotinylation by antibody recognition—a method for proximity labeling, Published online: 18 December 2017; doi:10.1038/nmeth.4533

Proximity-based labeling represents a useful approach for mapping protein environment, but current methods for this are limited to application to cell lines. This approach is now extended to primary human tissues with a method that uses antibodies to guide proximity labeling.
Categories: Journal Articles

Resolving systematic errors in widely used enhancer activity assays in human cells

Nature Methods - 11 December 2017 - 12:00am

Resolving systematic errors in widely used enhancer activity assays in human cells

Resolving systematic errors in widely used enhancer activity assays in human cells, Published online: 11 December 2017; doi:10.1038/nmeth.4534

Using the ORI of plasmids used in enhancer assays as the sole core promoter and inhibiting the interferon I response triggered by plasmid transfection greatly reduces false positive and negative results in single-candidate and massively parallel enhancer assays and enables genome-wide enhancer screens.
Categories: Journal Articles

Mapping the 3D orientation of piconewton integrin traction forces

Nature Methods - 11 December 2017 - 12:00am

Mapping the 3D orientation of piconewton integrin traction forces

Mapping the 3D orientation of piconewton integrin traction forces, Published online: 11 December 2017; doi:10.1038/nmeth.4536

Molecular force microscopy employs a combination of fluorescence polarization microscopy and molecular tension sensors to determine the orientation of cellular forces. The technology is demonstrated for integrin-mediated forces in platelets and fibroblasts.
Categories: Journal Articles

BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance

Nature Methods - 11 December 2017 - 12:00am

BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance

BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance, Published online: 11 December 2017; doi:10.1038/nmeth.4535

Mouse tumor organoids are characterized as a model to study tumor biology and drug resistance.
Categories: Journal Articles

NetSig: network-based discovery from cancer genomes

Nature Methods - 4 December 2017 - 12:00am

NetSig: network-based discovery from cancer genomes

NetSig: network-based discovery from cancer genomes, Published online: 04 December 2017; doi:10.1038/nmeth.4514

NetSig is a network-based statistic that identifies cancer driver genes with high accuracy and can be combined with gene-based statistical tests; results are validated with a large-scale in vivo tumorigenesis assay.
Categories: Journal Articles

Programmable full-adder computations in communicating three-dimensional cell cultures

Nature Methods - 4 December 2017 - 12:00am

Programmable full-adder computations in communicating three-dimensional cell cultures

Programmable full-adder computations in communicating three-dimensional cell cultures, Published online: 04 December 2017; doi:10.1038/nmeth.4505

Designer cells executing rationally assembled genetic programs that can process input signals with programmable logic are combined in a 3D cell culture that performs three-input, two-output full-adder computations.
Categories: Journal Articles

The new 2D Superresolution mode for ZEISS Airyscan

Nature Methods - 30 November 2017 - 12:00am

The new 2D Superresolution mode for ZEISS Airyscan

The new 2D Superresolution mode for ZEISS Airyscan, Published online: 30 November 2017; doi:10.1038/nmeth.f.404

The new 2D Superresolution mode for ZEISS Airyscan
Categories: Journal Articles

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

Nature Methods - 30 November 2017 - 12:00am

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data, Published online: 30 November 2017; doi:10.1038/nmeth.4499

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data
Categories: Journal Articles

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