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University Imaging Centers - Where the University sees the future

Journal Articles

Single-cell ChIP

Nature Methods - 30 July 2019 - 12:00am

Nature Methods, Published online: 30 July 2019; doi:10.1038/s41592-019-0523-7

Single-cell ChIP
Categories: Journal Articles

Multi-omics single-cell analysis

Nature Methods - 30 July 2019 - 12:00am

Nature Methods, Published online: 30 July 2019; doi:10.1038/s41592-019-0519-3

Multi-omics single-cell analysis
Categories: Journal Articles

Publisher Correction: Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9

Nature Methods - 23 July 2019 - 12:00am

Nature Methods, Published online: 23 July 2019; doi:10.1038/s41592-019-0533-5

Publisher Correction: Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9
Categories: Journal Articles

Addendum: Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA

Nature Methods - 19 July 2019 - 12:00am

Nature Methods, Published online: 19 July 2019; doi:10.1038/s41592-019-0505-9

Addendum: Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA
Categories: Journal Articles

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

Nature Methods - 15 July 2019 - 12:00am

Nature Methods, Published online: 15 July 2019; doi:10.1038/s41592-019-0466-z

Conos constructs a joint graph between single cells in different samples based on multiple pairwise alignments of the samples and identifies recurrent subpopulations across all of the datasets.
Categories: Journal Articles

A genetically encoded fluorescent sensor for in vivo imaging of GABA

Nature Methods - 15 July 2019 - 12:00am

Nature Methods, Published online: 15 July 2019; doi:10.1038/s41592-019-0471-2

The genetically encoded GABA sensor iGABASnFR allows visualizing GABA signaling in vivo. Its application is demonstrated in mouse slices, in the awake mouse and in behaving zebrafish.
Categories: Journal Articles

Machine-learning-guided directed evolution for protein engineering

Nature Methods - 15 July 2019 - 12:00am

Nature Methods, Published online: 15 July 2019; doi:10.1038/s41592-019-0496-6

This review provides an overview of machine learning techniques in protein engineering and illustrates the underlying principles with the help of case studies.
Categories: Journal Articles

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling

Nature Methods - 15 July 2019 - 12:00am

Nature Methods, Published online: 15 July 2019; doi:10.1038/s41592-019-0467-y

DIVERS uses replicate sampling and spike-in sequencing to distinguish temporal and spatial variations from noise in microbial samples.
Categories: Journal Articles

High-affinity free ubiquitin sensors for quantifying ubiquitin homeostasis and deubiquitination

Nature Methods - 15 July 2019 - 12:00am

Nature Methods, Published online: 15 July 2019; doi:10.1038/s41592-019-0469-9

High-affinity sensors for free ubiquitin can be used to quantify intracellular ubiquitin pools, visualize ubiquitin levels by microscopy of fixed cells and enable real-time deubiquitination assays of diverse ubiquitin–protein conjugates.
Categories: Journal Articles

A genetically encodable cell-type-specific protein synthesis inhibitor

Nature Methods - 15 July 2019 - 12:00am

Nature Methods, Published online: 15 July 2019; doi:10.1038/s41592-019-0468-x

A genetically encodable protein synthesis inhibitor (gePSI) for cell-specific inhibition of protein synthesis that is efficient and reversible enables the study of structural plasticity following single-synapse activation in neurons.
Categories: Journal Articles

Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9

Nature Methods - 15 July 2019 - 12:00am

Nature Methods, Published online: 15 July 2019; doi:10.1038/s41592-019-0473-0

CombiSEAL is a high-throughput platform for seamlessly assembling barcoded combinatorial genetic units, offering an approach for protein optimization such as screening SpCas9 variants.
Categories: Journal Articles

EPIC: software toolkit for elution profile-based inference of protein complexes

Nature Methods - 15 July 2019 - 12:00am

Nature Methods, Published online: 15 July 2019; doi:10.1038/s41592-019-0461-4

A software tool, EPIC, is developed to determine protein complex membership using chromatographic fractionation–mass spectrometry data, and is applied to map the global Caenorhabditis elegans interactome.
Categories: Journal Articles

Mechanistic investigation of mEos4b reveals a strategy to reduce track interruptions in sptPALM

Nature Methods - 8 July 2019 - 12:00am

Nature Methods, Published online: 08 July 2019; doi:10.1038/s41592-019-0462-3

The red form of the photoconvertible fluorescent protein mEos4b has a long-lived dark state with specific chromophore conformation. Weak 488-nm light depopulates this state, improving track lengths in single-particle tracking experiments.
Categories: Journal Articles

Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction

Nature Methods - 8 July 2019 - 12:00am

Nature Methods, Published online: 08 July 2019; doi:10.1038/s41592-019-0458-z

This Perspective highlights recent applications of deep learning in fluorescence microscopy image reconstruction and discusses future directions and limitations of these approaches.
Categories: Journal Articles

Quantitative analysis of super-resolved structures using ASAP

Nature Methods - 1 July 2019 - 12:00am

Nature Methods, Published online: 01 July 2019; doi:10.1038/s41592-019-0472-1

The automated structures analysis program (ASAP) enables rapid and objective detection, classification and analysis of cellular assemblies in super-resolution images.
Categories: Journal Articles

Ana J. García Sáez

Nature Methods - 28 June 2019 - 12:00am

Nature Methods, Published online: 28 June 2019; doi:10.1038/s41592-019-0463-2

Analyzing super-res microscopy images ASAP, strengthened by Ultimate Frisbee.
Categories: Journal Articles

Pole-to-pole ocean viromes

Nature Methods - 27 June 2019 - 12:00am

Nature Methods, Published online: 27 June 2019; doi:10.1038/s41592-019-0480-1

A global-scale survey of the ocean viral metagenome (virome) broadens views on marine viruses and their roles in ecosystems.
Categories: Journal Articles

Expanded CIBERSORTx

Nature Methods - 27 June 2019 - 12:00am

Nature Methods, Published online: 27 June 2019; doi:10.1038/s41592-019-0486-8

Expanded CIBERSORTx
Categories: Journal Articles

Best practices and benchmarks for intact protein analysis for top-down mass spectrometry

Nature Methods - 27 June 2019 - 12:00am

Nature Methods, Published online: 27 June 2019; doi:10.1038/s41592-019-0457-0

The Consortium for Top-Down Proteomics presents a decision-tree-based guide to sample preparation and analysis protocols for researchers performing top-down mass-spectrometry-based analysis of intact proteins.
Categories: Journal Articles

Guiding human development in a dish

Nature Methods - 27 June 2019 - 12:00am

Nature Methods, Published online: 27 June 2019; doi:10.1038/s41592-019-0464-1

Understanding of fundamental questions in human embryology is hampered by limited access to in utero developmental events. Manfrin et al. have engineered an in vitro platform that recapitulates early morphogenic events of human development with unprecedented spatial and temporal control.
Categories: Journal Articles

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