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Nature Methods

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Nature Methods is a science methodology journal publishing laboratory techniques and methods papers in the life sciences and areas of chemistry relevant to the life sciences.
Updated: 3 days 15 hours ago

Molecular resolution imaging by repetitive optical selective exposure

9 September 2019 - 12:00am

Nature Methods, Published online: 09 September 2019; doi:10.1038/s41592-019-0544-2

Repetitive optical selective exposure (ROSE) is an interferometric single-molecule localization microscopy method offering twofold improvement in lateral resolution with the same photon budget compared with conventional approaches.
Categories: Journal Articles

Supervised classification enables rapid annotation of cell atlases

9 September 2019 - 12:00am

Nature Methods, Published online: 09 September 2019; doi:10.1038/s41592-019-0535-3

Garnett uses a hierarchical markup language and machine learning to define cell types and their marker genes and identifies these cell types in scRNA-seq datasets from tissues and whole organisms and across species.
Categories: Journal Articles

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

9 September 2019 - 12:00am

Nature Methods, Published online: 09 September 2019; doi:10.1038/s41592-019-0547-z

Single-nucleus methyl-3C sequencing jointly interrogates 3D chromatin organization and DNA methylation in human cells, and these joint measurements more accurately distinguish different cell types than either unimodal method.
Categories: Journal Articles

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

9 September 2019 - 12:00am

Nature Methods, Published online: 09 September 2019; doi:10.1038/s41592-019-0589-2

Publisher Correction: Oblique-plane single-molecule localization microscopy for tissues and small intact animals
Categories: Journal Articles

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

9 September 2019 - 12:00am

Nature Methods, Published online: 09 September 2019; doi:10.1038/s41592-019-0529-1

CellAssign uses a probabilistic model to assign single cells to a given cell type defined by known marker genes, enabling automated annotation of cell types present in a tumor microenvironment.
Categories: Journal Articles

High-definition spatial transcriptomics for in situ tissue profiling

9 September 2019 - 12:00am

Nature Methods, Published online: 09 September 2019; doi:10.1038/s41592-019-0548-y

A dense, spatially barcoded bead array captures RNA from histological tissue sections for spatially resolved gene expression analysis.
Categories: Journal Articles

Supervised clustering for single-cell analysis

9 September 2019 - 12:00am

Nature Methods, Published online: 09 September 2019; doi:10.1038/s41592-019-0534-4

A widely used concept from machine learning is put to use for single-cell analysis
Categories: Journal Articles

Robust and automated detection of subcellular morphological motifs in 3D microscopy images

9 September 2019 - 12:00am

Nature Methods, Published online: 09 September 2019; doi:10.1038/s41592-019-0539-z

A computational workflow combining image segmentation, computer graphics and supervised machine learning enables automated and robust 3D analysis of the coupling of cell shape and signaling.
Categories: Journal Articles

PPI discovery using proteome coevolution

30 August 2019 - 12:00am

Nature Methods, Published online: 30 August 2019; doi:10.1038/s41592-019-0566-9

An improved method to detect coevolving residues at protein interfaces allows proteome-wide screening of PPIs.
Categories: Journal Articles

Data denoising with transfer learning in single-cell transcriptomics

30 August 2019 - 12:00am

Nature Methods, Published online: 30 August 2019; doi:10.1038/s41592-019-0537-1

SAVER-X trains a deep neural network for transfer learning that improves the quality of scRNA-seq data using prior information learnt from existing public studies.
Categories: Journal Articles

Laser particles in hundreds of colors

30 August 2019 - 12:00am

Nature Methods, Published online: 30 August 2019; doi:10.1038/s41592-019-0565-x

The development of biologically compatible microdisk lasers enables massively multiplexed cell tracking.
Categories: Journal Articles

Markov models — hidden Markov models

30 August 2019 - 12:00am

Nature Methods, Published online: 30 August 2019; doi:10.1038/s41592-019-0532-6

“Everything we see hides another thing, we always want to see what is hidden by what we see” — Rene Magritte
Categories: Journal Articles

Looking at <i>Hydra</i> cells one at a time

30 August 2019 - 12:00am

Nature Methods, Published online: 30 August 2019; doi:10.1038/s41592-019-0569-6

Single-cell sequencing of Hydra results in a resource for studying differentiation trajectories, regeneration and nervous system development.
Categories: Journal Articles

Assessment of network module identification across complex diseases

30 August 2019 - 12:00am

Nature Methods, Published online: 30 August 2019; doi:10.1038/s41592-019-0509-5

In this DREAM challenge, 75 methods for the identification of disease-relevant modules from molecular networks are compared and validated with GWAS data. The authors provide practical guidelines for users and establish benchmarks for network analysis.
Categories: Journal Articles

A nanorotor for amplifying molecular movements

30 August 2019 - 12:00am

Nature Methods, Published online: 30 August 2019; doi:10.1038/s41592-019-0556-y

A DNA origami rotor amplifies and tracks DNA movements during biochemical reactions, uncovering action mechanisms of genome-processing enzymes.
Categories: Journal Articles

Machine intelligence rules in molecular design

30 August 2019 - 12:00am

Nature Methods, Published online: 30 August 2019; doi:10.1038/s41592-019-0563-z

Machine intelligence rules in molecular design
Categories: Journal Articles

An efficient auxin-inducible degron system with low basal degradation in human cells

26 August 2019 - 12:00am

Nature Methods, Published online: 26 August 2019; doi:10.1038/s41592-019-0512-x

An optimized F-box protein–degron pair enables efficient auxin-mediated protein degradation with minimal basal degradation in human cells and is suitable for transmembrane, cytoplasmic and nuclear proteins.
Categories: Journal Articles

A five-level classification system for proteoform identifications

26 August 2019 - 12:00am

Nature Methods, Published online: 26 August 2019; doi:10.1038/s41592-019-0573-x

A five-level classification system for proteoform identifications
Categories: Journal Articles

Transmission-mode MALDI-2 mass spectrometry imaging of cells and tissues at subcellular resolution

26 August 2019 - 12:00am

Nature Methods, Published online: 26 August 2019; doi:10.1038/s41592-019-0536-2

Adapting a t-MALDI-2 ion source to an Orbitrap mass analyzer enables mass spectrometry imaging of cells and tissues with (sub)cellular resolution.
Categories: Journal Articles

Parameter-free image resolution estimation based on decorrelation analysis

26 August 2019 - 12:00am

Nature Methods, Published online: 26 August 2019; doi:10.1038/s41592-019-0515-7

Decorrelation analysis offers an improved method for assessing image resolution that works on a single image and is insensitive to common image artifacts. The method can be applied generally to any type of microscopy images.
Categories: Journal Articles

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