Nature Methods
A scientific journal publishing cutting-edge methods, tools, analyses, resources, reviews, news and commentary, supporting life sciences research. Posts by the editors.
- A universal AI-powered pipeline enables precise 3D analysis of cell morphology and topology within organoid structures. www.nature.com/articles/s41...
- Our May issue is now live! 🥳 nature.com/nmeth/volume... We are thrilled to share our May Focus issue on bond-selective imaging! (see thread below) Cover art: hyperspectral stimulated Raman scattering image of the mouse brain, by Tao Chen, Marzia Savini and Meng Wang.
- PUPS - prediction of unseen proteins' subcellular localization - uses machine learning models to predict the localization of unseen proteins in unseen cell lines from sequence and cellular images. www.nature.com/articles/s41...
- The Mass Spectrometry Query Language (MassQL) is an open-source language for instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and expressive queries without the need for programming skills. www.nature.com/articles/s41...
- For a quick summary of the paper, read the Research Briefing here: www.nature.com/articles/s41...
- A Dark sectioning algorithm removes background and provides single-frame optical sectioning in fluorescence microscopy, facilitating improved deep-tissue segmentation accuracy. www.nature.com/articles/s41...
- Introducing FISHnet, a graph-theory-based method for sensitive and specific identification of chromatin domains from single-cell sequential Oligopaints data. www.nature.com/articles/s41...
- SeReNet is an accurate and efficient physics-driven self-supervised reconstruction network for light-field microscopy, enabling long and high-speed 3D intravital imaging. www.nature.com/articles/s41...
- A Dark sectioning algorithm removes background and provides single-frame optical sectioning in fluorescence microscopy, facilitating improved deep-tissue segmentation accuracy. www.nature.com/articles/s41...
- Exciting news...Nature Methods is hiring a new editor! This exciting and dynamic role will be shared with the Nature Research Cross-Journal Editorial Team. Apply here by June 1! springernature.wd3.myworkdayjobs.com/SpringerNatu...
- Excited to announce this new paper from the Kirchhausen and Hatzakis labs on DeepSPT, a deep learning framework for single-particle/vesicle tracking. www.nature.com/articles/s41...
- An extended 2D gastruloid system enables modeling the human mesoderm development and morphogenesis. www.nature.com/articles/s41...
- For a quick summary of GLORI 2.0/3.0, read the Research Briefing here: www.nature.com/articles/s41...
- Introducing GLORI 2.0 and 3.0, experimental methods for sensitive m6A quantification from RNA inputs as low as a few hundred cells. www.nature.com/articles/s41...
- Global efforts in microscopy dissemination have revealed the importance of setting technology adoption capable of producing scientific outcome as an end goal. Learn more here in a Comment from Leong Chew and colleagues! @scopeshifu.bsky.social www.nature.com/articles/s41...
- In this month's Technology Feature, journalist @virginiagewin.bsky.social explores how scientists working in the ecology, biodiversity and conservation fields are adopting AI tools to accelerate their research. Read it here: www.nature.com/articles/s41...
- A Review from experts in cryo-EM and X-ray crystallography describes the latest and greatest strategies for time-resolved structural biology. www.nature.com/articles/s41...
- Introducing GLORI 2.0 and 3.0, experimental methods for sensitive m6A quantification from RNA inputs as low as a few hundred cells. www.nature.com/articles/s41...
- From the lab of @don-b-arnold.bsky.social : ATLAS is a tool for circuit tracing, demonstrated here in rodents. It allows anterograde transsynaptic tracing, starting from genetically defined neurons. www.nature.com/articles/s41...
- A suite of nontoxic and permeable CarboTag probes in various colors enables live quantitative imaging of a range of plant cell wall characteristics and dynamic, high-resolution mapping of cell wall changes in response to growth or perturbations. www.nature.com/articles/s41...
- The NeuroXiv platform allows AI-powered open mining of a database of reconstructions of more than 175k mouse neurons, registered to the Common Coordinate Framework and supports queries about connectivity, projection patterns and other morphological features. www.nature.com/articles/s41...
- Please check out BiaPy from Muñoz-Barrutia, Arganda-Carreras, and colleagues for user-friendly deployment of deep learning tools for bioimage analysis. www.nature.com/articles/s41...
- New from the Dai and Li labs: Meta-learning-empowered reflective lattice light-sheet virtual structured illumination microscopy (Meta-rLLS-VSIM) offers near-isotropic resolution for fast and versatile super-resolution imaging of subcellular dynamics www.nature.com/articles/s41...
- A new paper from Kohli, Waller, and colleagues describes ring deconvolution microscopy for fast and straightforward correction of spatially varying aberrations across diverse microscopy modalities. www.nature.com/articles/s41...
- Out today from the Ruan lab! ChAIR, a droplet-based tri-omic tool, enables the simultaneous profiling of the transcriptome, chromatin accessibility and chromatin conformation in single cells. www.nature.com/articles/s41...
- Tissue-expansion method compatible with mass-spectrometry imaging (TEMI) enables the profiling of lipids, metabolites, peptides, proteins, and N-glycans in complex tissues with high spatial resolution, advancing spatially resolved multi-omics mapping. www.nature.com/articles/s41...
- A Perspective by Jina Ko and colleagues @pennpathlabmed.bsky.social explores advances and future directions in spatiotemporal omics methods for 4D profiling. www.nature.com/articles/s41...
- CHIMERYS is a spectrum-centric and data acquisition method-agnostic algorithm that deconvolves any MS2 spectrum, regardless of whether it was acquired by DDA, DIA or PRM, thus unifying analysis of bottom-up proteomics data. @msaid-de.bsky.social @kusterlab.bsky.social www.nature.com/articles/s41...
- Neural Perturbational Inference is an approach for estimating effective connectivity, in which virtual perturbations to a surrogate brain allow gaining insights into human brain functions. www.nature.com/articles/s41...
- An excellent Review from Jonathan Liu and colleagues discusses current 2D and 3D microscopy methods for imaging three-dimensional cell cultures and emerging strategies to address key challenges. www.nature.com/articles/s41...
- scMultiSim is a comprehensive single-cell and spatial data simulator generating realistic multi-omics data based on modeling gene regulatory networks, cell-cell interactions, and other biological and technical factors. www.nature.com/articles/s41...
- Happy to announce a new paper on a very promising monomeric red fluorescent protein (mScarlet3-H) from the Wu, Zheng, Piatkevich, and Fu labs. mScarlet3-H is bright, photostable, and physically stable, making it versatile for advanced bioimaging. www.nature.com/articles/s41...
- A Perspective from the Ecker lab discusses the progress and challenges of using computer vision approaches for behavior studies of primates in natural environments. www.nature.com/articles/s41...
- In this month's Editorial we discuss why basic research is the backbone of advances in medicine and improvements to the human condition - and that basic research needs essential support from government funding. www.nature.com/articles/s41...
- Read the News & Views highlighting this cool work here! www.nature.com/articles/s41...
- Perturb-tracing integrates CRISPR screening with barcode readout and chromatin tracing for loss-of-function screens, facilitating the study of chromatin folding regulators. www.nature.com/articles/s41...
- The integration of duplex sequencing with cost-effective Ultima sequencing enhances the accuracy of whole-genome circulating cell-free DNA profiling. www.nature.com/articles/s41...
- PTM-Mamba: a post-translational modification-aware protein language model, for protein modeling and design. www.nature.com/articles/s41...
- Perturb-tracing integrates CRISPR screening with barcode readout and chromatin tracing for loss-of-function screens, facilitating the study of chromatin folding regulators. www.nature.com/articles/s41...
- Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks. www.nature.com/articles/s41...
- Out this week from the MICrONS consortium: CAVE, Connectome Annotation Versioning Engine, a platform for proofreading, annotating and analyzing petascale EM datasets. www.nature.com/articles/s41...
