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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...

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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...

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An extended 2D gastruloid system enables modeling the human mesoderm development and morphogenesis. www.nature.com/articles/s41...

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For a quick summary of GLORI 2.0/3.0, read the Research Briefing here: www.nature.com/articles/s41...

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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...

submitted 5 days ago • 1 comment

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...

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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...

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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...

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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...

submitted 10 days ago • 1 comment

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...

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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...

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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...

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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...

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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...

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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...

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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...

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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...

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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...

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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...

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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...

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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...

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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...

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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...

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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...

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Read the News & Views highlighting this cool work here! www.nature.com/articles/s41...

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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...

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PTM-Mamba: a post-translational modification-aware protein language model, for protein modeling and design. www.nature.com/articles/s41...

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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...

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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...

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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...

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Our April issue is live! 🌧️🌷 nature.com/nmeth/volume... On the cover, Spotiphy projects scRNA-seq and histological image data onto the spatial transcriptome. Artwork by Jiyuan Yang @stjuderesearch.bsky.social. Paper: www.nature.com/articles/s41...

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Research Highlight by Nina Vogt: "Strolling down rats’ memory lane". www.nature.com/articles/s41...

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Research Highlight by Arunima Singh: "Chemical space exploration with quantum computing" www.nature.com/articles/s41...

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Research Highlight by Lin Tang: "Optimal transport for single-cell genomics" www.nature.com/articles/s41...

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Research Highlight by @ritastrack.bsky.social: "Structural biology at the plasma membrane" www.nature.com/articles/s41...

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In this month's Technology Feature, @carolineseydel.bsky.social explores how researchers are using label-free microscopy techniques to study complex biological systems, from living creatures to peptides. www.nature.com/articles/s41...

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A Comment from leaders in the field of biomolecular simulations brings attention to a need to establish FAIR principles for trajectory storage and sharing to favor reuse under an open science paradigm. www.nature.com/articles/s41...

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And check out the Research Briefing for a quick summary of the work, here! www.nature.com/articles/s41...

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xTrimo protein general language model (xTrimoPGLM) is a unified pretraining framework and foundation model designed for various protein-related tasks, including protein understanding and generation or design. www.nature.com/articles/s41...

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This month's Points of Significance column features propensity score weighting. Check it out! @martin-krzywinski.bsky.social www.nature.com/articles/s41...

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A new Perspective outlines the datasets, data standards, infrastructure, governance and community engagement approaches of the Human Tumor Atlas Network. #HTAN www.nature.com/articles/s41...

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LigandMPNN is a deep-learning-based protein sequence design method that can explicitly model all nonprotein components of biomolecular systems. www.nature.com/articles/s41...

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Out today! Spectral Denoising removes chemical and electronic noise from mass spectrometry data to improve metabolite annotation. www.nature.com/articles/s41...

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An important Perspective on global image sharing in the life sciences out today. The piece urges the community and funders to support FAIR bioimage data sharing and offers clear, actionable guidance on what is needed. www.nature.com/articles/s41...

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Uncalled4: a toolkit for nanopore signal alignment, analysis and visualization of DNA and RNA modifications. www.nature.com/articles/s41...

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Paired-Damage-seq is an in situ labeling-by-repair strategy for joint profiling of oxidative and ssDNA damage alongside gene expression, in single cells. www.nature.com/articles/s41...

submitted 44 days ago • 1 comment

A Resource paper defines connectivity types of neurons based on a spatially registered database containing more than 20,000 neuronal reconstructions. A brain connectivity map is also generated using such connectivity features. www.nature.com/articles/s41...

submitted 51 days ago • 0 comments