Nature Methods @naturemethods Twitter profile

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Nature Methods

5 months

It's that time of year!! 🎉We are so excited to announce our 2023 pick for Nature Methods' Method of the Year: methods for modeling development. Read the Editorial to find out why we chose this as our pick. #moty2023

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Nature Methods

@naturemethods

2 years

It’s finally here!! Our Method of the Year 2021 is….Protein Structure Prediction!!

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Nature Methods

@naturemethods

2 years

Are you curious about using organic dyes in your microscopy experiments but not sure where to start? This Perspective from @rhodamine110 and @jonathangrimm introduces readers to the world of dyes and their pros and cons for biological applications.

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Nature Methods

@naturemethods

2 years

Out today and freely available, a tool many in the image analysis community have been waiting for! PyImageJ: A library for integrating ImageJ and Python @EliceiriK @UWMadisonLOCI @ctrueden @CiminiLab @DrAnneCarpenter

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Nature Methods

@naturemethods

3 years

Method of the Year 2020 is...spatially resolved transcriptomics! Read about why we selected this topic this year in our Editorial.

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Nature Methods

@naturemethods

1 year

It's finally here!! Our Method of the Year 2022 is....long-read sequencing! 🎉 Read our (free!) Editorial to learn why we felt the time was right to select this class of powerful technologies as the Method of the Year.

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Nature Methods

@naturemethods

3 years

A Review paper from Peter Kharchenko @KharchenkoLab covers computational methods for scRNA-seq analyses, including their current limitations.

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Nature Methods

@naturemethods

4 years

The first complete assembly of a human chromosome!

Tim Stearns

@StearnsLab

4 years

20 years after the announcement of the "working draft" of the human genome, we have the first complete assembly of a human chromosome. It's hard work to chase down every last base!

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Nature Methods

@naturemethods

10 months

For this Focus issue, we asked experts in bioimaging from around the world to tell us what excited them about the future of bioimage analysis for the next 5-20 years. (1/n) All Focus content can also be found here:

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Nature Methods

@naturemethods

10 months

Out today: SCENIC+ is a comprehensive toolbox for inferring and analyzing enhancer-driven gene regulatory networks (eGRN) using single-cell multiomic data. @steinaerts @seppe_winter @Bravo_Potato

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

Nature Methods - SCENIC+ is a comprehensive toolbox for inferring and analyzing enhancer-driven gene regulatory networks using single-cell multiomic data.

www.nature.com

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Nature Methods

@naturemethods

3 years

By using a new deep learning architecture, Enformer leverages long-range information to improve prediction of gene expression based on DNA sequence. @deepmind @calico Open access paper:

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Nature Methods

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2 years

From the Mougous and Wiggins labs comes Omnipose! A versatile tool for segmenting diverse and arbitrarily shaped cells in microscopy images, with an emphasis on challenging bacterial shapes.

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Nature Methods

@naturemethods

2 years

The WashU Epigenome Browser now facilitates integrative visualization and exploration of 1D, 2D and 3D genomic data in a single webpage. #4DN

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Nature Methods

@naturemethods

2 years

A new benchmarking study compares 16 methods for integrating complex single-cell RNA and ATAC datasets and provides a guide to method choice. @MDLuecken @fabian_theis @colomemaria_epi @ICBMunich @HelmholtzMunich

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Nature Methods

@naturemethods

3 years

Out today! DeepImageJ offers a user-friendly solution in ImageJ to run trained deep learning models for biomedical image analysis. It includes guiding tools for reliable analyses, contributing to the democratization of deep learning in microscopy.

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Nature Methods

@naturemethods

3 years

Method to Watch by Nina Vogt: Assembloids are emerging models for studying human brain development, complex neural circuits or interactions between different tissues.

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Nature Methods

@naturemethods

3 years

Introducing Mitometer, an algorithm for automated segmentation and tracking of mitochondria in live-cell 2D and 3D time-lapse images. @michelledigman @Austin_Lefebvre

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Nature Methods

@naturemethods

6 years

Organoids are Method of the Year @naturemethods

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Nature Methods

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1 year

Excited to announce the Spatial Omics DataBase (SODB), a web-based platform for sharing and analyzing >25 types of spatial omics data. SODB promotes data reuse, offers novel viz tools and can streamline development of omics analysis tools.

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Nature Methods

@naturemethods

3 years

Single-cell methods are becoming the norm, but what about proteins? Chirlmin Joo and colleagues provide a detailed survey of the emerging landscape of single-molecule protein sequencing technologies in a Review out today!

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Nature Methods

@naturemethods

5 months

mStayGold, a monomeric derivative of the extremely photostable GFP StayGold, offers improved protein tagging while maintaining desirable photophysical properties. mStayGold extends the possibilities of what can be achieved with fluorescent protein labels.

StayGold variants for molecular fusion and membrane-targeting applications

Nature Methods - Monomeric and tandem dimer derivatives of the bright and photostable green fluorescent protein StayGold offer versatile tools for tagging target proteins and membranes in extended...

www.nature.com

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Nature Methods

@naturemethods

5 years

The estimation of effect sizes and their uncertainty allows researchers to move from the question ‘Does it?’ to ‘How much?’ DABEST () is a tool to generate such estimation graphics.

Moving beyond P values: data analysis with estimation graphics

Nature Methods - Moving beyond P values: data analysis with estimation graphics

www.nature.com

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Nature Methods

@naturemethods

3 years

Tangram is a versatile tool for aligning single-cell and single-nucleus RNA-seq data to spatially-resolved transcriptomics data using deep learning. @broadinstitute @tbyanc @gabo_scalia OA paper:

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Nature Methods

@naturemethods

9 months

Love napari but missing some ImageJ functions? Look no further than napari-imagej, which provides an accessible and comprehensive solution to ImageJ ecosystem access from napari.

napari-imagej: ImageJ ecosystem access from napari

Nature Methods - napari-imagej: ImageJ ecosystem access from napari

www.nature.com

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Nature Methods

@naturemethods

2 years

The Yin group from Wuhan University leverages a pair of pegRNAs to efficiently insert DNA fragments up to 250bp without the need of donor DNA, named GRAND editing.

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Nature Methods

@naturemethods

2 years

Squidpy from @fabian_theis and colleagues enables comprehensive analysis and visualization of spatial omics data with high efficiency. OA paper:

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Nature Methods

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2 months

Out today from the Stegle, Theis, and Moore labs! SpatialData is a user-friendly computational framework for exploring, analyzing, annotating, aligning and storing spatial omics data that can seamlessly handle large multimodal datasets.

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Nature Methods

@naturemethods

3 years

Out today! Best practices and tools for reporting reproducible fluorescence microscopy methods!! These are the among the most comprehensive guidelines we've seen, and we hope they become second nature to microscopists and improve rigor and reproducibility.

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Nature Methods

@naturemethods

2 years

Henikoff, @NadiyaKhyzha and @KamiAhmad3 introduce RT&Tag that enables mapping RNA molecules in proximity to a protein of interest in intact nuclei. OA paper:

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Nature Methods

@naturemethods

1 year

Bioinformatics advancements unleash the full potential of long-read sequencing in various areas of genomics. A Comment from Michael Schatz ( @mike_schatz ) and colleagues highlights this thriving domain of active methods development. @JohnsHopkins

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Nature Methods

@naturemethods

3 years

It's finally here! The May issue of @NatureSMB is LIVE and we are excited to share these gorgeous covers with you! 🎉 We split this painting depicting the transport and release of antibody-filled vesicles (from a B-cell) by @dsgoodsell to create these matching covers for #PDB50 !

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Nature Methods

@naturemethods

4 years

scRNA-seq offers a snapshot of transcriptomes but not RNA dynamics. scNT-seq from the Wu lab @hao_wu_7 integrates metabolic labeling and droplet sequencing to perform parallel analysis of newly-transcribed and pre-existing mRNAs.

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Nature Methods

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3 years

A Perspective highlights workflow managers - useful for developing and managing complex bioinformatics pipelines. @JonathanGoeke @goekelab @me_myself_andY @astar_gis

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Nature Methods

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3 years

Out today, a fantastic Review on spatial omics and multiplexed imaging methods for exploring cancer biology from Shalin Naik and Kelly Rogers @shalinhnaik @KRogers1001

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Nature Methods

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2 years

Tomorrow will be a big day....we will announce our Method of the Year 2021! We can't wait to share this special issue! Stay tuned! 🥳

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Nature Methods

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8 months

This Review from @OliverStegle and @BrittaVelten discusses statistical and computational strategies for analyzing various spatial and temporal omics data types, with an emphasis on the common modeling principles.

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Nature Methods

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4 years

The Meltome Atlas compiles the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans, providing a resource for analyzing protein stability in the context of function and interactions. @kusterlab @savitski_lab

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Nature Methods

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2 years

In their Comment, AlphaFold developers John Jumper and @demishassabis of @DeepMind describe the design of AlphaFold’s neural network and give their views on how it will transform the field of structural biology.

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Nature Methods

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2 years

Researchers present a comprehensive benchmarking analysis of computational methods that integrate spatial and single-cell transcriptomics data for transcript distribution prediction and cell type deconvolution.

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2 years

Out yesterday from @adam_k_glaser and @jonliu123 , a versatile hybrid open top light sheet microscope for imaging of large cleared samples. Check out their images! 🤩

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Nature Methods

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7 months

Long-read sequencing tools can capture the full picture of genomes and transcriptomes. An Analysis assesses the performance of long-read RNA sequencing analysis tools including isoform detection and differential expression analysis workflows.

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Nature Methods

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1 month

Is cell segmentation a solved problem? Maybe not yet, but the results of this multimodality cell segmentation challenge get us closer! (Spoiler, the winner is a generalist Transformer-based model). @BoWang87

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Nature Methods

@naturemethods

4 months

A clever strategy for multiplexed immunolabeling out today from Peng Yin's lab. "Thermal-plex" uses DNA probes that fluoresce sequentially when, and only when, activated with transient exposure to heating spikes at designated temperatures.

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Nature Methods

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3 years

Out today! Hierarchical phase-contrast tomography (HiP-CT) enables multiscale imaging of any region within an intact human organ down to cellular resolution.

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Nature Methods

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3 years

Out today! Pycro-Manager: open-source software for customized and reproducible microscope control.

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Nature Methods

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3 years

Come see CellPose from the Pachitariu lab for your image segmentation needs! Cellpose is a generalist, deep learning-based approach for segmenting structures in a wide range of image types. @marius10p

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Nature Methods

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2 years

Using a sequence-based deep neural network, scBasset facilitates various tasks of single-cell ATAC-seq analysis in a unified framework. @HY3952 @drklly @calico

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Nature Methods

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2 years

We're very excited to share this Perspective out today, which provides guidance for high-quality multiplexed antibody-based tissue imaging!!

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2 years

In a new Analysis paper, researchers compare the performance of 9 computational methods to identify and rank reprogramming transcription factors for 8 target cell types.

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2 years

Our March issue is live! 🎉 On the cover, multiplexed tissue imaging evokes a stained glass window. This gorgeous image was created by Stefan Uderhardt @red_ven and Andrea Radtke.

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Nature Methods

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3 years

Nanopore sequencing allows profiling long-range patterns on single molecules. nanoNOMe uses nanopore sequencing to profile CpG methylation and chromatin accessibility in human cells. @timp0

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Nature Methods

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5 years

So excited to be sharing this Perspective online today from Hamprecht and Kreshuk on Ilastik! Ilastik is a powerful tool for bringing sophisticated image analysis to biologists. Read it here or for free here

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2 years

An iterative approach for improving #AlphaFold protein model quality using experimental density maps, where rebuilt models are used as templates in new AlphaFold predictions, from @TerwillTom and colleagues. OA paper:

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Nature Methods

@naturemethods

6 months

Exciting new work on genetically encoded multimeric tags for subcellular protein localization in cryo-EM from the Cuylen-Haering & Mahamid labs.

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Nature Methods

@naturemethods

1 year

Out today! Radial Symmetry-FISH (RS-FISH) -- an accurate, fast, and user-friendly software for spot detection in 2D and 3D images. Bring on your smFISH, spatial transcriptomics, or spatial genomics applications! @kisharrington @successprocess @preibischs

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Nature Methods

@naturemethods

2 years

CellRank infers directed cell state transitions and cell fates using RNA velocity information from single-cell data. @MariusLange8 , @dana_peer , @fabian_theis , @sloan_kettering , @ICBmunich OA paper:

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4 years

A head-mounted 3P microscope from Jason Kerr’s lab enables imaging of neuronal activity in freely moving rats.

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3 years

Out today! nnU-Net is a deep learning-based image segmentation method that automatically configures itself for diverse biological and medical image segmentation tasks. And its performance is impressive!

nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation

Nature Methods - nnU-Net is a deep learning-based image segmentation method that automatically configures itself for diverse biological and medical image segmentation tasks. nnU-Net offers...

www.nature.com

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Nature Methods

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6 months

A cool chemical biology paper from the Loh lab! Adaptable, turn-on maturation (ATOM) biosensors use mono/nanobody targeting to control fluorescent protein maturation, enabling bright and specific cellular biosensing.

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Nature Methods

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4 years

From Strauss and Jungman, concatenated probes help yield up to 100-fold faster DNA-PAINT!

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2 years

CODA is a method for 3D reconstruction of large tissues at subcellular resolution from serially sectioned H&E images, from Pei-Hsun Wu, @deniswirtz and colleagues. @johnshopkins @ashleykiemen

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Nature Methods

@naturemethods

4 years

Microbial eukaryotes are important, but often overlooked, organisms in the global ecosystem. A Resource, supported by a community effort, describes valuable transformation tools for marine protists that have been challenging to genetically manipulate.

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2 years

Out today from the Johnsson lab: HaloTag variants that change the brightness and fluorescence lifetimes of rhodamines compared to HaloTag7. Lots of potential for multiplexed FLIM, including new lifetime-based cell cycle reporters. Open access!

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Nature Methods

@naturemethods

3 years

GlycoRNA is a thing!! 😮 (this eloquent tweet by @rita_strack , twitter takeover)

Ryan Flynn

@raflynn5

3 years

Excited to share my work w/ @CarolynBertozzi describing the discovery of glycoRNA today @CellCellPress . Since our @biorxivpreprint we uncovered an unexpected twist: glycoRNAs are on the surface of cells+some Siglec receptors have RNA-dependent cell binding

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4 years

The Trump administration in the US has interfered with scientific research and ignored scientific knowledge. Read our take here, and most importantly, VOTE!!!

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2 months

Pre-trained using over 33 million single cell RNA-seq profiles, scGPT is a foundation model facilitating a broad spectrum of downstream single-cell analysis tasks by transfer learning. @BoWang87 @HAOTIANCUI1 @ChloeXWang1 @UofT @VectorInst @UHN

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Nature Methods

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2 years

Out today from @bewersdorflab ! Two-color fluorogenic DNA-PAINT introduces self-quenching, kinetics-optimized probe designs. This approach improves imaging speed 26-fold and eliminates the need for optical sectioning.

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2 years

What's new in spatial 'omics? Light-seq from the @SinemKSaka1 , Kishi, Cepko, and Yin labs! Light-Seq uses light-directed DNA barcoding in fixed cells and tissues for multiplexed spatial indexing and subsequent next gen sequencing of even rare cell types.

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2 years

Introducing STELLAR: a geometric deep learning method for cell type discovery and identification in spatially resolved single-cell datasets. @jure @GarryPNolan @SnyderShot

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2 years

Ever wonder why nm localization precisions often don't translate to similar resolution below 10 nm? A paper from @LabSauer points to RET between fluorophores as a major factor. and see the accompanying N&V from @LMoeckl

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2 years

Our February issue is live! 🎉 On the cover, a beautiful example of cryo-expansion microscopy (Cryo-ExM) used to observe a human cell in mitosis, from @MarineLaporte8 of @CentrioleLab . OA paper here:

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3 years

As part of our commitment to increasing transparency in our editorial and peer review processes, we are very pleased to announce that we are now publishing peer review reports (including editorial decisions letters and author rebuttals) for original research papers.

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11 months

The PanGenome Research Tool Kit (PGR-TK) achieves flexible and scalable representation, visualization, and analysis of genomic variation using pangenome graphs. @infoecho @sedlazeck @GenomeInABottle @psudmant @srbehera11

Multiscale analysis of pangenomes enables improved representation of genomic diversity for repeti...

Nature Methods - The PanGenome Research Tool Kit (PGR-TK) achieves flexible and scalable representation, visualization and analysis of genomic variation using pangenome graphs.

www.nature.com

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4 years

Check it out: a nanobody for GFP that can be switched on and off with small molecules, from the Johnsson group.

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2 years

Our May issue is now live! 🎉 On the cover, a beautiful optically cleared mouse brain imaged with a hybrid open-top light-sheet microscope, from @adam_k_glaser (paper here: ).

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3 years

The Signac framework enables end-to-end analysis of single-cell chromatin data and offers interoperability with the Seurat package for multimodal analysis. @timoast @satijalab @nygenome

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2 years

Our August issue is now live!

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1 year

A new paper presents a statistical framework for power analysis of spatial omics studies, facilitated by an in silico tissue generation method. @ethanagb @DenisSchapiro @mssanjavickovic @broadinstitute @HiTSatHarvard OA paper:

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3 years

Method of the Year: In a Comment, Joakim Lundeberg and colleagues summarize sequencing-based approaches for spatially resolved transcriptomics.

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9 months

Extra-long tandem repeats (ETRs) such as centromeres and immunoglobulin loci are difficult to align. UniAligner is a computational method for efficiently and accurately aligning ETRs, facilitating analysis of their variation and evolution. @AndreyBzikadze

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8 months

Really pleased to publish this timely set of checklists to help improve the presentation and reproducibility of microscopy data. Wonderful community effort led by @ChriSchmied @helenajambor @tischitischer

Community-developed checklists for publishing images and image analyses

Nature Methods - Community-developed checklists offer best-practice guidance for biologists preparing light microscopy images and describing image analyses for publications.

www.nature.com

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2 years

Using transcriptomic similarity and spatial coordinates, PASTE allows aligning and integrating spatial transcriptomics data generated from adjacent tissue slices. @RonZeira @benjraphael

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Nature Methods

@naturemethods

10 months

A Review provides an overview of computational methods recently developed for detecting and analyzing structural variants using long-read sequencing data.

A survey of algorithms for the detection of genomic structural variants from long-read sequencing...

Nature Methods - This Review provides an overview of computational methods recently developed for detecting and analyzing structural variants using long-read sequencing data.

www.nature.com

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9 months

Research Highlight by @DrArunimaSingh : @cees_dekker and colleagues @tudelft have expanded nanopore-based single-molecule sequencing technology to post-translational modifications. They demonstrate the detection of phosphorylation along single peptides.

Nanopore-based detection of phosphorylation

Nature Methods - Nanopore-based detection of phosphorylation

www.nature.com

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2 years

An automated multi-scale 3D imaging platform enables both organoid culture and high-content imaging on a single instrument. @Viasnofflab @BeghinTeam

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3 years

CoTECH uses split-pool barcoding strategy to jointly profile histone modifications and transcriptome in single cells, which offers a multiomics tool to study epigenetic regulations during development. @AibinHe @PKU1898

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3 years

Out today from the @davidvanvalen lab! DeepCell Kiosk: cloud-native software that dynamically scales deep learning workflows to accommodate large imaging datasets.

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2 years

We are so pleased to announce that this month, we are officially launching a new article format for comparative analyses of established, related tools or methods, called Registered Reports. Read all about it in this month's Editorial:

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11 months

Out today! Trying to improve your spatial resolution for sequencing-based spatial transcriptomics? Look no further than Expansion Spatial Transcriptomics from the Lundeberg and Wang labs.

Expansion spatial transcriptomics - Nature Methods

Expansion spatial transcriptomics (Ex-ST) combines the power of tissue expansion with an improved RNA capture protocol for carrying out capture array-based spatial transcriptomics at high spatial...

www.nature.com

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10 months

The Tyson lab presents CheckM2, which leverages machine learning for improved estimation of completeness and contamination of metagenome-assembled genomes (MAGs) generated using metagenomics data. @CMR_QUT @AChklovski

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8 months

Interested in near-infrared fluorescent proteins but don't know where to start? Our very first Registered Report can help! In it Piatkevich and colleagues perform a quantitative comparison of NIR FPs (and some far-red) in vitro, in cells, and in vivo.

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6 months

Out today! Enhanced super-resolution radial fluctuations (eSRRF) for improved volumetric live-cell super-resolution imaging at high speeds. @HenriquesLab @christlet @Bassam_A_HAJJ

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4 months

Genetic modifications to the bioluminescence pathway in the fungus Neonothopanus nambi enhance bioluminescence by 1-2 orders of magnitude in plants and other eukaryotes.

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3 months

New from the @SandoghdarLab ! μkiss is a micropipette-based approach for delivering very small amounts of nanoparticles and small molecules to the cell surface with exquisite spatiotemporal control, enabling a wide range of biological investigations.

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3 years

The LIVECell dataset comprises annotated phase-contrast images of over 1.6 million cells from different cell lines during growth from sparse seeding to confluence for improved training of deep learning-based models of image segmentation.

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4 months

SHAPE-inspired RNA structure profiling at single-cell resolution!! Read about it in the paper out today from Jiaxu Wang and Yue Wan.

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8 months

The Tang group presents scNanoHi-C: a single cell Hi-C method based on nanopore long-read sequencing. scNanoHi-C allows researchers to capture high-order chromatin structures and detect genomic variations such as CNVs and SVs.

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2 years

So happy we've published TrackMate 7! @guijacquemet @jytinevez TrackMate 7 combines the benefits of deep learning-based image segmentation with accurate object tracking to enable improved 2D and 3D tracking of diverse objects in biological research.

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3 years

Cell interaction by multiplet sequencing (CIM-seq) by Martin Enge and colleagues is a RNA-seq-based method to analyze physical cell-cell interactions in complex tissues.

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3 years

Our latest Tech Feature 'Microscopy made to order' by @eisensteinium covers 'do-it-yourself' microscopy, and how open software and hardware tools are advancing science. (This gorgeous image brought to you by the mesoSPIM)

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