Nature Methods
@naturemethods
Followers
148K
Following
2K
Media
2K
Statuses
5K
Nature Methods publishes cutting-edge methods, tools, analyses, resources, reviews, news and commentary, supporting life sciences research. Tweets by editors.
New York
Joined March 2011
The wait is over!! We are thrilled to announce that we have chosen Spatial Proteomics as 2024’s Method of the Year! 🥳. For more on Spatial Proteomics and a road map to this special issue, please see this month’s Editorial or read on in this thread.
3
297
831
It’s finally here!! Our Method of the Year 2021 is….Protein Structure Prediction!!.
13
412
2K
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.
7
352
1K
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 .
12
338
1K
Out today from the Goodarzi lab! @genophoria SwitchSeeker combines computation and experiment to identify functional RNA structural switches. Applied to the human transcriptome, it identified a novel RNA switch in the 3ʹUTR of RORC, linked to NMD.
0
44
165
Method of the Year 2020 is. spatially resolved transcriptomics! Read about why we selected this topic this year in our Editorial.
17
315
897
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.
18
528
836
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.
11
238
652
A Review paper from Peter Kharchenko @KharchenkoLab covers computational methods for scRNA-seq analyses, including their current limitations.
3
248
617
The first complete assembly of a human chromosome!.
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!
3
155
583
This month's Focus on advanced AI in biology also contains a series of Comments from leaders in their respective fields, who discuss the broad impacts that AI-based methods are likely to have on many areas of biological research.
3
67
221
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:.
2
241
537
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.
1
204
498
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.
2
132
447
The WashU Epigenome Browser now facilitates integrative visualization and exploration of 1D, 2D and 3D genomic data in a single webpage. #4DN .
2
123
445
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.
1
156
440
In a new Comment, Eric Betzig describes his vision for the future of bioimaging and bioimage analysis. He further recommends "Cell Observatories" as a path forward for addressing complex outstanding biological questions. @Eric_Betzig .
0
54
148
DynaMight from @SjorsScheres @MRC_LMB models continuous structural heterogeneity in cryo-EM datasets, leading to an improved reconstruction of the consensus structure. The study also explores the issue of overfitting when modeling structural flexibility.
0
36
131
OpenFold developed by @gahdritz, @NazimBouatta, and @MoAlQuraishi is a trainable, open-source implementation of AlphaFold2. It is fast and memory efficient, and the code and training data are available under a permissive license.
6
145
404
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.
1
110
363
Generative AI, large language models, transformers, foundation models - what does it all mean and what is the potential impact on your research? Whether you're an AI novice or an AI expert, we invite you to read our Focus issue on advanced AI in biology.
19
42
127
Introducing Mitometer, an algorithm for automated segmentation and tracking of mitochondria in live-cell 2D and 3D time-lapse images. @michelledigman @Austin_Lefebvre.
6
100
337
Method to Watch by Nina Vogt: Assembloids are emerging models for studying human brain development, complex neural circuits or interactions between different tissues.
2
79
326
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!
1
112
313
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.
1
114
328
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.
2
105
319
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.
3
147
299
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:
3
103
320
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.
1
114
313
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.
3
78
300
Squidpy from @fabian_theis and colleagues enables comprehensive analysis and visualization of spatial omics data with high efficiency. OA paper:
0
76
300
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.
0
89
300
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.
5
84
286
Henikoff, @NadiyaKhyzha and @KamiAhmad3 introduce RT&Tag that enables mapping RNA molecules in proximity to a protein of interest in intact nuclei. OA paper:
2
85
286
RhoFold+ is an end-to-end language model-based deep learning approach for predicting 3D structures of RNAs.
3
76
302
Out today: BioNumPy is a Python package for efficient array programming on biological data.
5
79
295
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.
1
85
278
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!
4
54
268
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.
5
81
264
A Perspective highlights workflow managers - useful for developing and managing complex bioinformatics pipelines. .@JonathanGoeke @goekelab @me_myself_andY @astar_gis
1
118
257
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! 🥳.
3
17
267
Out today, a fantastic Review on spatial omics and multiplexed imaging methods for exploring cancer biology from Shalin Naik and Kelly Rogers @shalinhnaik @KRogers1001
2
92
262
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.
0
80
253
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
6
141
254
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.
1
74
259
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.
0
54
255
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.
0
51
251
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! 🤩
2
50
254
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.
1
88
258
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
1
52
257
Out today! Hierarchical phase-contrast tomography (HiP-CT) enables multiscale imaging of any region within an intact human organ down to cellular resolution.
1
49
238
Out today! Pycro-Manager: open-source software for customized and reproducible microscope control.
2
82
247
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
1
63
243
We're very excited to share this Perspective out today, which provides guidance for high-quality multiplexed antibody-based tissue imaging!! .
0
68
224
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.
4
50
209
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.
3
52
217
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
1
112
214
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 .
2
59
210
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:
3
70
204
Exciting new work on genetically encoded multimeric tags for subcellular protein localization in cryo-EM from the Cuylen-Haering & Mahamid labs.
1
53
203
scFoundation, with 100 million parameters covering about 20,000 genes, pretrained on over 50 million single-cell transcriptomics profiles, is a foundation model for diverse tasks of single-cell analysis.
0
68
213
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.
1
38
209
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:
0
66
204
A head-mounted 3P microscope from Jason Kerr’s lab enables imaging of neuronal activity in freely moving rats.
0
66
193
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
2
50
199
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!
0
54
202
From Strauss and Jungman, concatenated probes help yield up to 100-fold faster DNA-PAINT!
2
67
203
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.
0
65
198
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.
4
80
188
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!
3
55
196
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 .
3
52
204
DeepPBS is a deep-learning based model for the prediction of protein–DNA binding specificities. It makes use of physicochemical and geometric contexts and works across different protein families and on experimentally determined as well as predicted protein–DNA complex structures.
1
29
111
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.
3
59
193
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.
1
46
194
GlycoRNA is a thing!! 😮. (this eloquent tweet by @rita_strack, twitter takeover).
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
3
33
193
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:
1
40
192
Introducing STELLAR: a geometric deep learning method for cell type discovery and identification in spatially resolved single-cell datasets. @jure @GarryPNolan @SnyderShot
0
51
193
The Trump administration in the US has interfered with scientific research and ignored scientific knowledge. Read our take here, and most importantly, VOTE!!!
6
91
186
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.
6
38
186
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 .
1
76
185
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: .
0
39
178
Check it out: a nanobody for GFP that can be switched on and off with small molecules, from the Johnsson group.
3
90
182
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
0
59
183
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.
1
58
179
Method of the Year: In a Comment, Joakim Lundeberg and colleagues summarize sequencing-based approaches for spatially resolved transcriptomics.
1
46
182
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
1
74
181
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:
4
58
179
A Review provides an overview of computational methods recently developed for detecting and analyzing structural variants using long-read sequencing data.
1
66
175
Using transcriptomic similarity and spatial coordinates, PASTE allows aligning and integrating spatial transcriptomics data generated from adjacent tissue slices. @RonZeira @benjraphael.
1
54
168
An automated multi-scale 3D imaging platform enables both organoid culture and high-content imaging on a single instrument. @Viasnofflab @BeghinTeam
1
52
170
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.
1
54
177
Out today from the @davidvanvalen lab! DeepCell Kiosk: cloud-native software that dynamically scales deep learning workflows to accommodate large imaging datasets.
1
36
174
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:
4
49
166
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.
1
45
169