-
Benchmarking spatial clustering methods with spatially resolved transcriptomics data Nat. Methods (IF 48.0) Pub Date : 2024-03-15 Zhiyuan Yuan, Fangyuan Zhao, Senlin Lin, Yu Zhao, Jianhua Yao, Yan Cui, Xiao-Yong Zhang, Yi Zhao
-
Breaking up the StayGold dimer yields three photostable monomers Nat. Methods (IF 48.0) Pub Date : 2024-03-14 Joachim Goedhart, Theodorus W. J. Gadella
-
Unlocking cryo-EM’s multishot potential with square or rectangular beams Nat. Methods (IF 48.0) Pub Date : 2024-03-14 Xiaowei Zhao
-
Graphene sandwich for cryo-EM Nat. Methods (IF 48.0) Pub Date : 2024-03-12 Arunima Singh
A group of researchers from Tsinghua University and Peking University, China, led by Hong-wei Wang and Hailin Peng, have developed a graphene sandwich-based approach for cryo-EM specimen preparation in which the graphene film serves as both a coverslip and a slide. A small droplet of the sample is applied to an EM grid precoated with a layer of graphene film. Then another layer of graphene film is
-
MINSTED tracking of single biomolecules Nat. Methods (IF 48.0) Pub Date : 2024-03-13 Lukas Scheiderer, Henrik von der Emde, Mira Hesselink, Michael Weber, Stefan W. Hell
-
A leap for directed evolution Nat. Methods (IF 48.0) Pub Date : 2024-03-12 Rita Strack
Directed evolution has been instrumental in the development of biomolecules with unique and desired functions relative to their natural starting points. While many strategies work well for generating mutant libraries, doing continuous mutagenesis and selection in cells still represents a technical challenge, as the mutagenesis necessary to create sequence diversity can be detrimental to the host cell’s
-
Neural networks for biomechanics Nat. Methods (IF 48.0) Pub Date : 2024-03-12 Madhura Mukhopadhyay
First, the team trained a neural network on fluorescence microscopy images of the focal adhesion protein zyxin in fibroblasts paired with corresponding traction forces. They confirmed that the model could generalize and then accurately predict forces from an unseen test set that was validated by comparisons with experimental data. The team also confirmed that this model could be trained on other cytoskeletal
-
Long-term monosynaptic tracing Nat. Methods (IF 48.0) Pub Date : 2024-03-12 Nina Vogt
“Monosynaptic tracing has become a fairly standard tool in neuroscience,” says Ian Wickersham from the Massachusetts Institute of Technology in Cambridge. The technology is used to map neuronal circuitry predominantly in the mouse brain and relies on a deletion mutant of rabies virus and its complementation in a starter population of neurons. However, rabies virus is inherently cytotoxic, and therefore
-
-
Peer review demystified: part 1 Nat. Methods (IF 48.0) Pub Date : 2024-03-12
Peer review is at the heart of publishing scientific papers. In this first installment of a two-part Editorial, we explain how we manage the process at Nature Methods.
-
Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly Nat. Methods (IF 48.0) Pub Date : 2024-03-08 Joshua Casey Darian, Ritu Kundu, Ramesh Rajaby, Wing-Kin Sung
-
Creating diploid assemblies from Nanopore and Illumina reads with hypo-assembler Nat. Methods (IF 48.0) Pub Date : 2024-03-08
-
Square condenser apertures for square cameras in low-dose transmission electron microscopy Nat. Methods (IF 48.0) Pub Date : 2024-03-08 Hamish G. Brown, Dan Smith, Benjamin C. Wardle, Eric Hanssen
-
Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN Nat. Methods (IF 48.0) Pub Date : 2024-03-08 Barrett M. Powell, Joseph H. Davis
-
An optogenetic method for the controlled release of single molecules Nat. Methods (IF 48.0) Pub Date : 2024-03-08 Purba Kashyap, Sara Bertelli, Fakun Cao, Yulia Kostritskaia, Fenja Blank, Niranjan A. Srikanth, Claire Schlack-Leigers, Roberto Saleppico, Dolf Bierhuizen, Xiaocen Lu, Walter Nickel, Robert E. Campbell, Andrew J. R. Plested, Tobias Stauber, Marcus J. Taylor, Helge Ewers
-
Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry Nat. Methods (IF 48.0) Pub Date : 2024-03-05 Evolène Deslignière, Victor C. Yin, Eduard H. T. M. Ebberink, Amber D. Rolland, Arjan Barendregt, Tobias P. Wörner, Konstantin O. Nagornov, Anton N. Kozhinov, Kyle L. Fort, Yury O. Tsybin, Alexander A. Makarov, Albert J. R. Heck
-
Improved green and red GRAB sensors for monitoring spatiotemporal serotonin release in vivo Nat. Methods (IF 48.0) Pub Date : 2024-03-05 Fei Deng, Jinxia Wan, Guochuan Li, Hui Dong, Xiju Xia, Yipan Wang, Xuelin Li, Chaowei Zhuang, Yu Zheng, Laixin Liu, Yuqi Yan, Jiesi Feng, Yulin Zhao, Hao Xie, Yulong Li
-
Real-time detection of 20 amino acids and discrimination of pathologically relevant peptides with functionalized nanopore Nat. Methods (IF 48.0) Pub Date : 2024-03-05 Ming Zhang, Chao Tang, Zichun Wang, Shanchuan Chen, Dan Zhang, Kaiju Li, Ke Sun, Changjian Zhao, Yu Wang, Mengying Xu, Lunzhi Dai, Guangwen Lu, Hubing Shi, Haiyan Ren, Lu Chen, Jia Geng
-
Spatial landmark detection and tissue registration with deep learning Nat. Methods (IF 48.0) Pub Date : 2024-03-04 Markus Ekvall, Ludvig Bergenstråhle, Alma Andersson, Paulo Czarnewski, Johannes Olegård, Lukas Käll, Joakim Lundeberg
-
Collaborate, disseminate, accelerate Nat. Methods (IF 48.0) Pub Date : 2024-02-27 Vivien Marx
Collaborations between researchers and companies can progress swimmingly and teams quickly validate findings and mature methods. All too often, things can’t advance and the ‘Valley of Death’ looms. New ways to collaborate, underpinned by computational muscle, can help.
-
Early-career navigation tips Nat. Methods (IF 48.0) Pub Date : 2024-02-26
In a group interview, early-career researchers in proteomics share how they plan for the future and navigate divides over methods.
-
Bright and stable monomeric green fluorescent protein derived from StayGold Nat. Methods (IF 48.0) Pub Date : 2024-02-26 Hanbin Zhang, Gleb D. Lesnov, Oksana M. Subach, Wenhao Zhang, Tatyana P. Kuzmicheva, Anna V. Vlaskina, Valeriya R. Samygina, Liangyi Chen, Xianxin Ye, Alena Yu. Nikolaeva, Azat Gabdulkhakov, Stavrini Papadaki, Wenming Qin, Valentin Borshchevskiy, Maxim M. Perfilov, Alexey S. Gavrikov, Mikhail Drobizhev, Alexander S. Mishin, Kiryl D. Piatkevich, Fedor V. Subach
-
scGPT: toward building a foundation model for single-cell multi-omics using generative AI Nat. Methods (IF 48.0) Pub Date : 2024-02-26 Haotian Cui, Chloe Wang, Hassaan Maan, Kuan Pang, Fengning Luo, Nan Duan, Bo Wang
-
Genome-scale pan-cancer interrogation of lncRNA dependencies using CasRx Nat. Methods (IF 48.0) Pub Date : 2024-02-26 Juan J. Montero, Riccardo Trozzo, Maya Sugden, Rupert Öllinger, Alexander Belka, Ekaterina Zhigalova, Paul Waetzig, Thomas Engleitner, Marc Schmidt-Supprian, Dieter Saur, Roland Rad
-
Super-sectioning with multi-sheet reversible saturable optical fluorescence transitions (RESOLFT) microscopy Nat. Methods (IF 48.0) Pub Date : 2024-02-23 Andreas Bodén, Dirk Ollech, Andrew G. York, Alfred Millett-Sikking, Ilaria Testa
-
A-SOiD, an active-learning platform for expert-guided, data-efficient discovery of behavior Nat. Methods (IF 48.0) Pub Date : 2024-02-21 Jens F. Tillmann, Alexander I. Hsu, Martin K. Schwarz, Eric A. Yttri
-
A statistical method for quantifying progenitor cells reveals incipient cell fate commitments Nat. Methods (IF 48.0) Pub Date : 2024-02-20 Shanjun Deng, Han Gong, Di Zhang, Mengdong Zhang, Xionglei He
-
Using stem cells to model the human bone marrow in a dish Nat. Methods (IF 48.0) Pub Date : 2024-02-19
-
VIBRANT: a phenotyping method for drug discovery using vibrational spectroscopy Nat. Methods (IF 48.0) Pub Date : 2024-02-19
-
A biomimetic robotic antigen-presenting system for sensitive T cell recognition Nat. Methods (IF 48.0) Pub Date : 2024-02-19
-
TREX identifies region-specific protein interactors of RNA molecules Nat. Methods (IF 48.0) Pub Date : 2024-02-19
-
Uncovering hidden states driving biological outcomes using machine learning Nat. Methods (IF 48.0) Pub Date : 2024-02-19
-
TREX reveals proteins that bind to specific RNA regions in living cells Nat. Methods (IF 48.0) Pub Date : 2024-02-19 Martin Dodel, Giulia Guiducci, Maria Dermit, Sneha Krishnamurthy, Emilie L. Alard, Federica Capraro, Zeinab Rekad, Lovorka Stojic, Faraz K. Mardakheh
-
Generation of complex bone marrow organoids from human induced pluripotent stem cells Nat. Methods (IF 48.0) Pub Date : 2024-02-19 Stephanie Frenz-Wiessner, Savannah D. Fairley, Maximilian Buser, Isabel Goek, Kirill Salewskij, Gustav Jonsson, David Illig, Benedicta zu Putlitz, Daniel Petersheim, Yue Li, Pin-Hsuan Chen, Martina Kalauz, Raffaele Conca, Michael Sterr, Johanna Geuder, Yoko Mizoguchi, Remco T. A. Megens, Monika I. Linder, Daniel Kotlarz, Martina Rudelius, Josef M. Penninger, Carsten Marr, Christoph Klein
-
SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains Nat. Methods (IF 48.0) Pub Date : 2024-02-19 Javad Rahimikollu, Hanxi Xiao, AnnaElaine Rosengart, Aaron B. I. Rosen, Tracy Tabib, Paul M. Zdinak, Kun He, Xin Bing, Florentina Bunea, Marten Wegkamp, Amanda C. Poholek, Alok V. Joglekar, Robert A. Lafyatis, Jishnu Das
-
Multimodal probing of T-cell recognition with hexapod heterostructures Nat. Methods (IF 48.0) Pub Date : 2024-02-19 Xiaodan Huang, Lingyuan Meng, Guoshuai Cao, Aleksander Prominski, Yifei Hu, Chuanwang Yang, Min Chen, Jiuyun Shi, Charles Gallagher, Thao Cao, Jiping Yue, Jun Huang, Bozhi Tian
-
VIBRANT: spectral profiling for single-cell drug responses Nat. Methods (IF 48.0) Pub Date : 2024-02-19 Xinwen Liu, Lixue Shi, Zhilun Zhao, Jian Shu, Wei Min
-
Challenges and perspectives in computational deconvolution of genomics data Nat. Methods (IF 48.0) Pub Date : 2024-02-19 Lana X. Garmire, Yijun Li, Qianhui Huang, Chuan Xu, Sarah A. Teichmann, Naftali Kaminski, Matteo Pellegrini, Quan Nguyen, Andrew E. Teschendorff
-
OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data Nat. Methods (IF 48.0) Pub Date : 2024-02-16 Julianus Pfeuffer, Chris Bielow, Samuel Wein, Kyowon Jeong, Eugen Netz, Axel Walter, Oliver Alka, Lars Nilse, Pasquale Domenico Colaianni, Douglas McCloskey, Jihyung Kim, George Rosenberger, Leon Bichmann, Mathias Walzer, Johannes Veit, Bertrand Boudaud, Matthias Bernt, Nikolaos Patikas, Matteo Pilz, Michał Piotr Startek, Svetlana Kutuzova, Lukas Heumos, Joshua Charkow, Justin Cyril Sing, Ayesha Feroz
-
Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN Nat. Methods (IF 48.0) Pub Date : 2024-02-16 Yanay Rosen, Maria Brbić, Yusuf Roohani, Kyle Swanson, Ziang Li, Jure Leskovec
-
Multiscale biochemical mapping of the brain through deep-learning-enhanced high-throughput mass spectrometry Nat. Methods (IF 48.0) Pub Date : 2024-02-16 Yuxuan Richard Xie, Daniel C. Castro, Stanislav S. Rubakhin, Timothy J. Trinklein, Jonathan V. Sweedler, Fan Lam
-
Deciphering protein interaction network dynamics with a machine learning-based framework Nat. Methods (IF 48.0) Pub Date : 2024-02-15
-
Tapioca: a platform for predicting de novo protein–protein interactions in dynamic contexts Nat. Methods (IF 48.0) Pub Date : 2024-02-15 Tavis. J. Reed, Matthew. D. Tyl, Alicja Tadych, Olga. G. Troyanskaya, Ileana. M. Cristea
-
Development of the human head Nat. Methods (IF 48.0) Pub Date : 2024-02-12 Nina Vogt
The researchers focused on head development, and in particular on the development of the skull, head and neck muscles, the eyes and associated tissues, various glands and the vasculature. They began by screening antibodies to obtain a set of 36 that resulted in reproducible staining in whole-mount samples. These antibodies were then directly conjugated to fluorophores to facilitate multiplexed staining
-
Where imaging and metrics meet Nat. Methods (IF 48.0) Pub Date : 2024-02-12
When it comes to bioimaging and image analysis, details matter. Papers in this issue offer guidance for improved robustness and reproducibility.
-
Metrics reloaded: recommendations for image analysis validation Nat. Methods (IF 48.0) Pub Date : 2024-02-12 Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D. Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A. Riegler, Manuel Wiesenfarth, A. Emre Kavur, Carole H. Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis
-
Sharpen SV detection Nat. Methods (IF 48.0) Pub Date : 2024-02-12 Lin Tang
Boosted by the power of long-read sequencing, the frontiers of structural variation (SV) detection are advancing quickly. Accompanying and facilitating this progress, the toolbox of computational methods keeps expanding — although it is still far from being perfected. In 2018, Fritz Sedlazeck at Baylor College of Medicine and colleagues presented ‘Sniffles1’, which has since become a widely used tool
-
More deaminases towards precise editing Nat. Methods (IF 48.0) Pub Date : 2024-02-12 Lei Tang
Base editors hold great potential for correcting point mutations, which contribute to over 50% of identified disease-associated variations. Among the base editors that have been developed, adenine base editors (ABEs) and cytosine base editors — which enable the conversion of A to G and C to T, respectively — have been used in a range of biomedical applications. The deaminases used in ABEs are originally
-
Spotting T and B cell receptors Nat. Methods (IF 48.0) Pub Date : 2024-02-12 Madhura Mukhopadhyay
The antigen specificity of T and B lymphocytes is mediated by cognate antigen receptors on the cell surface. Although recent technical developments have enabled analyses of T and B cell receptors at the single-cell level, these methods have so far lacked spatial resolution. A recent paper in Science reports ‘Spatial VDJ’, a spatial transcriptomics-based method that maps full-length immunoglobulin (Ig)
-
Understanding metric-related pitfalls in image analysis validation Nat. Methods (IF 48.0) Pub Date : 2024-02-12 Annika Reinke, Minu D. Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A. Emre Kavur, Tim Rädsch, Carole H. Sudre, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M. Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A. Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker
-
A paintbrush for delivery of nanoparticles and molecules to live cells with precise spatiotemporal control Nat. Methods (IF 48.0) Pub Date : 2024-02-12 Cornelia Holler, Richard William Taylor, Alexandra Schambony, Leonhard Möckl, Vahid Sandoghdar
-
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses Nat. Methods (IF 48.0) Pub Date : 2024-02-12 Eric D. Sun, Rong Ma, Paloma Navarro Negredo, Anne Brunet, James Zou
-
CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2 Nat. Methods (IF 48.0) Pub Date : 2024-02-07 Ben Shor, Dina Schneidman-Duhovny
-
Single-cell probing of RNA structure Nat. Methods (IF 48.0) Pub Date : 2024-02-06 Elizabeth A. Jolley, Philip C. Bevilacqua
-
Correcting PCR amplification errors in unique molecular identifiers to generate accurate numbers of sequencing molecules Nat. Methods (IF 48.0) Pub Date : 2024-02-05 Jianfeng Sun, Martin Philpott, Danson Loi, Shuang Li, Pablo Monteagudo-Mesas, Gabriela Hoffman, Jonathan Robson, Neelam Mehta, Vicki Gamble, Tom Brown, Tom Brown, Stefan Canzar, Udo Oppermann, Adam P. Cribbs
-
From zero to hero in budget-making Nat. Methods (IF 48.0) Pub Date : 2024-02-05
The grant deadline approaches but budget details are still missing. Experienced budget-makers share how they manage budgets and the ‘boom–bust’ cycle.
-
Homotrimer barcodes enable accurate counting of RNA molecules during high-throughput RNA sequencing Nat. Methods (IF 48.0) Pub Date : 2024-02-05
-
Inside the chase after those elusive proteoforms Nat. Methods (IF 48.0) Pub Date : 2024-02-02 Vivien Marx
Human cells contain crowds of protein variants, but, especially in a time of funding challenges, chasing these proteoforms takes dogged persistence.
-
A prime editor that makes space for insertions Nat. Methods (IF 48.0) Pub Date : 2024-02-01
We developed a prime editing (PE) strategy by incorporating a 5′–3′ exonuclease activity, which enhanced the efficacy and precision of ≥30-nucleotide DNA insertions without a secondary nick. Our optimization of the PE complex revealed that recruiting the exonuclease via an RNA aptamer outperformed direct protein fusions.
-
Exonuclease-enhanced prime editors Nat. Methods (IF 48.0) Pub Date : 2024-02-01 Dong-Jiunn Jeffery Truong, Julian Geilenkeuser, Stephanie Victoria Wendel, Julius Clemens Heinrich Wilming, Niklas Armbrust, Eva Maria Hildegard Binder, Tobias Heinrich Santl, Annika Siebenhaar, Christoph Gruber, Teeradon Phlairaharn, Milica Živanić, Gil Gregor Westmeyer