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The multimodality cell segmentation challenge: toward universal solutions Nat. Methods (IF 48.0) Pub Date : 2024-03-26 Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Haofeng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Vojislav Gligorovski, Maxime Scheder, Sahand Jamal Rahi, Carly Kempster, Alice Pollitt, Leon Espinosa, Tâm Mignot, Jan Moritz Middeke, Jan-Niklas Eckardt
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DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes Nat. Methods (IF 48.0) Pub Date : 2024-03-26 Fabian Frommelt, Andrea Fossati, Federico Uliana, Fabian Wendt, Peng Xue, Moritz Heusel, Bernd Wollscheid, Ruedi Aebersold, Rodolfo Ciuffa, Matthias Gstaiger
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Closing in on cancer heterogeneity with organoids Nat. Methods (IF 48.0) Pub Date : 2024-03-25 Vivien Marx
Organoids are an emerging way to model the fraught complexity of tumors.
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Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis Nat. Methods (IF 48.0) Pub Date : 2024-03-25 Wenpin Hou, Zhicheng Ji
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Open-top multisample dual-view light-sheet microscope for live imaging of large multicellular systems Nat. Methods (IF 48.0) Pub Date : 2024-03-20 Franziska Moos, Simon Suppinger, Gustavo de Medeiros, Koen Cornelius Oost, Andrea Boni, Camille Rémy, Sera Lotte Weevers, Charisios Tsiairis, Petr Strnad, Prisca Liberali
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RoboEM: automated 3D flight tracing for synaptic-resolution connectomics Nat. Methods (IF 48.0) Pub Date : 2024-03-21 Martin Schmidt, Alessandro Motta, Meike Sievers, Moritz Helmstaedter
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A multicolor suite for deciphering population coding of calcium and cAMP in vivo Nat. Methods (IF 48.0) Pub Date : 2024-03-21 Tatsushi Yokoyama, Satoshi Manita, Hiroyuki Uwamori, Mio Tajiri, Itaru Imayoshi, Sho Yagishita, Masanori Murayama, Kazuo Kitamura, Masayuki Sakamoto
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Found: a skilled, courageous postdoctoral fellow Nat. Methods (IF 48.0) Pub Date : 2024-03-20
To select the best postdoctoral fellows for their labs, principal investigators assess scientific qualifications and more.
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SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms Nat. Methods (IF 48.0) Pub Date : 2024-03-20 Francisco J. Pardo-Palacios, Angeles Arzalluz-Luque, Liudmyla Kondratova, Pedro Salguero, Jorge Mestre-Tomás, Rocío Amorín, Eva Estevan-Morió, Tianyuan Liu, Adalena Nanni, Lauren McIntyre, Elizabeth Tseng, Ana Conesa
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SpatialData: an open and universal data framework for spatial omics Nat. Methods (IF 48.0) Pub Date : 2024-03-20 Luca Marconato, Giovanni Palla, Kevin A. Yamauchi, Isaac Virshup, Elyas Heidari, Tim Treis, Wouter-Michiel Vierdag, Marcella Toth, Sonja Stockhaus, Rahul B. Shrestha, Benjamin Rombaut, Lotte Pollaris, Laurens Lehner, Harald Vöhringer, Ilia Kats, Yvan Saeys, Sinem K. Saka, Wolfgang Huber, Moritz Gerstung, Josh Moore, Fabian J. Theis, Oliver Stegle
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scPROTEIN: a versatile deep graph contrastive learning framework for single-cell proteomics embedding Nat. Methods (IF 48.0) Pub Date : 2024-03-19 Wei Li, Fan Yang, Fang Wang, Yu Rong, Linjing Liu, Bingzhe Wu, Han Zhang, Jianhua Yao
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Multicenter integrated analysis of noncoding CRISPRi screens Nat. Methods (IF 48.0) Pub Date : 2024-03-19 David Yao, Josh Tycko, Jin Woo Oh, Lexi R. Bounds, Sager J. Gosai, Lazaros Lataniotis, Ava Mackay-Smith, Benjamin R. Doughty, Idan Gabdank, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D. White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J. Greenleaf, Pardis C. Sabeti
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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
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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
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Unlocking cryo-EM’s multishot potential with square or rectangular beams Nat. Methods (IF 48.0) Pub Date : 2024-03-14 Xiaowei Zhao
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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
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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
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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
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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
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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
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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.
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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
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Creating diploid assemblies from Nanopore and Illumina reads with hypo-assembler Nat. Methods (IF 48.0) Pub Date : 2024-03-08
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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
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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
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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
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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
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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
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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
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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
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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.
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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.
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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
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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
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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
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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
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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
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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
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Using stem cells to model the human bone marrow in a dish Nat. Methods (IF 48.0) Pub Date : 2024-02-19
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VIBRANT: a phenotyping method for drug discovery using vibrational spectroscopy Nat. Methods (IF 48.0) Pub Date : 2024-02-19
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A biomimetic robotic antigen-presenting system for sensitive T cell recognition Nat. Methods (IF 48.0) Pub Date : 2024-02-19
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TREX identifies region-specific protein interactors of RNA molecules Nat. Methods (IF 48.0) Pub Date : 2024-02-19
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Uncovering hidden states driving biological outcomes using machine learning Nat. Methods (IF 48.0) Pub Date : 2024-02-19
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Deciphering protein interaction network dynamics with a machine learning-based framework Nat. Methods (IF 48.0) Pub Date : 2024-02-15
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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
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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
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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.
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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
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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