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Quantification of absolute labeling efficiency at the single-protein level Nat. Methods (IF 48.0) Pub Date : 2024-04-24 Joschka Hellmeier, Sebastian Strauss, Shuhan Xu, Luciano A. Masullo, Eduard M. Unterauer, Rafal Kowalewski, Ralf Jungmann
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De novo identification of CD4+ T cell epitopes Nat. Methods (IF 48.0) Pub Date : 2024-04-24 Paul M. Zdinak, Nishtha Trivedi, Stephanie Grebinoski, Jessica Torrey, Eduardo Zarate Martinez, Salome Martinez, Louise Hicks, Rashi Ranjan, Venkata Krishna Kanth Makani, Mary Melissa Roland, Lyubov Kublo, Sanya Arshad, Mark S. Anderson, Dario A. A. Vignali, Alok V. Joglekar
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scRNA-seq: oh, the joys Nat. Methods (IF 48.0) Pub Date : 2024-04-23 Vivien Marx
To those who seek transcriptomic information at high resolution, scale and throughput, single-cell RNA sequencing brings the data. Scientists share tips and future plans as they reflect on the method’s rise to stardom.
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Can AlphaFold’s breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity? Nat. Methods (IF 48.0) Pub Date : 2024-04-23 Benjamin McMaster, Christopher Thorpe, Graham Ogg, Charlotte M. Deane, Hashem Koohy
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Simplifying deep learning to enhance accessibility of large-scale 3D brain imaging analysis Nat. Methods (IF 48.0) Pub Date : 2024-04-22
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Virtual reality-empowered deep-learning analysis of brain cells Nat. Methods (IF 48.0) Pub Date : 2024-04-22 Doris Kaltenecker, Rami Al-Maskari, Moritz Negwer, Luciano Hoeher, Florian Kofler, Shan Zhao, Mihail Todorov, Zhouyi Rong, Johannes Christian Paetzold, Benedikt Wiestler, Marie Piraud, Daniel Rueckert, Julia Geppert, Pauline Morigny, Maria Rohm, Bjoern H. Menze, Stephan Herzig, Mauricio Berriel Diaz, Ali Ertürk
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Single-cell immune repertoire analysis Nat. Methods (IF 48.0) Pub Date : 2024-04-18 Sergio E. Irac, Megan Sioe Fei Soon, Nicholas Borcherding, Zewen Kelvin Tuong
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LiMCA: Hi-C gets an RNA twist Nat. Methods (IF 48.0) Pub Date : 2024-04-15 Jane Kawaoka, Stavros Lomvardas
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Quest: my postdoc home Nat. Methods (IF 48.0) Pub Date : 2024-04-15
For a postdoctoral fellowship, it’s advisable to be selective about lab choice and to be clear about expectations.
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Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice Nat. Methods (IF 48.0) Pub Date : 2024-04-15 Honggui Wu, Jiankun Zhang, Fanchong Jian, Jinxin Phaedo Chen, Yinghui Zheng, Longzhi Tan, X. Sunney Xie
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Protein language models using convolutions Nat. Methods (IF 48.0) Pub Date : 2024-04-12 Lin Tang
The prowess of protein language models (PLMs) has been demonstrated in handling various tasks, such as protein structure prediction, function analysis and engineering, and novel protein design. Transformers, a deep learning architecture that excels in learning relationships in sequence data, have been commonly employed as the backbone of PLMs, first being pretrained on huge datasets of protein sequences
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A map of mouse embryogenesis Nat. Methods (IF 48.0) Pub Date : 2024-04-12 Madhura Mukhopadhyay
Mammalian embryogenesis is a highly orchestrated series of events leading to the development of a multicellular organism from a single cell. Although recent methods have enabled novel analyses of developmental dynamics, they have been unable to provide a comprehensive view of the processes involved. To generate a more continuous picture of development, a team at Washington University and Jackson Labs
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Protein–ligand structure prediction Nat. Methods (IF 48.0) Pub Date : 2024-04-12 Rita Strack
Zhuoran Qiao and Thomas Miller III of Iambic Therapeutics, Animashree Anandkumar of Nvidia Corporation and the California Institute of Technology, and colleagues sought to address this challenge and develop an approach that can predict protein–ligand complex structures using only protein sequences and molecular graphs of ligands as primary inputs. Qiao recalls that there were two main inspirations
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Modeling locomotion from environment to neurons Nat. Methods (IF 48.0) Pub Date : 2024-04-12 Nina Vogt
George says that when he started testing theoretical ideas about hippocampal function, he was looking for tools to help him model environments, trajectories or neuronal activity. However, “no unified toolkit existed to link this generation of behavior, motion trajectories and concurrent neural data from these various very stereotyped hippocampal cell types.” George says that the existing tools “are
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Peer review demystified: part 2 Nat. Methods (IF 48.0) Pub Date : 2024-04-12
We continue our explanation of the peer review process at Nature Methods.
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Pretraining a foundation model for generalizable fluorescence microscopy-based image restoration Nat. Methods (IF 48.0) Pub Date : 2024-04-12 Chenxi Ma, Weimin Tan, Ruian He, Bo Yan
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Accessible computing platforms democratize neuroimaging data analysis Nat. Methods (IF 48.0) Pub Date : 2024-04-11 Lucina Q. Uddin
Several research groups are making it easier for other neuroscientists to analyze large datasets by providing tools that can be accessed and used from anywhere in the world.
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brainlife.io: a decentralized and open-source cloud platform to support neuroscience research Nat. Methods (IF 48.0) Pub Date : 2024-04-11 Soichi Hayashi, Bradley A. Caron, Anibal Sólon Heinsfeld, Sophia Vinci-Booher, Brent McPherson, Daniel N. Bullock, Giulia Bertò, Guiomar Niso, Sandra Hanekamp, Daniel Levitas, Kimberly Ray, Anne MacKenzie, Paolo Avesani, Lindsey Kitchell, Josiah K. Leong, Filipi Nascimento-Silva, Serge Koudoro, Hanna Willis, Jasleen K. Jolly, Derek Pisner, Taylor R. Zuidema, Jan W. Kurzawski, Kyriaki Mikellidou, Aurore
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Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations Nat. Methods (IF 48.0) Pub Date : 2024-04-09 Srinivas Niranj Chandrasekaran, Beth A. Cimini, Amy Goodale, Lisa Miller, Maria Kost-Alimova, Nasim Jamali, John G. Doench, Briana Fritchman, Adam Skepner, Michelle Melanson, Alexandr A. Kalinin, John Arevalo, Marzieh Haghighi, Juan C. Caicedo, Daniel Kuhn, Desiree Hernandez, James Berstler, Hamdah Shafqat-Abbasi, David E. Root, Susanne E. Swalley, Sakshi Garg, Shantanu Singh, Anne E. Carpenter
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scGHOST: identifying single-cell 3D genome subcompartments Nat. Methods (IF 48.0) Pub Date : 2024-04-08 Kyle Xiong, Ruochi Zhang, Jian Ma
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Spike sorting with Kilosort4 Nat. Methods (IF 48.0) Pub Date : 2024-04-08 Marius Pachitariu, Shashwat Sridhar, Jacob Pennington, Carsen Stringer
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Selective-plane-activation structured illumination microscopy Nat. Methods (IF 48.0) Pub Date : 2024-04-05 Kenta Temma, Ryosuke Oketani, Toshiki Kubo, Kazuki Bando, Shunsuke Maeda, Kazunori Sugiura, Tomoki Matsuda, Rainer Heintzmann, Tatsuya Kaminishi, Koki Fukuda, Maho Hamasaki, Takeharu Nagai, Katsumasa Fujita
The background light from out-of-focus planes hinders resolution enhancement in structured illumination microscopy when observing volumetric samples. Here we used selective plane illumination and reversibly photoswitchable fluorescent proteins to realize structured illumination within the focal plane and eliminate the out-of-focus background. Theoretical investigation of the imaging properties and
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Creating a universal cell segmentation algorithm Nat. Methods (IF 48.0) Pub Date : 2024-04-01
Cell segmentation currently involves the use of various bespoke algorithms designed for specific cell types, tissues, staining methods and microscopy technologies. We present a universal algorithm that can segment all kinds of microscopy images and cell types across diverse imaging protocols.
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Building an automated three-dimensional flight agent for neural network reconstruction Nat. Methods (IF 48.0) Pub Date : 2024-04-01
RoboEM, an artificial intelligence (AI)-based flight agent, automatically steers through three-dimensional electron microscopy (3D-EM) images of brain tissue to follow neurites. RoboEM substantially improves state-of-the-art automated reconstructions, eliminating manual proofreading needs in complex connectomic analysis problems and paving the way for high-throughput, cost-effective, large-scale mapping
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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