Nature protocols

Keyphrases

Publications

volume 19, number 5, 2024

Mehrad Hajiaghabozorgi, Mathew Fischbach, Michael Albrecht, Wen Wang, Chad L Myers
BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS. Nature protocols 19 (5) (2024)
Bastian Hartmann, Lutz Fleischhauer, Monica Nicolau, Thomas Hartvig Lindkær Jensen, Florin-Andrei Taran, Hauke Clausen-Schaumann, Raphael Reuten
Profiling native pulmonary basement membrane stiffness using atomic force microscopy. Nature protocols 19 (5) (2024)
Andreas Müller, Deborah Schmidt, Jan Philipp Albrecht, Lucas Rieckert, Maximilian Otto, Leticia Elizabeth Galicia Garcia, Gunar Fabig, Michele Solimena, Martin Weigert
Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets. Nature protocols 19 (5) (2024)
Kailin Zhang, Xiang Shi, Haibo Jiang, Kaiwen Zeng, Zihao Zhou, Peng Zhai, Lihua Zhang, Huisheng Peng
Design and fabrication of wearable electronic textiles using twisted fiber-based threads. Nature protocols 19 (5) (2024)
Francisco M Barriga, Scott W Lowe
Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements). Nature protocols 19 (5) (2024)
John M Ball, Wei Li
Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models. Nature protocols 19 (5) (2024)
Aoxue Wang, Yejun Zou, Shuning Liu, Xiuze Zhang, Ting Li, Lijuan Zhang, Ruwen Wang, Yale Xia, Xie Li, Zhuo Zhang, Tiemin Liu, Zhenyu Ju, Ru Wang, Joseph Loscalzo, Yi Yang, Yu-Zheng Zhao
Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors. Nature protocols 19 (5) (2024)
Jessica D Ewald, Guangyan Zhou, Yao Lu, Jelena Kolic, Cara Ellis, James D Johnson, Patrick E Macdonald, Jianguo Xia
Web-based multi-omics integration using the Analyst software suite. Nature protocols 19 (5) (2024)

volume 19, number 6, 2024

Nolan K Newman, Matthew S Macovsky, Richard R Rodrigues, Amanda M Bruce, Jacob W Pederson, Jyothi Padiadpu, Jigui Shan, Joshua Williams, Sankalp S Patil, Amiran K Dzutsev, Natalia Shulzhenko, Giorgio Trinchieri, Kevin Scott Brown, Andrey Morgun
Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions. Nature protocols 19 (6) (2024)
Costanza Borrelli, Alessandra Gurtner, Isabelle Catherine Arnold, Andreas E Moor
Stress-free single-cell transcriptomic profiling and functional genomics of murine eosinophils. Nature protocols 19 (6) (2024)
Rafael Tapia-Rojo, Marc Mora, Sergi Garcia-Manyes
Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales. Nature protocols 19 (6) (2024)
Tim H H Coorens, Michael Spencer Chapman, Nicholas Williams, Iñigo Martincorena, Michael R Stratton, Jyoti Nangalia, Peter J Campbell
Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples. Nature protocols 19 (6) (2024)
Marley Downes, Christopher Eugene Shuck, Bernard McBride, Jeffrey Busa, Yury Gogotsi
Comprehensive synthesis of Ti 3 C 2 T x from MAX phase to MXene. Nature protocols 19 (6) (2024)
Lei Tian, Kyle Jackson, Leon He, Shadman Khan, Mathura Thirugnanasampanthar, Mellissa Gomez, Fereshteh Bayat, Tohid F Didar, Zeinab Hosseini-Doust
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination. Nature protocols 19 (6) (2024)
Anne-Sophie Gribling-Burrer, Patrick Bohn, Redmond P Smyth
Isoform-specific RNA structure determination using Nano-DMS-MaP. Nature protocols 19 (6) (2024)
Degong Ruan, Yiyi Xuan, Timothy Theodore Ka Ki Tam, ZhuoXuan Li, Xiao Wang, Shao Xu, Doris Herrmann, Heiner Niemann, Liangxue Lai, Xuefei Gao, Monika Nowak-Imialek, Pengtao Liu
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells. Nature protocols 19 (6) (2024)
David Falck, Dana L E Vergoossen
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC-MS readout. Nature protocols 19 (6) (2024)
David Falck, Dana L E Vergoossen
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC-MS readout. Nature protocols 19 (6) (2024)
Nolan K Newman, Matthew S Macovsky, Richard R Rodrigues, Amanda M Bruce, Jacob W Pederson, Jyothi Padiadpu, Jigui Shan, Joshua Williams, Sankalp S Patil, Amiran K Dzutsev, Natalia Shulzhenko, Giorgio Trinchieri, Kevin Scott Brown, Andrey Morgun
Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions. Nature protocols 19 (6) (2024)
Hongwei Yu, Yuli Li, Wentao Han, Lisui Bao, Fuyun Liu, Yuanting Ma, Zhongqi Pu, Qifan Zeng, Lingling Zhang, Zhenmin Bao, Guo-Hua Ding
Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nature protocols 19 (6) (2024)
Rafael Tapia-Rojo, Marc Mora, Sergi Garcia-Manyes
Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales. Nature protocols 19 (6) (2024)
Rafael Tapia-Rojo, Marc Mora, Sergi Garcia-Manyes
Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales. Nature protocols 19 (6) (2024)
Rafael Tapia-Rojo, Marc Mora, Sergi Garcia-Manyes
Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales. Nature protocols 19 (6) (2024)

volume 19, number 7, 2024

Yupeng Wang, Haibao Tang, Xiyin Wang, Ying Sun, Paule V Joseph, Andrew H Paterson
Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX. Nature protocols 19 (7) (2024)
Maria Alieva, Mario Barrera Román, Sam de Blank, Diana Petcu, Amber L Zeeman, Noël M M Dautzenberg, Annelisa M Cornel, Cesca van de Ven, Rob Pieters, Monique L Den Boer, Stefan Nierkens, Friso G J Calkoen, Hans Clevers, Jürgen Kuball, Zsolt Sebestyén, Ellen J Wehrens, Johanna F Dekkers, Anne C Rios
BEHAV3D: a 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response. Nature protocols 19 (7) (2024)
Shuo Han, Emma R Guiberson, Yuxin Li, Justin L Sonnenburg
High-throughput identification of gut microbiome-dependent metabolites. Nature protocols 19 (7) (2024)
Rebeccah A Warmack, Belinda B Wenke, Thomas Spatzal, Douglas C Rees
Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins. Nature protocols 19 (7) (2024)
Mohamed Abdelrahim, Quan Gao, Yichuan Zhang, Weishuo Li, Qi Xing, Mark Bradley, Jin Geng
Light-mediated intracellular polymerization. Nature protocols 19 (7) (2024)
Rebeccah A Warmack, Belinda B Wenke, Thomas Spatzal, Douglas C Rees
Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins. Nature protocols 19 (7) (2024)
Emma J Vontalge, Tamar Kavlashvili, Steven N Dahmen, Matthew T Cranford, James M Dewar
Control of DNA replication in vitro using a reversible replication barrier. Nature protocols 19 (7) (2024)
Mohamed Abdelrahim, Quan Gao, Yichuan Zhang, Weishuo Li, Qi Xing, Mark Bradley, Jin Geng
Light-mediated intracellular polymerization. Nature protocols 19 (7) (2024)
Shuo Han, Emma R Guiberson, Yuxin Li, Justin L Sonnenburg
High-throughput identification of gut microbiome-dependent metabolites. Nature protocols 19 (7) (2024)
Shuo Han, Emma R Guiberson, Yuxin Li, Justin L Sonnenburg
High-throughput identification of gut microbiome-dependent metabolites. Nature protocols 19 (7) (2024)
Alberto John Taurozzi, Patrick L Rüther, Ioannis Patramanis, Claire Koenig, Ryan Sinclair Paterson, Palesa P Madupe, Florian Simon Harking, Frido Welker, Meaghan Mackie, Jazmin Ramos-Madrigal, Jesper Velgaard Olsen, Enrico Cappellini
Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel. Nature protocols 19 (7) (2024)
Michael G J Doyle, Braeden A Mair, Anna Sib, Odey Bsharat, Maxime Munch, Volker Derdau, Benjamin H Rotstein, Rylan J Lundgren
A practical guide for the preparation of C1-labeled α-amino acids using aldehyde catalysis with isotopically labeled CO 2 . Nature protocols 19 (7) (2024)
Nils Kriedemann, Wiebke Triebert, Jana Teske, Mira Mertens, Annika Franke, Kevin Ullmann, Felix Manstein, Lika Drakhlis, Alexandra Haase, Caroline Halloin, Ulrich Martin, Robert Zweigerdt
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks. Nature protocols 19 (7) (2024)
Emma J Vontalge, Tamar Kavlashvili, Steven N Dahmen, Matthew T Cranford, James M Dewar
Control of DNA replication in vitro using a reversible replication barrier. Nature protocols 19 (7) (2024)
Aude-Anais Olijnik, Antonio Rodriguez-Romera, Zoë C Wong, Yuqi Shen, Jasmeet S Reyat, Natalie J Jooss, Julie Rayes, Bethan Psaila, Abdullah Obaid Khan
Generating human bone marrow organoids for disease modeling and drug discovery. Nature protocols 19 (7) (2024)

volume 19, number 8, 2024

Chao Chen, Xiaoyan Zhang, Zhiyuan Gao, Guangxue Feng, Dan Ding
Preparation of AIEgen-based near-infrared afterglow luminescence nanoprobes for tumor imaging and image-guided tumor resection. Nature protocols 19 (8) (2024)
Martin Peter Schwalm, Krishna Saxena, Susanne Müller, Stefan Knapp
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nature protocols 19 (8) (2024)
Jia Ping Tan, Xiaodong Liu, Mohammad Mahfuz Chowdhury
Reprogramming fibroblast into human iBlastoids. Nature protocols 19 (8) (2024)
Ruotian Chen, Chenwei Ni, Jian Zhu, Fengtao Fan, Can Li
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles. Nature protocols 19 (8) (2024)
Brian L Hie, Soochi Kim, Thomas A Rando, Bryan Bryson, Bonnie Berger
Scanorama: integrating large and diverse single-cell transcriptomic datasets. Nature protocols 19 (8) (2024)
Kristýna Kantnerová, Nils Kuhlbusch, Dieter Juchelka, Andreas Hilkert, Sebastian H Kopf, Cajetan Neubauer
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS. Nature protocols 19 (8) (2024)
Rory M Power, Aline Tschanz, Timo Zimmermann, Jonas Ries
Build and operation of a custom 3D, multicolor, single-molecule localization microscope. Nature protocols 19 (8) (2024)
Jacob Bobonis, Alessio Ling Jie Yang, Carlos Geert Pieter Voogdt, Athanasios Typas
TAC-TIC, a high-throughput genetics method to identify triggers or blockers of bacterial toxin-antitoxin systems. Nature protocols 19 (8) (2024)
Brian L Hie, Soochi Kim, Thomas A Rando, Bryan Bryson, Bonnie Berger
Scanorama: integrating large and diverse single-cell transcriptomic datasets. Nature protocols 19 (8) (2024)
Ying Chen, Yiwei Yang, Fan Zhang
Noninvasive in vivo microscopy of single neutrophils in the mouse brain via NIR-II fluorescent nanomaterials. Nature protocols 19 (8) (2024)
Bhaskar Paul, Sabuj Kundu
The use of methanol as a C1 building block. Nature protocols 19 (8) (2024)
Brian L Hie, Soochi Kim, Thomas A Rando, Bryan Bryson, Bonnie Berger
Scanorama: integrating large and diverse single-cell transcriptomic datasets. Nature protocols 19 (8) (2024)