Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes
Nature Protocols, Published online: 24 January 2024; doi:10.1038/s41596-024-00961-9Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes (Source: Nature Protocols)
Source: Nature Protocols - January 24, 2024 Category: Biomedical Science Authors: Marianna Penzo Domenica Carnicelli Lorenzo Montanaro Maurizio Brigotti Source Type: research
OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds
Nature Protocols, Published online: 23 January 2024; doi:10.1038/s41596-023-00942-4A web-based tool to guide the lead optimization process by improving calculation of substructure modifications of candidate compounds with improved absorption, distribution, metabolism, excretion, and toxicity profiles. (Source: Nature Protocols)
Source: Nature Protocols - January 23, 2024 Category: Biomedical Science Authors: Jiacai Yi Shaohua Shi Li Fu Ziyi Yang Pengfei Nie Aiping Lu Chengkun Wu Yafeng Deng Changyu Hsieh Xiangxiang Zeng Tingjun Hou Dongsheng Cao Source Type: research
An end-to-end workflow for nondestructive 3D pathology
Nature Protocols, Published online: 23 January 2024; doi:10.1038/s41596-023-00934-4A detailed workflow covering 3D pathology, including tissue preparation, imaging with light-sheet fluorescence microscopy, tools for initial data processing in Python (e.g., stitching, intensity leveling and false coloring) and data quality control. (Source: Nature Protocols)
Source: Nature Protocols - January 23, 2024 Category: Biomedical Science Authors: Kevin W. Bishop Lindsey A. Erion Barner Qinghua Han Elena Baraznenok Lydia Lan Chetan Poudel Gan Gao Robert B. Serafin Sarah S. L. Chow Adam K. Glaser Andrew Janowczyk David Brenes Hongyi Huang Dominie Miyasato Lawrence D. True Soyoung Kang Joshua C. Vaug Source Type: research
Irreversible light-activated SpyLigation mediates split-protein assembly in 4D
Nature Protocols, Published online: 22 January 2024; doi:10.1038/s41596-023-00938-0Light-activated assembly of split-protein fragment pairs using the covalent SpyTag/SpyCatcher peptide–protein reaction can be used to modulate biological protein activity in solution, biomaterials and cells. (Source: Nature Protocols)
Source: Nature Protocols - January 22, 2024 Category: Biomedical Science Authors: Brizzia G. Munoz-Robles Cole A. DeForest Source Type: research
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution
Nature Protocols, Published online: 22 January 2024; doi:10.1038/s41596-023-00937-1The formation and functional relevance of N6-methyladenosine sites are key unanswered questions in the field of RNA biology. The protocol describes an unbiased sequencing-based method for the characterization of the global distribution and stoichiometry of N6-methyladenosine sites. (Source: Nature Protocols)
Source: Nature Protocols - January 22, 2024 Category: Biomedical Science Authors: Weiguo Shen Hanxiao Sun Cong Liu Yunpeng Yi Yongkang Hou Ye Xiao Yufei Hu Bo Lu Jinying Peng Jing Wang Chengqi Yi Source Type: research
Production and use of antigen tetramers to study antigen-specific B cells
Nature Protocols, Published online: 19 January 2024; doi:10.1038/s41596-023-00930-8Antigen-specific B cells constitute a small proportion of the total B cell population, making identification for downstream analysis challenging. Here, this is achieved by pairing fluorescent antigen tetramer probes with a sensitive enrichment approach. (Source: Nature Protocols)
Source: Nature Protocols - January 19, 2024 Category: Biomedical Science Authors: Allyssa Phelps Diego Pazos-Castro Francesca Urselli Emily Grydziuszko Olivia Mann-Delany Allison Fang Tina D. Walker Rangana Talpe Guruge Jaime Tome-Amat Araceli Diaz-Perales Susan Waserman Jim Boonyaratanakornkit Manel Jordana Justin J. Taylor Joshua F. Source Type: research
Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0
Nature Protocols, Published online: 18 January 2024; doi:10.1038/s41596-023-00931-7Genome-scale metabolic models enable mathematical exploration of metabolism under various defined conditions. This protocol describes GECKO, a method for enhancing a genome-scale metabolic model with enzymatic constraints using kinetic and omics data (e.g., proteomics). (Source: Nature Protocols)
Source: Nature Protocols - January 18, 2024 Category: Biomedical Science Authors: Yu Chen Johan Gustafsson Albert Tafur Rangel Mihail Anton Iv án Domenzain Cheewin Kittikunapong Feiran Li Le Yuan Jens Nielsen Eduard J. Kerkhoven Source Type: research
Hyperspectral confocal imaging for high-throughput readout and analysis of bio-integrated microlasers
Nature Protocols, Published online: 18 January 2024; doi:10.1038/s41596-023-00924-6A customized hyperspectral confocal microscope enables the tracking of living cells and sensing of cellular processes by characterizing bio-integrated microlasers with high spectral resolution. (Source: Nature Protocols)
Source: Nature Protocols - January 18, 2024 Category: Biomedical Science Authors: Vera M. Titze Soraya Caixeiro Vinh San Dinh Matthias K önig Matthias R übsam Nachiket Pathak Anna-Lena Schumacher Maximilian Germer Christian Kukat Carien M. Niessen Marcel Schubert Malte C. Gather Source Type: research
Bacterial genome engineering using CRISPR-associated transposases
Nature Protocols, Published online: 12 January 2024; doi:10.1038/s41596-023-00927-3This protocol provides extensive guidelines and detailed steps to generate novel bio-engineered bacterial strains using CRISPR-associated transposase (CAST) systems, with available plasmids and standard molecular biology techniques. (Source: Nature Protocols)
Source: Nature Protocols - January 12, 2024 Category: Biomedical Science Authors: Diego Rivera Gelsinger Phuc Leo H. Vo Sanne E. Klompe Carlotta Ronda Harris H. Wang Samuel H. Sternberg Source Type: research
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy
Nature Protocols, Published online: 11 January 2024; doi:10.1038/s41596-023-00941-5A light sheet fluorescence microscopy approach for the analysis of immune cell composition, vascularization, tissue perfusion and hypoxia enables spatial imaging of the tissue microenvironment in cancer and cardiovascular diseases. (Source: Nature Protocols)
Source: Nature Protocols - January 11, 2024 Category: Biomedical Science Authors: Duo Zhang Abigail H. Cleveland Elisavet Krimitza Katherine Han Chenlong Yi Andrea L. Stout Wei Zou Jay F. Dorsey Yanqing Gong Yi Fan Source Type: research
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA
Nature Protocols, Published online: 03 January 2024; doi:10.1038/s41596-023-00952-2Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA (Source: Nature Protocols)
Source: Nature Protocols - January 3, 2024 Category: Biomedical Science Authors: Shuo Li Ran Hu Colin Small Ting-Yu Kang Chun-Chi Liu Xianghong Jasmine Zhou Wenyuan Li Source Type: research
Streamlining spatial omics data analysis with Pysodb
Nature Protocols, Published online: 22 December 2023; doi:10.1038/s41596-023-00925-5The procedure guides inexperienced users interested in handling spatial omics data in a Python environment to streamline data analysis and to facilitate benchmarking analysis via the spatial omics database. (Source: Nature Protocols)
Source: Nature Protocols - December 22, 2023 Category: Biomedical Science Authors: Senlin Lin Fangyuan Zhao Zihan Wu Jianhua Yao Yi Zhao Zhiyuan Yuan Source Type: research
Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution
Nature Protocols, Published online: 21 December 2023; doi:10.1038/s41596-023-00932-6Mapping of chromatin states at single-cell resolution is still challenging. This protocol describes nano-CT, a novel method to simultaneously characterize up to three epigenetic modalities at single-cell resolution. (Source: Nature Protocols)
Source: Nature Protocols - December 21, 2023 Category: Biomedical Science Authors: Jos é Ramón Bárcenas-Walls Federico Ansaloni Bastien Herv é Emilia Strandback Tomas Nyman Gon çalo Castelo-Branco Marek Barto šovič Source Type: research
Collections from Nature Protocols
Nature Protocols, Published online: 19 December 2023; doi:10.1038/s41596-023-00946-0In 2023, Nature Protocols launched four new collections (on organoids, neural probes, cognitive neuroscience frameworks and neurostimulation) to help readers navigate our content and highlight areas of particular current interest. (Source: Nature Protocols)
Source: Nature Protocols - December 19, 2023 Category: Biomedical Science Source Type: research
Profiling human brain vascular cells using single-cell transcriptomics and organoids
Nature Protocols, Published online: 15 December 2023; doi:10.1038/s41596-023-00929-1A protocol extension describing the purification of prenatal human brain endothelial and mural cells with FACS and their utilization in downstream applications, including cell culture, organoid transplantation and single-cell transcriptomics. (Source: Nature Protocols)
Source: Nature Protocols - December 15, 2023 Category: Biomedical Science Authors: Elizabeth E. Crouch Loukas N. Diafos Edward J. Valenzuela Kaylee Wedderburn-Pugh Janeth Ochoa Birrueta Jaela Caston Tara Joseph Madeline G. Andrews Aparna Bhaduri Eric J. Huang Source Type: research
