Review Articles

This Tutorial provides guide for how to evaluate, select and use publicly available computational tools for predicting intrinsic disorder in proteins, with a focus on performance and ease of use results, exemplified using results from the Critical Assessment of protein Intrinsic Disorder prediction experiment.

This tutorial provides guidelines for imputing human leukocyte antigen alleles, including standard quality control measures for input genotyping data and best practice recommendations for association testing and fine-mapping to identify causal alleles.

This tutorial outlines common strategies for analysis of bulk RNA-sequencing (RNA-seq) data in the context of tumor immunity and immunotherapy response and presents a comprehensive computational pipeline integrating these tools to streamline RNA-seq analysis.

This new tutorial from Braun and colleagues details how to design and execute in vivo CRISPR screens in mice to investigate a variety of phenotypes.

This review explores factors to consider when introducing electronic laboratory notebooks, including discussion of integration with research data management and the functionalities to compare when evaluating specific software packages.

The authors describe three-dimensional imaging pipelines available to analyze archival patient specimens. The pipelines facilitate the visualization of both large and small volumes of tissue with subcellular resolution.

This tutorial describes how to develop a nanoinjection workflow, including the selection of nanoneedle devices, approaches to loading cargo, strategies for interfacing to biological systems and assays to evaluate the efficacy of intracellular delivery.

Mass-spectrometry-based proteomics is a powerful approach for discovering disease biomarkers. This tutorial provides advice on the study design, including cohort selection, evaluating statistical power, blinding and randomization, and quality control.

Understanding the heterogeneity of extracellular vesicles is crucial for unraveling their functions. This review describes the benefits, challenges and contributions of the state-of-the art methods used in single-vesicle analysis.

This tutorial provides guidelines for interpreting single-cell transcriptomic maps to identify cell types, states and other biologically relevant patterns.

This tutorial provides guidance for selecting and optimizing tissue-clearing protocols for specific samples and biological questions. In addition, instructions are provided for developing an imaging strategy and processing the resulting data.

This tutorial explains how to evaluate and benchmark metagenome assembly, binning and profiling methods using standards and software provided by the CAMI initiative.

In this review article, the authors compare in vitro cytotoxicity assays (including chromium release, bioluminescence, impedance and flow cytometry assays) with respect to their experimental setup, appropriate uses, advantages and disadvantages and measures to overcome their limitations.

This review illustrates the power of on-resin multicomponent reaction protocols to create complexity and diversity in biomolecular skeletons such as peptides and oligonucleotides, including strategies to assemble, label and conjugate them.

In this Tutorial Review, Hemberg et al. present an overview of the computational workflow involved in processing single-cell RNA sequencing data.

Off-target effects of programmable nucleases remain a critical issue for therapeutic applications of genome editing. This review compares experimental and computational tools for off-target analysis and provides recommendations for better assessments of off-target effects.

This tutorial describes how to design nanoparticle-based LFAs for detecting biomolecules. The authors provide guidance on how to select the appropriate lateral-flow strip components and bioreceptors as well as detection strategies.

This tutorial describes a set of essential performance tests for characterization of neural interface electrodes. The authors provide guidelines for standardized implementation and reporting on electrode performances.

Neural interfaces with implantable electrodes are used to modulate and restore function to the peripheral nervous system. Hybrid modeling described in this protocol is used to optimize each aspect of the implantable electrode design and operation.

This tutorial describes the main causes of sample-induced spherical aberration artifacts in 3D microscopy. In addition, the authors provide a practical ImageJ/Fiji-based solution to correct these aberrations during or after image acquisition.