Review Articles

Life cycle assessment quantifies environmental impacts during the full life cycle of a product or process. This tutorial uses ReCiPe to perform the impact assessment phase, where the magnitude and significance of environmental impacts are evaluated.

We present best practice guidelines for the use of concurrent TMS-fMRI, experimental design, technical requirements and data interpretation, illustrated via 12 use cases.

In this Tutorial, we provide guidelines for the use of ML models to mine genomes and proteomes for the discovery of antimicrobial peptides, discussing the various stages of the ML workflow, recent advances in ML models and how to experimentally validate the computational predictions.

In this Tutorial, the authors provide guidelines for quality control of whole-exome and whole-genome sequencing data for population-scale association analyses. They explain how to filter samples and variants, and compare commonly used software programs for quality control of sequencing data.

This tutorial describes a complete pipeline for structural connectomics, including fundamental aspects of diffusion MRI and its applications for exploring structural connectomics, including fiber tracking and constructing a structural network.

A Tutorial review on the measurement of membrane mechanical forces reported via fluorescence lifetime variations induced by conformational changes of the Flipper probes.

This tutorial provides guidelines on oncolytic virus design, production and testing in cancer immunotherapy. Best practice recommendations for preclinical and clinical use of oncolytic viruses as an immunotherapy tool and related future challenges are also considered.

Attempts to reproduce the computational steps described in published omics research often fail. This review provides guidelines for the packaging and containerization of software so that readers can use the exact programs used in published work.

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.