This Review discusses mass spectrometry techniques that have been instrumental for identifying protein-protein interactions. Examples from diverse disease contexts illustrate the potential of these approaches for revealing disease mechanisms and therapeutic targets.

A new approach integrates multi-omics datasets with a prior knowledge network spanning signaling, metabolism and allosteric regulations. Application to a kidney cancer patient cohort captures relevant cross-talks among deregulated processes.

This Review discusses the emerging challenges and potential pitfalls of current RNA velocity modeling approaches and provides guidance on how to address them.

Tissue-clearing methods have allowed imaging intact biological specimens and understanding biology at a whole-organism and systems-level. This Review provides a guide for scientists who would like to setup a clearing protocol, with an emphasis on DISCO methods.

Over 100 resources are integrated into OmniPath, a comprehensive knowledge base of intra- and inter-cellular signaling. Workflows are provided and illustrated in case studies analyzing omics data in SARS-CoV-2 infection and ulcerative colitis.

Single cell sequencing and multiplex single-molecule RNA FISH analyses on SARS-CoV-2 infected human intestinal organoids characterize the tropism of SARS-CoV-2 and identify strategies developed by the virus to interfere with the host intrinsic innate immune response.

COVID-19 Disease Map is a large-scale collection of curated computational models and diagrams of molecular mechanisms involved in SARS-CoV-2 infection. The map supports the computational exploration of pathways affected by the virus.

This study demonstrates the ability of scVI to integrate single-cell RNA-seq datasets in a variety of settings and presents scANVI, a new development based on scVI for automated annotation of cell types and states.