Bioinformatics articles from across Nature Portfolio

The analysis of longitudinal bulk and single-cell multi-omics data is a highly complex task. Here, the authors introduce PALMO, a software platform with five modules to analyse longitudinal bulk and single-cell multi-omics data, which is extensively tested in external datasets that include multiple omics modalities.

RiPP discovery has expanded the scope of post-translational modification chemistry, but genome mining of RiPP classes remains an unsolved challenge. Here, the authors employed bioinformatics and synthetic biology approaches to discover and characterize an unknown class of RiPPs, defined by an unusual amino-modified C-terminus.

Analysing the regulatory consequences of mutations and splice variants at large scale in cancer requires efficient computational tools. Here, the authors develop RegTools, a software package that can identify splice-associated variants from large-scale genomics and transcriptomics data with efficiency and flexibility.

This study comprehensively benchmarks 18 state-of-the-art methods for cellular deconvolution of spatial transcriptomics and provide decision-tree-style guidelines and recommendations for method selection.

Integration of single-cell RNA sequencing data between different samples has been a major challenge for analyzing cell populations. Here the authors benchmark 46 workflows for differential expression analysis of single-cell data with multiple batches and suggest several high-performance methods under different conditions based on simulation and real data analyses.