Nature Reviews Genetics, Published online: 13 May 2025; doi:10.1038/s41576-025-00841-2Barbadilla-Martínez et al. review recent progress in deep-learning-based sequence-to-expression models, which predict gene expression levels solely from DNA sequence. These models are providing new insights into the complex combinatorial logic underlying cis-regulatory control of gene expression.

Summary: Leveraging the Python/C API, eccLib was developed as a high-performance library designed for parsing genomic files and analysing genomic contexts. To the best of the authors' knowledge, it…

As in many diploid organisms with genetic sex determination, haploid-dominant organisms have also evolved sex chromosomes or extensive genomic regi...

Nature Reviews Genetics, Published online: 28 March 2025; doi:10.1038/s41576-025-00822-5Long-read sequencing technologies can directly profile methylation modifications across the genome. In this Review, Fu et al. overview the long-read computational tools to identify and compare methylation signals, as well as tools that use these methylation signals to analyse cell-type diversity and gain additional genomic insights.

Nature Reviews Genetics, Published online: 28 March 2025; doi:10.1038/s41576-025-00828-zAdvances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read RNA sequencing, including experimental and computational tools, current applications, challenges and opportunities.

A team of scientists from University College Cork (UCC), the University of Connecticut, and the Natural History Museum of Vienna have uncovered how plants responded to catastrophic climate changes 250...

Chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a significant role in the evolution of adaptations in those species. Inversions are thought to op...