Gene expression articles from across Nature Portfolio

Ctyper is a genotyping method for copy number variation and complex genes that produces sequence-resolved genotypes by directly comparing sequencing reads to pangenome haplotypes, achieving increased robustness and copy number sensitivity with efficiency scalable to biobank analysis.

FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

For the 25th anniversary of Nature Reviews Genetics, we reflect on exciting progress towards decoding the regulatory genome and its mechanisms, a central goal in genetics that must be solved with interdisciplinary research to yield widespread insights into evolution, development and disease.

Studies of human regulatory genomics are being performed at biobank scales, with data from tens of thousands of individuals. Stephen Montgomery describes how these datasets will advance our understanding of how variation in gene regulation shapes human traits and disease.

Two deep-learning frameworks — GHIST and iSCALE — turn routine histology images into a rich molecular resource, and predict spatial gene expression at single-cell resolution (GHIST) and at super-resolution across large tissue sections (iSCALE), for scalable, data-driven tissue biology.