December 1, 2025 – This month Genome Research ( https://genome.org ) publishes a special issue highlighting novel advances in computational biology.
In collaboration with the 29th International Conference on Research in Computational Molecular Biology (RECOMB), Genome Research publishes a collection of novel computational methods and their applications in genomics, including single-cell and spatial transcriptomics. These include algorithmic innovations in haplotype assembly and phasing, the analysis of genomic variation and its association to phenotype, and metagenomic data analyses. Several of these studies are highlighted below.
LLOKI (Haber et al. 2025) is a method for integrating image-based spatial transcriptomics data across multiple platforms by incorporating feature alignment across gene panels and batch alignment across technologies. When tested on real data, LLOKI outperforms existing methods at identifying spatial gene programs in normal physiology and disease.
Chandra et al. (2025) present a method, Pangenome-based Haplotype Inference (PHI), that uses pangenome references to improve genotyping accuracy from short-read sequencing data. When tested on a sample dataset of haploid genomes, this method accurately estimates haplotype sequences in low-coverage inputs and repeat-rich regions.
Methods that aim to improve metagenomic analyses are also presented. Shaw et al. (2025) present devider, a method for haplotyping small sequences from long-read sequencing data including in heterogeneous mixtures like viral coinfection and metagenomes.
Long-read approaches like optical genome mapping (OGM) offer an accurate approach for measuring large structural variations. OMKar (Raeisi Dehkordi et al. 2025) generates virtual karyotypes from OGM data to robustly detect constitutional genetic abnormalities.
This partnership between RECOMB and Genome Research brings novel computational methodologies to a broader genomics audience. Additional cutting-edge computational methods that advance studies across genome biology are also included in this Special Issue.
