Genome assembly in the telomere-to-telomere era | Nature Reviews Genetics
Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly — the process of reconstructing the genome sequence of an organism from sequencing reads — has been a central problem in bioinformatics for four decades. Until recently, genomes were typically assembled into fragments of a few megabases at best, but now technological advances in long-read sequencing enable the near-complete assembly of each chromosome — also known as telomere-to-telomere assembly — for many organisms. Here, the authors review recent progress on assembly algorithms and protocols, with a focus on how to derive near-telomere-to-telomere assemblies.
hadge: a comprehensive pipeline for donor deconvolution in single-cell studies | Genome Biology
Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. Researchers develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution.
Prospective de novo drug design with deep interactome learning | Nature Communications
De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. Researchers present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of drug-like molecules. This method capitalizes on the unique strengths of both graph neural networks and chemical language models, offering an alternative to the need for application-specific reinforcement, transfer, or few-shot learning. It enables the “zero-shot” construction of compound libraries tailored to possess specific bioactivity, synthesizability, and structural novelty.