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Zhang, Hou, Ma et al. present PROFIT-seq, a sequencing strategy that involves adaptive sampling of transcriptome libraries to enrich genes of interest and allows unbiased quantification of the whole transcriptome.
Dardano et al. generate human pluripotent stem cell-derived cardiac organoids capable of undergoing endothelial-to-haematopoietic transition and producing haematopoietic cells.
Dimitrov et al. present LIANA+, a framework that unifies and extends approaches to study inter- and intracellular signalling from diverse mediators, captured from single-cell, spatially resolved and multi-omics data.
Cao et al. describe the development and application of an engineered protein system (MARS) derived from PLEKHA5 that allows mitosis-specific recruitment of proteins to the plasma membrane to study protein function in cell division.
Hamazaki, Yang et al. report that an early pulse of retinoic acid robustly induces human gastruloids with a neural tube, segmented somites and more advanced cell types than conventional gastruloids.
Qin, Liu and colleagues develop a tool that combines CRISPR technology with G-quadruplex (G4)-stabilizing protein or ligand to specifically target DNA G4 structures. This tool provides better understanding of G4 functions and enables G4-based drug development.
Huang, Qin, Shang et al. profile double-strand breaks (DSBs) generated by C-to-G base editors (CGBEs) and find that HMCES protects abasic sites and reduces CGBE-triggered DSBs.
Noack and Vangelisti et al. present 3DRAM-seq, which simultaneously profiles genome organization, chromatin accessibility and DNA methylation at high resolution and allows mapping cell-type-specific epigenetic regulation in human neurogenesis.
Huang et al. provide a method to generate human gastric stem cell-derived pancreatic islet-like organoids that are capable of restoring glucose homeostasis in diabetic mice.
Berg et al. describe Metaboverse, a tool for automated discovery and visualization of metabolic data. Metaboverse enhances the user’s ability to extract meaningful patterns from multi-omics datasets to describe metabolic responses and signatures.
Lotfollahi et al. present ExpiMap, a deep-learning model enabling interpretable reference mapping of RNA sequencing data using biologically defined entities, offering end-to-end analysis from dataset integration to functional interpretation.
Stewart-Morgan et al. present isolation of DNA by 5-ethynyl-deoxyuridine labelling for mass spectrometry, a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. They apply it to study DNA methylation and hydroxymethylation propagation.
Lim et al. developed a fluorescence resonance energy transfer-based assay to identify anti-CRISPR molecules and discovered an SpCas9 inhibitor that is twofold more efficient in inhibiting Cas9 at diverse genomic loci than existing inhibitors and easy to synthesize.
Truong et al. report a system to monitor RNA expression by modifying an intron within a gene of interest. This additional engineered transcript then hijacks nuclear export machinery for subsequent translation of a reporter gene.
Zou et al. use a single multi-target guide RNA to direct Cas9 to a high number of loci mapped by high-throughput short-read sequencing. This multi-target CRISPR system allows detailed studies of genome editing and DNA repair.
Rosebrock, Arora et al. report a method to overcome limited cortical cellular diversity in human organoids, thus mirroring fundamental features of cortical development and offering a basis for organoid-based disease modelling.
John Peter et al. develop METALIC (Mass tagging-Enabled TrAcking of Lipids In Cells), an approach to track interorganelle lipid flux in live cells using organelle-targeted enzymatic labelling of lipid subpopulations and mass spectrometry.
Lummertz da Rocha et al. present CellComm, an algorithm that analyses cell–cell communication to predict signalling and regulatory networks, and identify regulators of haematopoietic development in the aorta–gonad–mesonephros region.
