Nanopore sequencing has emerged as a transformative technology in the study of the central nervous system (CNS), particularly in understanding complex transcriptomic landscapes and diagnosing infections. One significant application is highlighted in the study by Ramirez, which utilized long-read sequencing to analyze the adult Drosophila brain transcriptome under both physiological and pathological conditions. This approach allowed for the accurate reconstruction of highly processed RNA transcripts, overcoming the limitations of traditional short-read sequencing methods. By capturing full-length transcripts, the study revealed a vast diversity of RNA isoforms, which is crucial for understanding the intricate post-transcriptional modifications that neurons undergo (ref: Ramirez doi.org/10.1186/s12864-025-12111-w/). In the realm of CNS infections, Shi developed a targeted nanopore sequencing (tNPS) technology that integrates high-throughput sequencing with multiplex PCR amplification. This innovative diagnostic tool targets 17 prevalent CNS pathogens, including bacteria, fungi, and DNA viruses, enhancing the detection capabilities for CNS infections that pose significant public health risks. The dual detection strategy employed in this study not only amplifies pathogen-specific sequences but also includes universal primers for comprehensive analysis of 16S rRNA and internal transcribed spacer regions, thereby improving diagnostic accuracy (ref: Shi doi.org/10.2147/IDR.S540638/). Furthermore, Wang's case analysis on Parkinson's disease and herpes simplex virus type 1 underscores the potential of nanopore sequencing in clinical settings, particularly for patients with neurodegenerative disorders who are at risk of infections from drug-resistant pathogens. This study emphasizes the need for advanced sequencing technologies to monitor and manage infections in vulnerable populations (ref: Wang doi.org/10.1016/j.bbrep.2025.102310/).