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Masaaki Furuno is a leading figure in functional genomics, best known for his pivotal contributions to the FANTOM (Functional Annotation of the Mammalian Genome) consortium. His research centers on deciphering the transcriptional regulatory landscape of mammalian genomes, with a particular focus on transcription initiation and non-coding RNA biology. Furuno’s most impactful work is the landmark 2017 FANTOM5 study, which has garnered over 360 citations. In this project, he and his team mapped transcription initiation events across thousands of human and mouse samples at single base-pair resolution using Cap Analysis of Gene Expression (CAGE) coupled with single-molecule sequencing. This comprehensive atlas of promoters and enhancers fundamentally reshaped our understanding of gene regulation, revealing the pervasive nature of bidirectional transcription and the complexity of the transcriptome. Beyond this flagship paper, Furuno has been instrumental in developing bioinformatics pipelines for large-scale sequencing data, enabling the systematic annotation of mammalian genomes. His work has provided an essential resource for researchers studying development, disease, and evolution, cementing his reputation as a key architect of modern transcriptomics.