Yoshitaka Sakamoto

Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes

PRCGAP provides a haplotype-resolved analysis of cancer genomes, detecting variants missed by standard references and revealing new insights into structural variants and fusion events in leukemia.

A near-complete human pancreatic cancer genome

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing

The paper introduces mm2-ivh, an algorithm that improves overlap detection in alpha satellite HORs by distinguishing identical k-mers from different repeats, leading to more accurate haplotype reconstruction.

Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations

This paper uses rare k-mers to identify centromere haplogroups in human populations and cancer translocations, revealing structural diversity and translocation mechanisms.

Long read sequencing reveals a novel class of structural aberrations in cancers: identification and characterization of cancerous local amplifications

The paper identifies a novel class of structural aberrations in lung cancers using long-read sequencing and shows their occurrence in vivo and in cancer-related genes.

MoMI-G: Modular Multi-scale Integrated Genome Graph Browser

MoMI-G is a web-based genome browser for visualizing structural variants and other genomic annotations, enabling intuitive exploration of large and nested variants.