Author

Toshiyuki Yokoyama

The University of TokyoORCID 0000-0002-7345-6397Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Assay:whole-genome sequencing· 4 Research Focus:database / resource· 2 Organism:human· 2 Research Focus:software / tool· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:genome assembly· 1

Frequent Co-Authors

Masahiro KasaharaiD· 3 shared Masahide SekiiD· 2 shared Yoshitaka SakamotoiD· 2 shared Adam M. NovakiD· 1 shared Akihiro OhashiiD· 1 shared Asako MatsumotoiD· 1 shared Atsushi ToyodaiD· 1 shared Ayako IzunoiD· 1 shared

Activity by Year

2019-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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3 shared papersGenomics

Masahiro KasaharaORCID

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4 papers

Recent·Most cited

A chromosome-level genome assembly of amodel conifer plant, the Japanese cedar,Cryptomeria japonica D. Don

Takeshi Fujino, Katsushi Yamaguchi, Toshiyuki Yokoyama, Toshiya Hamanaka, Yoritaka Harazono, Hiroaki Kamada, Wataru Kobayashi, Tokuko Ujino‐Ihara, Kentaro Uchiyama, Asako Matsumoto, Ayako Izuno, Yoshihiko Tsumura, Atsushi Toyoda, Shuji Shigenobu, Yoshinari Moriguchi, , Masahiro Kasahara

The paper presents a chromosome-level genome assembly for the Japanese cedar, using long-read and Hi-C sequencing to achieve high contiguity and accuracy.

BMC Genomics · Nov 5, 2024Peer-reviewedGenomics

Efficient indexing and querying of annotations in a pangenome graph

Adam M. Novak, Dickson Chung, Glenn Hickey, Sarah Djebali, Toshiyuki Yokoyama, Erik P. Garrison, Giuseppe Narzisi, Benedict Paten, Jean Monlong

The paper introduces tools to efficiently index and query annotations in pangenome graphs using GAF format, demonstrating applications on human pangenome data.

bioRxiv · Oct 12, 2024 · PreprintBioinformatics

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

Yoshitaka Sakamoto, Liu Xu, Masahide Seki, Toshiyuki Yokoyama, Masahiro Kasahara, Yukie Kashima, Akihiro Ohashi, Yoko Shimada, Noriko Motoi, Katsuya Tsuchihara, Susumu S. Kobayashi, Takashi Kohno, Yuichi Shiraishi, Ayako Suzuki, Yutaka Suzuki

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.

Genome Research · Sep 1, 2020Peer-reviewedGenomics

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

Toshiyuki Yokoyama, Yoshitaka Sakamoto, Masahide Seki, Yutaka Suzuki, Masahiro Kasahara

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

BMC Bioinformatics · Nov 5, 2019Peer-reviewedBioinformatics