Publications | Yuichi Shiraishi

Preprint

Iida N, Okada A, Kobayashi Y, Chiba K, Yatabe Y, Shiraishi Y. Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data. bioRxiv, doi: https://doi.org/10.1101/2024.02.21.581470. Portal site.
Shiraishi Y, Chiba K, Okada A. SF3B1ness score: screening SF3B1 mutation status from over 60,000 transcriptomes based on a machine learning approach. bioRxiv, doi: https://doi.org/10.1101/572834. Software.

Peer reviewed

The only peer-reviewed journals to which I have contributed as a first, co-first or corresponding author are shown. The more comprehensive list may be found here.

Nakamura W, Hirata M, Oda S, Chiba K, Okada A, Mateos RN, Sugawa M, Iida N, Ushiama M, Tanabe N, Sakamoto H, Sekine S, Hirasawa A, Kawai Y, Tokunaga K; NCBN Controls WGS Consortium; Tsujimoto SI, Shiba N, Ito S, Yoshida T, Shiraishi Y. Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes. NPJ Genom Med. 2024 Feb 17;9(1):11.
Shiraishi Y*, Koya J, Chiba K, Okada A, Arai Y, Saito Y, Shibata T, Kataoka K. Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv. Nucleic Acids Res. 2023 Jun 20;gkad526. Software.
Shiraishi Y*, Okada A* et al. Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data. Nat Commun. 2022 Sep 29;13(1):5357. Portal site.
PCAWG Transcriptome Core Group et al. Genomic basis for RNA alterations in cancer. Nature. 2020 Feb;578(7793):129-136.
Shiraishi Y, Kataoka K, Chiba K, Okada A, Kogure Y, Tanaka H, Ogawa S, Miyano S. A comprehensive characterization of cis-acting splicing-associated variants in human cancer. Genome Res. 2018 Aug;28(8):1111-1125.
Okada A, Chiba K, Tanaka H, Miyano S, Shiraishi Y. A framework for generating interactive reports for cancer genome analysis. Journal of Open Source Software. 2017 2(20),457, doi:10.21105/joss.00457. Software.
Kataoka K*, Shiraishi Y*, Takeda Y* et al. Aberrant PD-L1 expression through 3’-UTR disruption in multiple cancers. Nature. 2016 Jun 16;534(7607):402-6.
Shiraishi Y, Tremmel G, Miyano S, Stephens M. A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures. PLoS Genet. 2015 Dec 2;11(12):e1005657. Software.
Kataoka K*, Nagata Y*, Kitanaka A*, Shiraishi Y*, Shimamura T*, Yasunaga J*, Totoki Y* et al. Integrated molecular analysis of adult T cell leukemia/lymphoma. Nat Genet. 2015 Nov;47(11):1304-15.
Chiba K*, Shiraishi Y*, Nagata Y, Yoshida K, Imoto S, Ogawa S, Miyano S. Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data. Bioinformatics. 2015 Jan 1;31(1):116-8. Software.
Shiraishi Y, Fujimoto A, Furuta M et al. Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers. PLoS One. 2014 Dec 19;9(12):e114263.
Sato Y*, Yoshizato T*, Shiraishi Y*, Maekawa S*, Okuno Y* et al. Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet. 2013 Aug;45(8):860-7.
Shiraishi Y, Sato Y, Chiba K, Okuno Y, Nagata Y, Yoshida K, Shiba N, Hayashi Y, Kume H, Homma Y, Sanada M, Ogawa S, Miyano S. An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Res. 2013 Apr;41(7):e89. Software.
Yoshida K*, Sanada M*, Shiraishi Y*, Nowak D*, Nagata Y* et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature. 2011 Sep 11;478(7367):64-9.
Shiraishi Y, Okada-Hatakeyama M, Miyano S. A rank-based statistical test for measuring synergistic effects between two gene sets. Bioinformatics. 2011 Sep 1;27(17):2399-405. Software.
Shiraishi Y, Kimura S, Okada M. Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. Bioinformatics. 2010 Apr 15;26(8):1073-81.