Publications

* Co-first authors (equal contribution). † Corresponding author.

Preprint

• Sakamoto Y, Ochi Y, Kogure Y, Kato S, Sato-Otsubo A, Sugawa M, Tanaka Y, Tsujimura T, Mikami T, Nagae G, Chiba K, Okada A, Ito Y, Suzuki H, Yamamoto T, Aburatani H, Koga Y, Kato I, Takita J, Mano H, Ogawa S, Kataoka K, Kato M, Shiraishi Y†. Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes. bioRxiv, doi: https://doi.org/10.64898/2026.05.28.728591. Software.

• Yano Y, Okada A, Ono M, Mateos RN, Nakayama T†, Shiraishi Y†. CrosSplice: A Pipeline for Identifying Rare Splice-Site Creating Variants from Cross-Tissue Transcriptome Data. medRxiv, doi: https://doi.org/10.64898/2025.12.21.25342246.

• 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.

• Shiraishi Y†, Ochi Y, Sugawa M, Sakamoto Y, Kimura K, Tsujimura T, Okada A, Okuda R, Namba S, Hori T, Kobayashi Y, Miyauchi T, Mateos RN, Suzuki H, Chiba K, Ito Y, Nakamura W, Ohka F, Motomura K, Yamamoto T, Kawai Y, Okada Y, Suzuki H, Fukagawa T, Kato M, Saito R, Garrison E, Logsdon GA, Ogawa S. Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations. Cell. 2026 Oct 13. doi: 10.1016/j.cell.2026.08.053. Software.

• Suzuki H†, Sugawa M, Sakamoto Y, Shiraishi Y†. mm2-ivh: simple and precise overlap detection in alpha satellite HORs with interval hashing. Bioinformatics. 2025 Dec 3;btaf648.

• 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. Nat Commun. 2025 Jan 9;16(1):426. Portal site.

• Mateos RN, Winardi W, Chiba K, Okada A, Suzuki A, Mitsuishi Y†, Shiraishi Y†. Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system. NPJ Syst Biol Appl. 2024 Dec 6;10(1):147.

• 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*, Chiba K, Kawachi A, Omori I, Mateos RN, Iida N, Yamauchi H, Kosaki K, Yoshimi A. 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*; Calabrese C*, Davidson NR*, Demircioğlu D*, Fonseca NA*, He Y*, Kahles A*, Lehmann KV*, Liu F*, Shiraishi Y*, Soulette CM*, Urban L*, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group; Brazma A†, Brooks AN†, Göke J, Rätsch G†, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. Genomic basis for RNA alterations in cancer. Nature. 2020 Feb;578(7793):129-136.

• Ochiai H, Chiba K, Okada A, Shiraishi Y. hotsub: A batch job engine for cloud services with ETL framework. Journal of Open Source Software. 2018 3(31),1069, doi:10.21105/joss.01069. Software.

• 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*, Sakata S, Matsumoto M, Nagano S, Maeda T, Nagata Y, Kitanaka A, Mizuno S, Tanaka H, Chiba K, Ito S, Watatani Y, Kakiuchi N, Suzuki H, Yoshizato T, Yoshida K, Sanada M, Itonaga H, Imaizumi Y, Totoki Y, Munakata W, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Masuda K, Minato N, Kashiwase K, Izutsu K, Takaori-Kondo A, Miyazaki Y, Takahashi S, Shibata T, Kawamoto H, Akatsuka Y, Shimoda K, Takeuchi K, Seya T, Miyano S, Ogawa S†. 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*, Chiba K, Sato-Otsubo A, Nagae G, Ishii R, Muto S, Kotani S, Watatani Y, Takeda J, Sanada M, Tanaka H, Suzuki H, Sato Y, Shiozawa Y, Yoshizato T, Yoshida K, Makishima H, Iwanaga M, Ma G, Nosaka K, Hishizawa M, Itonaga H, Imaizumi Y, Munakata W, Ogasawara H, Sato T, Sasai K, Muramoto K, Penova M, Kawaguchi T, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Nakamaki T, Ishiyama K, Miyawaki S, Yoon SS, Tobinai K, Miyazaki Y, Takaori-Kondo A, Matsuda F, Takeuchi K, Nureki O, Aburatani H, Watanabe T, Shibata T, Matsuoka M, Miyano S, Shimoda K, Ogawa S†. 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, Tanaka H, Chiba K, Boroevich KA, Abe T, Kawakami Y, Ueno M, Gotoh K, Ariizumi S, Shibuya T, Nakano K, Sasaki A, Maejima K, Kitada R, Hayami S, Shigekawa Y, Marubashi S, Yamada T, Kubo M, Ishikawa O, Aikata H, Arihiro K, Ohdan H, Yamamoto M, Yamaue H, Chayama K, Tsunoda T, Miyano S, Nakagawa H†. 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*, Kamura T, Shimamura T, Sato-Otsubo A, Nagae G, Suzuki H, Nagata Y, Yoshida K, Kon A, Suzuki Y, Chiba K, Tanaka H, Niida A, Fujimoto A, Tsunoda T, Morikawa T, Maeda D, Kume H, Sugano S, Fukayama M, Aburatani H, Sanada M, Miyano S, Homma Y, Ogawa S†. 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*, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, Chalkidis G, Suzuki Y, Shiosaka M, Kawahata R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Ishiyama K, Mori H, Nolte F, Hofmann WK, Miyawaki S, Sugano S, Haferlach C, Koeffler HP, Shih LY, Haferlach T, Chiba S, Nakauchi H, Miyano S, Ogawa S†. 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, Fukumizu K. Statistical approaches to combining binary classifiers for multi-class classification. Neurocomputing. 2011 Feb;74(5):680-688.

• 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.

• Shiraishi Y. Game theoretical analysis of the simple one-vs.-all classifier. Neurocomputing. 2008 Aug;71(13-15):2747-2753.

• Shiraishi Y. An upper bound on the convergence time of the Gibbs sampler in Ising models. J Stat Comput Simul. 2007 Oct;77(10):839-850.