The ProteomeXchange consortium at 10 years: 2023 update.
Deutsch, E. W., Bandeira, N., Perez-Riverol, Y., Sharma, V., Carver, J. J., Mendoza, L., Kundu, D. J., Wang, S., Bandla, C., Kamatchinathan, S., Hewapathirana, S., Pullman, B. S., Wertz, J., Sun, Z., Kawano, S., Okuda, S., Watanabe, Y., MacLearn B., MacCoss, M. J., Zhu, Y., Ishihama, Y.,Vizcaíno, J. A. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res. 51(D1):D1539-D1548(2022).
New method to construct a reference amino acid sequence database for metaproteome analysis.
Miura, N., Ishihama, Y., Okuda, S. New method to construct a reference amino acid sequence database for metaproteome analysis. HUPO2021, Stockholm/Hybrid (2021/11/18).
Construction of amino acid sequence database for metaproteome analysis using genomes of closely related species.
Miura, N., Ishihama, Y., Okuda, S. Construction of amino acid sequence database for metaproteome analysis using genomes of closely related species. ASMS2021, Philadelphia/Hybrid (2021/10/31).
The jPOST project promoting FAIR data principles in proteomics
AOHUPO2021, “The jPOST project promoting FAIR data principles in proteomics”, Online (2021/7/1).
The jPOST Repository as a Public Data Repository for Shotgun Proteomics.
Watanabe, Y., Yoshizawa, A. C., Ishihama, Y., Okuda, S. The jPOST Repository as a Public Data Repository for Shotgun Proteomics. Methods Mol. Biol. 2259:309-322(2021).
The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics.
Deutsch, E. W., Bandeira, N., Sharma, V., Perez-Riverol, Y., Carver, J. J., Kundu, D. J., García-Seisdedos, D., Jarnuczak, A. F., Hewapathirana, S., Pullman, B. S., Wertz, J., Sun, Z., Kawano, S., Okuda, S., Watanabe, Y., Hermjakob, H., MacLean, B., MacCoss, M. J., Zhu, Y., Ishihama, Y., Vizcaíno, J. A. The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics. Nucleic Acids Res. 48(D1):D1145-D1152 (2020).
Network analysis of proteogenomics data in lung cancer cell lines.
Watanabe, Y., Ling, Y., Uemura, H., Yoshizawa, A. C., Ishihama, Y., Okuda, S. Network analysis of proteogenomics data in lung cancer cell lines. HUPO2019, Adelaide (2019/9/17).
Promotion of proteomic data sharing through a specialized data journal.
Kawano, S., Okuda, S., Matsumoto, M., Ishihama, Y. Promotion of proteomic data sharing through a specialized data journal. HUPO2019, Adelaide (2019/9/16).
The jPOST environment: an integrated proteomics data repository and database.
Moriya, Y., Kawano, S., Okuda, S., Watanabe, Y., Matsumoto, M., Takami, T., Kobayashi, D., Yamanouchi, Y., Araki, N., Yoshizawa, A. C., Tabata, T., Iwasaki, M., Sugiyama, N., Tanaka, S., Goto, S., Ishihama, Y. The jPOST environment: an integrated proteomics data repository and database. Nucleic Acids Res. 47(D1):D1218-D1224 (2019).
Computational approaches towards understanding human genome, proteome, and proteogenome data
2018 Taiwan-Japan Joint Conference for Genomics and Proteogenomics and Annual Retreat of Taiwan Genomics and Genetics Society, “Computational approaches towards understanding human genome, proteome, and proteogenome data”, DoubleTree by Hilton Hotel Naha Shuri Castle, Japan (2018/8/31).