Department of Computational and Systems Biology

27  articles.  
* There may be some overlapped articles listed due to the difference of format.

  1. Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer. 2023.01; 42 (1): 111929. ( PubMed , DOI )

  1. Bayesian statistical method for detecting structural and topological diversity in polymorphic proteins. 2022.11; 20 6519-6525. ( PubMed , DOI )

  2. Nucleic Acid-triggered Tumoral Immunity Propagates pH-selective Therapeutic Antibodies through Tumor-driven Epitope Spreading. 2022.09; 114 (1): 321-338. ( PubMed , DOI )

  1. Mizuno S, Yamaguchi R, Hasegawa T, Hayashi S, Fujita M, Zhang F, Koh Y, Lee SY, Yoon SS, Shimizu E, Komura M, Fujimoto A, Nagai M, Kato M, Liang H, Miyano S, Zhang Z, Nakagawa H, Imoto S: Immunogenomic pan-cancer landscape reveals immune escape mechanisms and immunoediting histories. Scientific reports. 2021.08; 11 (1): 15713. ( PubMed , DOI )

  1. Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, , , Gordon Saksena, Kyle Ellrott, Michael C Wendl, David A Wheeler, Gad Getz, Jared T Simpson, Mark B Gerstein, Li Ding, : Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020.09; 11 (1): 4748. ( PubMed , DOI )

  2. Hasegawa T, Hayashi S, Shimizu E, Mizuno S, Niida A, Yamaguchi R, Miyano S, Nakagawa H, Imoto S: Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens. Bioinformatics (Oxford, England). 2020.09; 36 (18): 4813-4816. ( PubMed , DOI )

  3. Constance H Li, Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, Paul C Boutros, PCAWG Consortium (Satoru Miyano, et al.): Sex differences in oncogenic mutational processes. Nat Commun. 2020.08; 11 (1): 4330. ( PubMed , DOI )

  4. Fujita M, Yamaguchi R, Hasegawa T, Shimada S, Arihiro K, Hayashi S, Maejima K, Nakano K, Fujimoto A, Ono A, Aikata H, Ueno M, Hayami S, Tanaka H, Miyano S, Yamaue H, Chayama K, Kakimi K, Tanaka S, Imoto S, Nakagawa H: Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations. EBioMedicine. 2020.03; 53 102659. ( PubMed , DOI )

  5. Pan-cancer analysis of whole genomes. Nature. 2020.02; 578 (7793): 82-93. ( PubMed , DOI )

  6. Pathway and network analysis of more than 2500 whole cancer genomes 2020.02; 11 (1): ( DOI )

  7. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns 2020.02; 11 (1): ( DOI )

  8. Divergent mutational processes distinguish hypoxic and normoxic tumours 2020.02; 11 (1): ( DOI )

  9. Inferring structural variant cancer cell fraction 2020.02; 11 (1): ( DOI )

  10. Integrative pathway enrichment analysis of multivariate omics data 2020.02; 11 (1): ( DOI )

  11. Yiqun Zhang, Fengju Chen, Nuno A Fonseca, Yao He, Masashi Fujita, Hidewaki Nakagawa, Zemin Zhang, Alvis Brazma, Chad J Creighton, PCAWG Consortium (Satoru Miyano, et al.): High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2020.02; 11 (1): 736. ( PubMed , DOI )

  12. Lina Sieverling, Chen Hong, Sandra D Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M Braun, Isidro Cortés-Ciriano, Ruibin Xi, Rolf Kabbe, Peter J Park, Roland Eils, Matthias Schlesner, , Benedikt Brors, Karsten Rippe, David T W Jones, Lars Feuerbach, PCAWG Consortium (Satoru Miyano, et al.): Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun. 2020.02; 11 (1): 733. ( PubMed , DOI )

  13. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis 2020.02; 3 (1): ( DOI )

  14. Combined burden and functional impact tests for cancer driver discovery using DriverPower 2020.02; 11 (1): ( DOI )

  15. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig 2020.02; 11 (1): ( DOI )

  16. Tomoko Saito, Atsushi Niida, Ryutaro Uchi, Hidenari Hirata, Hisateru Komatsu, Shotaro Sakimura, Shuto Hayashi, Sho Nambara, Yosuke Kuroda, Shuhei Ito, Hidetoshi Eguchi, Takaaki Masuda, Keishi Sugimachi, Taro Tobo, Haruto Nishida, Tsutomu Daa, Kenichi Chiba, Yuichi Shiraishi, Tetsuichi Yoshizato, Masaaki Kodama, Tadayoshi Okimoto, Kazuhiro Mizukami, Ryo Ogawa, Kazuhisa Okamoto, Mitsutaka Shuto, Kensuke Fukuda, Yusuke Matsui, Teppei Shimamura, Takanori Hasegawa, Yuichiro Doki, Satoshi Nagayama, Kazutaka Yamada, Mamoru Kato, Tatsuhiro Shibata, Masaki Mori, Hiroyuki Aburatani, Kazunari Murakami, Yutaka Suzuki, Seishi Ogawa, Satoru Miyano, Koshi Mimori: A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer. Nat Commun. 2020; 9 (1): 2884. ( PubMed , DOI )

  1. A Bayesian model integration for mutation calling through data partitioning 2019.11; 35 (21): 4247-4254. ( PubMed , DOI )

  2. Alphlard-nt: Bayesian method for human leukocyte antigen genotyping and mutation calling through simultaneous analysis of normal and tumor whole-genome sequence data 2019.09; 26 (9): 923-937. ( PubMed , DOI )

  3. Quantifying immune-based counterselection of somatic mutations 2019.07; 15 (7): e1008227. ( PubMed , DOI )

  1. ALPHLARD: A Bayesian method for analyzing HLA genes from whole genome sequence data 2018.11; 19 (1): 790. ( PubMed , DOI )

  2. 藤田 征志, 井元 清哉, 山口 類, 長谷川 嵩矩, 林 周斗, 垣見 和宏, 宮野 悟, 山上 裕機, 茶山 一彰, 中川 英刀: 肝臓がんにおける免疫抑制機構のゲノム解析(Genomic insights into immune suppression in liver cancer) 日本癌学会総会記事. 2018.09; 77回 906. ( ichushi )

  1. 小関準, 小嶋泰弘, 林周斗, 廣瀬遥香, NAM Hyunha, 島村徹平: Topological data analysis for protein structural changes caused by some mutations 分子科学討論会講演プログラム&要旨(Web). 2021; 15th

  1. Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto: An in silico automated pipeline to identify tumor specic neoantigens from whole genome and exome sequencing data Proceeding of 12th International Symposium on Bioinformatics Research and Applications. 2016;

To the head of this page.▲