2024

1. Single-cell Colocalization analysis using a generative model, Yasuhiro Kojima, Shinji Mii, Shuto Hayashi, Haruka Hirose, Masato Ishikawa, Masashi Akiyama, Atsushi Enomoto, Teppei Shimamura,
   Cell Syst.,Vol.15,Issue2, 180-192.e7,2024.  

2023

1. RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations, Masato Ishikawa,Seiichi Sugino,Yoshie Masuda,Yusuke Tarumoto, Yusuke Seto, Nobuko Taniyama, Fumi Wagai, Yuhei Yamauchi, Yasuhiro Kojima, Hisanori Kiryu, Kosuke Yusa, Mototsugu Eiraku, Atsushi Mochizuki, Commun. Biol., Vol.6, Ariticle Number1290, 2023
2. Hypoxia activates SREBP2through Golgidisassembly in bone marrow-derived monocytesfor enhanced tumor growth,Ryuichi Nakahara, Sho Aki, Maki Sugaya, Haruka Hirose, Miki Kato, Keisuke Maeda,Daichi M Sakamoto, Yasuhiro Kojima, Miyuki Nishida, Ritsuko Ando, Masashi Muramatsu, Melvin Pan, Rika Tsuchida, Yoshihiro Matsumura, Hideyuki Yanai, Hiroshi Takano, Ryoji Yao, Shinsuke Sando, Masabumi Shibuya, Juro Sakai, Tatsuhiko Kodama, Hiroyasu Kidoya, Teppei Shimamura, Tsuyoshi Osawa, EMBO J., DOI:10.15252/embj.2023114032
3. Automated time-lapse data segmentation reveals in vivo cell state dynamics, Miriam Genuth, Yasuhiro Kojima(Co-First), Dörthe Jülich, Hisanori Kiryu, Scott Holley, Sci. Adv.,Vol.9,Issue22, DOI: 10.1126/sciadv.adf1814.,2023
4. Topological data analysis of protein structure and inter/intra-molecular interaction changes attributable to amino acid mutations,Jun Koseki, Shuto Hayashi, Yasuhiro Kojima, Haruka Hirose, Teppei Shimamura,  Comput. Struct. Biotechnol. J., Vol.21, 2950-2959, 2023.
5. Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer, Yuki Ozato, Yasuhiro Kojima(Co-First), Yuta Kobayashi, Yuuichi Hisamatsu, Takeo Toshima, Yusuke Yonemura, Takaaki Masuda, Kouichi Kagawa, Yasuhiro Goto, Mitsuaki Udo, Ayako Gamachi, Kiyomi Imamura, Yuta Kuze, Jyunko Zenkou, Ayako Suzuki, Atsushi Niida, Takeharu Sakamoto, Haruka Hirose, Shuto Hayashi, Jun Koseki, Eiji Oki, Satoshi Fukuchi, Masanobu Oshima, Taro Tobo, Satoshi Nagayama, Yuichiro Doki, Hidetoshi Eguchi, Masaki Mori, Tatsuhiro Shibata, Yutaka Suzuki, Teppei Shimamura, Koshi Mimori, Cell Reports, Vol. 42, Issue 1, 111929, 2023.
   

2022

1. A bifurcation concept for B-lymphoid/plasmacytoid dendritic cells with largely fluctuating transcriptome dynamics, Keiki Nagaharu, Yasuhiro Kojima (Co-First), Haruka Hirose, Kodai Minoura, Kunihiko Hinohara, Hirohito Minami, Yuki Kageyama, Yuka Sugimoto, Masahiro Masuya, Shigeru Nii, Masahide Seki, Yutaka Suzuki, Isao Tawara, Teppei Shimamura, Naoyuki Katayama, Hiroyoshi Nishikawa, Kohshi Ohishi,  Cell Reports, Vol.40, Issue 9, 111260, 2022.

2021

1. Cancer immunotherapy with PI3K and PD-1 dual-blockade via optimal modulation of T cell activation signal, Sho Isoyama, Shigeyuki Mori, Daisuke Sugiyama, Yasuhiro Kojima, Yasuko Tada, Kohei Shitara Kunihiko Hinohara, Shingo Dan, Hiroyoshi Nishikawa, J. ImmunoTher. Cancer, Vol.9, Issue 8, e002279, 2021.

2020

1. Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations, Yasuhiro Kojima, Hirotaka Matsumoto, Hisanori Kiryu, Bioinformatics, Vol.36, Issue 1, 221-231, 2020.

2019

1. TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column,Hisanori Kiryu, Yuto Ichikawa, Yasuhiro Kojima, Algorithms Mol. Bio., Vol.14, Issue23, 2019.